diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000..6e9a708 --- /dev/null +++ b/.coveragerc @@ -0,0 +1,21 @@ +# .coveragerc to control coverage.py +[run] +branch = True +source = pycgtool + +[report] +# Regexes for lines to exclude from consideration +exclude_lines = + # Have to re-enable the standard pragma + pragma: no cover + + # Don't complain about missing debug-only code: + def __repr__ + + # Don't complain if tests don't hit defensive assertion code: + raise AssertionError + raise NotImplementedError + +ignore_errors = True +show_missing = True +sort = miss diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..8399d25 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,61 @@ +name: Publish + +on: + release: + types: + - created + +jobs: + publish: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v1 + with: + python-version: "3.8" + + - name: Install Poetry + uses: snok/install-poetry@v1.1.4 + + - name: Publish + env: + PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} + run: | + poetry config pypi-token.pypi $PYPI_TOKEN + poetry publish --build + + build-release-artifacts: + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, macos-latest] + + runs-on: ${{ matrix.os }} + + steps: + - uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v1 + with: + python-version: "3.8" + + - name: Install prerequisites + run: | + python -m pip install --upgrade pip + pip install pyinstaller + pip install . + + - name: Build distributable + run: | + pyinstaller pycgtool/__main__.py --name pycgtool-${{ matrix.os }} --onefile --collect-data mdtraj --hidden-import xdrlib + + - uses: ncipollo/release-action@v1 + with: + allowUpdates: true + artifacts: dist/pycgtool-${{ matrix.os }} + omitBodyDuringUpdate: true + token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index a40a081..ba5aada 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -5,16 +5,16 @@ name: Python package on: push: - branches: [ master ] + branches: [ master, dev ] pull_request: - branches: [ master ] + branches: [ master, dev ] jobs: build: strategy: fail-fast: false matrix: - python-version: [3.7, 3.8, 3.9] + python-version: ["3.6", "3.7", "3.8", "3.9"] os: [ubuntu-latest, macos-latest] runs-on: ${{ matrix.os }} @@ -27,13 +27,30 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Install project and dependencies + - name: Update pip run: | - pip install --upgrade pip - pip install -r requirements.txt mdtraj - pip install pytest coverage + python -m pip install --upgrade pip - - name: Test with pytest + - name: Get pip cache dir + id: pip-cache run: | - coverage run --source=pycgtool -m pytest - coverage report --skip-covered + echo "::set-output name=dir::$(pip cache dir)" + + - name: Cache pip + uses: actions/cache@v2 + with: + # This path is specific to Ubuntu + path: ${{ steps.pip-cache.outputs.dir }} + # Look to see if there is a cache hit for the corresponding requirements file + key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }} + restore-keys: | + ${{ runner.os }}-pip- + ${{ runner.os }}- + + - name: Install dependencies + run: | + pip install tox + + - name: Run tests / linter + run: | + tox diff --git a/.gitignore b/.gitignore index 2ad0dd5..666cfbd 100644 --- a/.gitignore +++ b/.gitignore @@ -36,4 +36,4 @@ settings.json .cache/ /notes/ *.offsets -*.pkl \ No newline at end of file +*.pkl diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000..b3423e0 --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,12 @@ +version: 2 + +sphinx: + configuration: docs/conf.py + +python: + version: 3.7 + install: + - method: pip + path: . + extra_requirements: + - docs diff --git a/.requirements-test.txt b/.requirements-test.txt deleted file mode 100644 index a878829..0000000 --- a/.requirements-test.txt +++ /dev/null @@ -1,3 +0,0 @@ -scipy -mdtraj -pytest diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..313b86a --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,89 @@ +# Changelog + +All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines. + +## [2.0.0-beta.5](https://github.com/jag1g13/pycgtool/compare/v1.0.2...v2.0.0-beta.5) (2021-11-14) + + +### Features + +* add flag to get version number ([f3660f7](https://github.com/jag1g13/pycgtool/commit/f3660f7081b7265a39569338e693d32a1d4030ec)) + + +### Bug Fixes + +* catch updated exception from MDTraj 1.9.7 ([b1d1e6d](https://github.com/jag1g13/pycgtool/commit/b1d1e6db76a1ce5c9273f6cf0833440c337aa302)) +* skip NaNs in bond sample output ([ef5a977](https://github.com/jag1g13/pycgtool/commit/ef5a97750dde27d48f83dc0f8472b4cc88f645aa)) + +## [2.0.0-beta.4](https://github.com/jag1g13/pycgtool/compare/v2.0.0-beta.3...v2.0.0-beta.4) (2021-10-09) + + +### Bug Fixes + +* add data files to installable package ([a9fdae8](https://github.com/jag1g13/pycgtool/commit/a9fdae85d5f9d2bff9dcfd4fe0fbc8a683dbe773)) +* backup forcefield directories instead of overwrite ([19b4054](https://github.com/jag1g13/pycgtool/commit/19b40540b0254c47d7a70eef12c2200bb96a4b9d)) +* backup frame and forcefield output files ([626cc3a](https://github.com/jag1g13/pycgtool/commit/626cc3a839a21699ac4c28eab55f385c6a199327)) +* create output directory if it doesn't exist ([c4694e8](https://github.com/jag1g13/pycgtool/commit/c4694e811201c7538819757bc52ea21ecd9f196f)) +* **tests:** add missing mapping test file ([db0be76](https://github.com/jag1g13/pycgtool/commit/db0be763bab6f629706597da1cb43d4ce3ff0914)) +* use correct reference coordinate for virtual bead calc ([a0a61f2](https://github.com/jag1g13/pycgtool/commit/a0a61f2dd2ae38d63b6de5a516f324865e93fe04)) + +## [2.0.0-beta.3](https://github.com/jag1g13/pycgtool/compare/v2.0.0-beta.2...v2.0.0-beta.3) (2021-08-14) + + +### Bug Fixes + +* avoid bond calc and traj output when no atoms ([ba0e5ab](https://github.com/jag1g13/pycgtool/commit/ba0e5ab1339f1f2821a0edb08a5b7f661c9ac29f)), closes [#51](https://github.com/jag1g13/pycgtool/issues/51) +* catch zero volume PDB box and warn ([61a5b80](https://github.com/jag1g13/pycgtool/commit/61a5b809e0cd4dffaf3e2e2bbe2ab74fcc0488aa)) +* handle empty output frames correctly ([3d4b9ad](https://github.com/jag1g13/pycgtool/commit/3d4b9adccce32c95d4114c994133d3db6efd1556)), closes [#51](https://github.com/jag1g13/pycgtool/issues/51) + +## [2.0.0-beta.2](https://github.com/jag1g13/pycgtool/compare/v2.0.0-beta.1...v2.0.0-beta.2) (2021-05-28) + + +### Bug Fixes + +* use absolute imports in entrypoint script ([1509247](https://github.com/jag1g13/pycgtool/commit/15092476496724e61a7c2f1367cdaa8ebe5fe0f2)) + +## [2.0.0-beta.1](https://github.com/jag1g13/pycgtool/compare/v2.0.0-alpha.5...v2.0.0-beta.1) (2021-05-10) + + +### Features + +* add initial trial for backmapping ([ab97010](https://github.com/jag1g13/pycgtool/commit/ab97010846815df7309b646d0bfe9f9e246890ba)) + + +### Bug Fixes + +* add missing changes to poetry lockfile ([3edf562](https://github.com/jag1g13/pycgtool/commit/3edf562f1dfb71599dc40d78e5b824c0c2417eca)) +* attempt fix to ci config ([4551eb5](https://github.com/jag1g13/pycgtool/commit/4551eb5c46d70c9dadbc1397150705a1bd726b82)) +* avoid warnings with unnecessary topology file ([717c227](https://github.com/jag1g13/pycgtool/commit/717c22723c4b5857f5e4a2bd7f956ecafb3258d3)) +* cast unitcell to float32 to avoid numpy warn ([a89d2ce](https://github.com/jag1g13/pycgtool/commit/a89d2cee5e789ad7c85f593f1a8b9d73ba1e50e6)) +* **ci:** remove unused numpy import ([bb27619](https://github.com/jag1g13/pycgtool/commit/bb276195d9f1f76668d3133607a49f07ce4a8de4)) +* fix count of frames in trajectory ([d02cd34](https://github.com/jag1g13/pycgtool/commit/d02cd3485cd474cf539a7e628dddfc4eaa953e51)) +* Move bond dump files to output directory ([1439235](https://github.com/jag1g13/pycgtool/commit/1439235f3a48da84af4b3fe064e1da9b39aa71e9)) +* python 3.10 this time - not 3.1 ([5143191](https://github.com/jag1g13/pycgtool/commit/51431910aeb8b70bef90aba82183d040282d6912)) +* remove 3.10 - it's not in the cache yet ([80a90e1](https://github.com/jag1g13/pycgtool/commit/80a90e1c62f245dab2f85e2533612c8b19a7c9d0)) +* replace reference to requirements.txt in CI ([3d1bd7f](https://github.com/jag1g13/pycgtool/commit/3d1bd7f5fde17b5c0300f70300cfa3b0f42cb3f1)) +* update tests to match refactoring in __main__ ([0dbce7d](https://github.com/jag1g13/pycgtool/commit/0dbce7d50e35fa1ffed959a40f7c9a2aa6dda873)) + +## [2.0.0-alpha.5](https://github.com/jag1g13/pycgtool/compare/v1.0.1...v2.0.0-alpha.5) (2020-09-23) + + +### Features + +* Add option for performance profiling ([cbd56ed](https://github.com/jag1g13/pycgtool/commit/cbd56ed8177e17bfc43284d4b09320fc24b8b939)) + + +### Bug Fixes + +* Account for MDTraj renaming in mol mappings ([6c7c07f](https://github.com/jag1g13/pycgtool/commit/6c7c07f748c5aabd21b3ba8997dfd9ae7d97f1b9)) +* Call CI tools from inside Poetry env ([60e3e9d](https://github.com/jag1g13/pycgtool/commit/60e3e9db94f61dfb33840bd17716d5e48499f5c9)) +* Distinguish between failure cases in traj cmp ([0ede47c](https://github.com/jag1g13/pycgtool/commit/0ede47c99d8667cae1ff38023c1a877b22ca0db7)) +* Drop support for Python 3.5 ([d50adb2](https://github.com/jag1g13/pycgtool/commit/d50adb2820b8519eaa3d77af95f4f45deb399e35)) +* Fix CI failing to find Flake8 ([4b8e375](https://github.com/jag1g13/pycgtool/commit/4b8e37563cd5f7ce8e4d3b0c55f0bf869f39c3b9)) +* Fix err in file comparison when diff lengths ([6994993](https://github.com/jag1g13/pycgtool/commit/69949934801986578e52a73e3da0e18dd546be2f)) +* Fix error when reading zero size box ([c44f621](https://github.com/jag1g13/pycgtool/commit/c44f62171a5d9b37b591736f3869e892e3d49a32)) +* Fix failing bond dump test ([8d7d06f](https://github.com/jag1g13/pycgtool/commit/8d7d06f9e90ca5cbceadc29630e8d8208829eff3)) +* Fix linting errors raised by pyflakes ([d275329](https://github.com/jag1g13/pycgtool/commit/d2753290f96181b1b4ed00d92a70cad244abd2a3)) +* Fix remaining test failures ([50ec715](https://github.com/jag1g13/pycgtool/commit/50ec7156e790a8ed475414c95196e5861027e006)) +* Replace time.clock with time.process_time ([d1f6981](https://github.com/jag1g13/pycgtool/commit/d1f69810475e2e3af4beb2652688c05d11b73a86)) +* Update Poetry lock file ([f08dd83](https://github.com/jag1g13/pycgtool/commit/f08dd839fde66c739e52920a1ca92d5b7ec2b135)) diff --git a/LICENSE.md b/LICENSE similarity index 100% rename from LICENSE.md rename to LICENSE diff --git a/README.md b/README.md index a948b60..7255951 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,24 @@ -[![Build Status](https://travis-ci.org/jag1g13/pycgtool.svg?branch=master)](https://travis-ci.org/jag1g13/pycgtool) [![Documentation Status](https://readthedocs.org/projects/pycgtool/badge/?version=master)](http://pycgtool.readthedocs.io/en/master/?badge=master) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.259330.svg)](https://doi.org/10.5281/zenodo.259330) - # PyCGTOOL -Please see http://pycgtool.readthedocs.io/en/master/ for full documentation. - -A Python program for automated generation of coarse-grained molecular dynamics models from atomistic simulation trajectories. - -The aim of this project is to provide a tool to aid in parametrising coarse-grained (CG) molecular mechanics models. PyCGTOOL generates coarse-grained models from atomistic simulation trajectories using a user-provided mapping. Equilibrium values and force constants of bonded terms are calculated by Boltzmann Inversion of bond distributions collected from the input trajectory. +[![License](https://img.shields.io/github/license/jag1g13/pycgtool.svg)](LICENSE) +[![Python package](https://github.com/jag1g13/pycgtool/actions/workflows/python-package.yml/badge.svg?branch=dev)](https://github.com/jag1g13/pycgtool/actions) +[![Documentation](https://readthedocs.org/projects/pycgtool/badge/?version=dev)](http://pycgtool.readthedocs.io/en/dev) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.598143.svg)](https://doi.org/10.5281/zenodo.598143) +[![PyPi Version](https://img.shields.io/pypi/v/pycgtool.svg)](https://pypi.python.org/pypi/pycgtool/) +[![conda-forge Version](https://anaconda.org/conda-forge/pycgtool/badges/version.svg)](https://anaconda.org/conda-forge/pycgtool/badges/version.svg) -Alternatively map-only mode (behaving similarly to MARTINIZE) may be used to generate initial coordinates to use with existing CG topologies such as the MARTINI lipid models. For instance, a pre-equilibrated atomistic membrane may be used to create starting coordinates for a MARTINI membrane simulation. +Generate coarse-grained molecular dynamics models from atomistic trajectories. -PyCGTOOL makes it easy to test multiple variations in mapping and bond topology by making simple changes to the config files. +PyCGTOOL is a tool to aid in parametrising coarse-grained (CG) molecular mechanics models of small molecules, for example for simulations using the popular MARTINI model. +It generates coarse-grained model parameters from atomistic simulation trajectories using a user-provided mapping. +Equilibrium values and force constants of bonded terms are calculated by Boltzmann Inversion of bond distributions collected from the input trajectory. -This version has several advantages over the original C++ implementation CGTOOL: -* PyCGTOOL is able to run anywhere the necessary library dependencies are available (all available from pip) -* Does not require that residues are present in contiguous sorted blocks -* May map multiple residues with a single pass -* Support for polymers such as DNA or proteins making use of GROMACS' pdb2gmx -* Much more automated testing ensures that regressions will be identified quickly +Alternatively map-only mode (behaving similarly to MARTINIZE) may be used to generate initial coordinates to use with existing CG topologies such as the MARTINI lipid models. +For instance, a pre-equilibrated atomistic membrane may be used to create starting coordinates for a CG membrane simulation. -If you experience problems or wish to see a new feature added please [file an issue](https://github.com/jag1g13/pycgtool/issues). +PyCGTOOL makes it quick and easy to test multiple variations in mapping and bond topology by making simple changes to the config files. -If you find PyCGTOOL useful, please cite our JCIM paper https://doi.org/10.1021/acs.jcim.7b00096. +If you find PyCGTOOL useful, please cite our JCIM paper (https://doi.org/10.1021/acs.jcim.7b00096) and the code itself (https://doi.org/10.5281/zenodo.598143). ```bibtex @article{Graham2017, @@ -39,28 +36,82 @@ If you find PyCGTOOL useful, please cite our JCIM paper https://doi.org/10.1021/ } ``` -## Usage -Input to PyCGTOOL is GROMACS GRO and XTC files, along with two custom files: MAP and BND. These files provide the atomistic-to-CG mapping and bonded topology respectively. Example files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory. The format of these files is described in the [full documentation](http://pycgtool.readthedocs.io/en/master/). +## Install + +PyCGTOOL requires Python 3.6 or higher and may be installed using either `pip` or `conda`: +``` +pip install pycgtool +``` + +``` +conda install -c conda-forge pycgtool +``` -To run PyCGTOOL: -`pycgtool.py -g -x -m -b ` +Alternatively, you may download a pre-packaged version for your operating system from the [releases page](https://github.com/jag1g13/pycgtool/releases) on GitHub. +These pre-packaged versions include all dependencies and should be suitable in cases where you cannot install packages using one of the above methods. +**Warning**: This installation method is not extensively tested - installing via `pip` or `conda` should be prefered in most cases. -To run PyCGTOOL in map-only mode: -`pycgtool.py -g -m ` +### MDTraj on macOS -To see the help text: -`pycgtool.py -h` +On some versions macOS, with some versions of the Clang compiler, MDTraj may fail to load GROMACS XTC simulation trajectories. +If you encounter this issue, please make sure you have the latest version of MDTraj installed. + +For more information see [MDTraj/#1572](https://github.com/mdtraj/mdtraj/issues/1572). + +## Usage + +Input to PyCGTOOL is an atomistic simulation trajectory in the form of a topology (e.g. PDB, GRO, etc.) and a trajectory file (e.g. XTC, DCD, etc.), along with two custom files which describe the CG model to be generated: mapping (`.map`) and bonding (`.bnd`). +These files provide the atomistic-to-CG mapping and bonded topology respectively and use a format similar to GROMACS `.itp` files. +Topology and trajectory files are processed using [MDTraj](https://www.mdtraj.org) so most common formats are accepted. + +Example mapping and bond files are present in the [test/data](https://github.com/jag1g13/pycgtool/tree/master/test/data) directory. +The format of these files is described fully in the [documentation page on file formats](https://pycgtool.readthedocs.io/en/dev/file-formats.html). For more information, see [the tutorial](https://pycgtool.readthedocs.io/en/master/tutorial.html). -It is important to perform validation of any new parameter set; a brief example is present at the end of the tutorial. +It is important to perform validation of any new parameter set - a brief example is present at the end of the tutorial. + +For a full list of options, see the [documentation](https://pycgtool.readthedocs.io/en/master/index.html) or use: +``` +pycgtool -h +``` + +### Generate a Model + +To generate a CG model from an atomistic simulation: +``` +pycgtool -m -b +``` + +### Map Only + +To use PyCGTOOL to convert a set of atomistic simulation coordinates to CG coordinates: +``` +pycgtool -m +``` + +Or to convert a complete simulation trajectory: +``` +pycgtool -m +``` + +## Maintainers + +James Graham ([@jag1g13](https://github.com/jag1g13)) + +## Contributing + +If you experience problems using PyCGTOOL or wish to see a new feature added please [open an issue](https://github.com/jag1g13/pycgtool/issues/new). + +To help develop PyCGTOOL, you can create a fork of this repository, clone your fork and install PyCGTOOL in development mode using [Poetry](https://python-poetry.org/): +``` +poetry install +``` + +This will result in an editable mode install (similar to `pip install -e .`) along with all the necessary runtime and development dependencies. +Testing and linting is handled by [Tox](https://tox.readthedocs.io/en/latest/) - use `tox` to run the full test suite and linter as they are configured in the Continuous Integration pipeline. -## Requirements -PyCGTOOL requires: -* Python3 -* [NumPy](http://www.numpy.org/) -* [simpletraj](https://github.com/arose/simpletraj) +When you're ready for your work to be merged, please submit a Pull Request. -The bundled test code may be run using your preferred Python testing frontend although py.test or nose2 is recommended. -All library dependencies may be installed from pip using the command `pip install -r requirements.txt` +## License -This program is a reimplementation of the earlier [CGTOOL](https://bitbucket.org/jag1g13/cgtool). +[GPL-3.0](LICENSE) © James Graham, University of Southampton diff --git a/clean.sh b/clean.sh deleted file mode 100755 index f257ab0..0000000 --- a/clean.sh +++ /dev/null @@ -1,2 +0,0 @@ -rm *.itp* *.gro* *.dat* *.json* *.xtc* -rm -r *.ff diff --git a/data/atom_masses.json b/data/atom_masses.json deleted file mode 100644 index cea07cf..0000000 --- a/data/atom_masses.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "H": 1.0080, - "C": 12.0110, - "N": 14.0067, - "O": 15.9994, - "P": 30.9738, - "S": 32.0600 -} diff --git a/doc/Makefile b/doc/Makefile deleted file mode 100644 index 5339467..0000000 --- a/doc/Makefile +++ /dev/null @@ -1,223 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = build -SOURCEDIR = source - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source - -.PHONY: help -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " applehelp to make an Apple Help Book" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " xml to make Docutils-native XML files" - @echo " pseudoxml to make pseudoxml-XML files for display purposes" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - @echo " coverage to run coverage check of the documentation (if enabled)" - -.PHONY: clean -clean: - rm -rf $(BUILDDIR)/* - -.PHONY: html -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -.PHONY: dirhtml -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -.PHONY: singlehtml -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -.PHONY: pickle -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -.PHONY: json -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -.PHONY: htmlhelp -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -.PHONY: qthelp -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PyCGTOOL.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PyCGTOOL.qhc" - -.PHONY: applehelp -applehelp: - $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp - @echo - @echo "Build finished. The help book is in $(BUILDDIR)/applehelp." - @echo "N.B. You won't be able to view it unless you put it in" \ - "~/Library/Documentation/Help or install it in your application" \ - "bundle." - -.PHONY: devhelp -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/PyCGTOOL" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PyCGTOOL" - @echo "# devhelp" - -.PHONY: epub -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -.PHONY: latex -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -.PHONY: latexpdf -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -.PHONY: latexpdfja -latexpdfja: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through platex and dvipdfmx..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -.PHONY: text -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -.PHONY: man -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -.PHONY: texinfo -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." - -.PHONY: info -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." - -.PHONY: gettext -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." - -.PHONY: changes -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -.PHONY: linkcheck -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -.PHONY: doctest -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." - -.PHONY: coverage -coverage: - $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage - @echo "Testing of coverage in the sources finished, look at the " \ - "results in $(BUILDDIR)/coverage/python.txt." - -.PHONY: xml -xml: - $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml - @echo - @echo "Build finished. The XML files are in $(BUILDDIR)/xml." - -.PHONY: pseudoxml -pseudoxml: - $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml - @echo - @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." - -.PHONY: apidoc -apidoc: - sphinx-apidoc -o $(SOURCEDIR) -ef ../pycgtool/ - @echo - @echo "Sphinx apidoc finished." diff --git a/doc/make.bat b/doc/make.bat deleted file mode 100644 index 5cf6991..0000000 --- a/doc/make.bat +++ /dev/null @@ -1,263 +0,0 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set BUILDDIR=build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source -set I18NSPHINXOPTS=%SPHINXOPTS% source -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^` where ^ is one of - echo. html to make standalone HTML files - echo. dirhtml to make HTML files named index.html in directories - echo. singlehtml to make a single large HTML file - echo. pickle to make pickle files - echo. json to make JSON files - echo. htmlhelp to make HTML files and a HTML help project - echo. qthelp to make HTML files and a qthelp project - echo. devhelp to make HTML files and a Devhelp project - echo. epub to make an epub - echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter - echo. text to make text files - echo. man to make manual pages - echo. texinfo to make Texinfo files - echo. gettext to make PO message catalogs - echo. changes to make an overview over all changed/added/deprecated items - echo. xml to make Docutils-native XML files - echo. pseudoxml to make pseudoxml-XML files for display purposes - echo. linkcheck to check all external links for integrity - echo. doctest to run all doctests embedded in the documentation if enabled - echo. coverage to run coverage check of the documentation if enabled - goto end -) - -if "%1" == "clean" ( - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - - -REM Check if sphinx-build is available and fallback to Python version if any -%SPHINXBUILD% 1>NUL 2>NUL -if errorlevel 9009 goto sphinx_python -goto sphinx_ok - -:sphinx_python - -set SPHINXBUILD=python -m sphinx.__init__ -%SPHINXBUILD% 2> nul -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -:sphinx_ok - - -if "%1" == "html" ( - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "dirhtml" ( - %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. - goto end -) - -if "%1" == "singlehtml" ( - %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. - goto end -) - -if "%1" == "pickle" ( - %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the pickle files. - goto end -) - -if "%1" == "json" ( - %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the JSON files. - goto end -) - -if "%1" == "htmlhelp" ( - %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run HTML Help Workshop with the ^ -.hhp project file in %BUILDDIR%/htmlhelp. - goto end -) - -if "%1" == "qthelp" ( - %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run "qcollectiongenerator" with the ^ -.qhcp project file in %BUILDDIR%/qthelp, like this: - echo.^> qcollectiongenerator %BUILDDIR%\qthelp\PyCGTOOL.qhcp - echo.To view the help file: - echo.^> assistant -collectionFile %BUILDDIR%\qthelp\PyCGTOOL.ghc - goto end -) - -if "%1" == "devhelp" ( - %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. - goto end -) - -if "%1" == "epub" ( - %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The epub file is in %BUILDDIR%/epub. - goto end -) - -if "%1" == "latex" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "latexpdf" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - cd %BUILDDIR%/latex - make all-pdf - cd %~dp0 - echo. - echo.Build finished; the PDF files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "latexpdfja" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - cd %BUILDDIR%/latex - make all-pdf-ja - cd %~dp0 - echo. - echo.Build finished; the PDF files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "text" ( - %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The text files are in %BUILDDIR%/text. - goto end -) - -if "%1" == "man" ( - %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The manual pages are in %BUILDDIR%/man. - goto end -) - -if "%1" == "texinfo" ( - %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. - goto end -) - -if "%1" == "gettext" ( - %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The message catalogs are in %BUILDDIR%/locale. - goto end -) - -if "%1" == "changes" ( - %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes - if errorlevel 1 exit /b 1 - echo. - echo.The overview file is in %BUILDDIR%/changes. - goto end -) - -if "%1" == "linkcheck" ( - %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck - if errorlevel 1 exit /b 1 - echo. - echo.Link check complete; look for any errors in the above output ^ -or in %BUILDDIR%/linkcheck/output.txt. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -if "%1" == "coverage" ( - %SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage - if errorlevel 1 exit /b 1 - echo. - echo.Testing of coverage in the sources finished, look at the ^ -results in %BUILDDIR%/coverage/python.txt. - goto end -) - -if "%1" == "xml" ( - %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The XML files are in %BUILDDIR%/xml. - goto end -) - -if "%1" == "pseudoxml" ( - %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. - goto end -) - -:end diff --git a/doc/source/conf.py b/doc/source/conf.py deleted file mode 100644 index d28e97f..0000000 --- a/doc/source/conf.py +++ /dev/null @@ -1,291 +0,0 @@ -#!/usr/bin/env python3 -# -*- coding: utf-8 -*- -# -# PyCGTOOL documentation build configuration file, created by -# sphinx-quickstart on Tue Feb 23 21:47:28 2016. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -import sys -import os - -import sphinx_rtd_theme - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -sys.path.insert(0, os.path.abspath('../../')) - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.coverage', - 'sphinx.ext.mathjax', - 'sphinx.ext.viewcode', -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The encoding of source files. -#source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = 'PyCGTOOL' -copyright = '2016, James Graham' -author = 'James Graham' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '0.1' -# The full version, including alpha/beta/rc tags. -release = '0.1' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -#today = '' -# Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = [] - -# The reST default role (used for this markup: `text`) to use for all -# documents. -#default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -#add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -#show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built documents. -#keep_warnings = False - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = 'sphinx_rtd_theme' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -#html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -#html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -#html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -#html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -# Add any extra paths that contain custom files (such as robots.txt or -# .htaccess) here, relative to this directory. These files are copied -# directly to the root of the documentation. -#html_extra_path = [] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -#html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -#html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -#html_additional_pages = {} - -# If false, no module index is generated. -#html_domain_indices = True - -# If false, no index is generated. -#html_use_index = True - -# If true, the index is split into individual pages for each letter. -#html_split_index = False - -# If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -#html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None - -# Language to be used for generating the HTML full-text search index. -# Sphinx supports the following languages: -# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja' -# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr' -#html_search_language = 'en' - -# A dictionary with options for the search language support, empty by default. -# Now only 'ja' uses this config value -#html_search_options = {'type': 'default'} - -# The name of a javascript file (relative to the configuration directory) that -# implements a search results scorer. If empty, the default will be used. -#html_search_scorer = 'scorer.js' - -# Output file base name for HTML help builder. -htmlhelp_basename = 'PyCGTOOLdoc' - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', - -# Latex figure (float) alignment -#'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'PyCGTOOL.tex', 'PyCGTOOL Documentation', - 'James Graham', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'pycgtool', 'PyCGTOOL Documentation', - [author], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - (master_doc, 'PyCGTOOL', 'PyCGTOOL Documentation', - author, 'PyCGTOOL', 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False diff --git a/doc/source/index.rst b/doc/source/index.rst deleted file mode 100644 index 5eece82..0000000 --- a/doc/source/index.rst +++ /dev/null @@ -1,182 +0,0 @@ -.. PyCGTOOL documentation master file, created by - sphinx-quickstart on Tue Feb 23 21:47:28 2016. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to PyCGTOOL's documentation! -==================================== - -.. toctree:: - :hidden: - - self - tutorial - mapping-only - Module Documentation - - -.. toctree:: - :maxdepth: 2 - -:doc:`tutorial` - -Features --------- -PyCGTOOL provides a means to quickly and easily generate coarse-grained molecular dynamics models within the MARTINI framework from all-atom or united-atom simulation trajectories. - -A user defined mapping is applied to the input trajectory and bonded terms (lengths, angles and dihedrals) are measured. From these measurements, equilibrium values and force constants are found and a GROMACS topology is created for the target molecules. - -Requirements ------------- -PyCGTOOL requires: - -- Python 3 -- Numpy (http://www.numpy.org/) -- simpletraj (https://github.com/arose/simpletraj) - -Optional: - -- MDTraj for pseudo-CG XTC output (http://mdtraj.org/1.7.2/) with own dependencies: - - - Scipy (https://www.scipy.org/) - - Cython (http://cython.org/) - -- Python testing framework (e.g. Nose2, py.test) -- Numba for increased performance (http://numba.pydata.org/) -- Sphinx to generate documentation yourself (http://www.sphinx-doc.org/en/stable/) - -Basic Usage ------------ -PyCGTOOL requires four input files to generate a coarse-grained model: - --g GROMACS gro coordinate file --x GROMACS xtc trajectory file --m PyCGTOOL mapping definition file --b PyCGTOOL bond definition file - -The program is called by:: - - pycgtool.py -g -x -m -b - -Example mapping and bond definition files are present in the ``test/data`` directory. Their format is explained below. - -After running PyCGTOOL two files, ``out.gro`` and ``out.itp`` will be created. The gro file contains the mapped coarse-grain coordinates with every molecule for which a mapping was provided. The itp file contains the parameters for each molecule type. - -It is important to perform validation of any new parameter set. -This is typically done by comparing properties between the reference simulation and simulations using the new CG model. -In the tutorial we use the radius of gyration, but there are many other suitable properties, depending on the class of molecule being parametrised. - -Mapping / Bond Definition Files -------------------------------- -The mapping and bond definition input files use a format similar to the GROMACS itp/top format. - -Mapping Definition -~~~~~~~~~~~~~~~~~~ -An example of mapping definition file for the monosaccharide allose taken from ``test/data/sugar.map`` is shown below. - -Molecule names (as present in the gro coordinate file) are used as section headers inside square brackets. Each of the following lines describes a single coarse-grained bead mapping. The items on a line are: the name of the bead, its MARTINI bead type, optionally the bead charge, and a list of all the atom names it should contain. All items on a line are whitespace separated. Multiple molecules may be specified in their own sections. -It is not recommended to provide a mapping for water since MARTINI water combines four molecules into a single bead which is not yet supported by PyCGTOOL. -Note that bead charges in the MARTINI framework are by convention integers and are used only for formally charged functional groups. An example of a molecule mapping using charges can be found in ``test/data/dppc.map``. :: - - ; comments begin with a semicolon - [ALLA] - C1 P3 C1 O1 - C2 P3 C2 O2 - C3 P3 C3 O3 - C4 P3 C4 O4 - C5 P2 C5 C6 O6 - O5 P4 O5 - - [SOL] - W P4 OW HW1 HW2 - -Bond Definition -~~~~~~~~~~~~~~~ -An example bond definition file for the monosaccharide allose taken from ``test/data/sugar.bnd`` is shown below. - -As in the mapping definition file, molecule names are used as section headers inside square brackets. The following lines define bonds lengths, angles and dihedrals between coarse-grained beads. Each line is a list of bead names, using the names defined in the mapping file. Two bead names on a line defines a bond length, three defines an angle, and four defines a dihedral. - -If no angles are defined for a molecule, PyCGTOOL will construct all angles from the list of bonds. This may also be enabled for dihedrals via the ``--advanced`` flag, but is not recommended as in most cases coarse-grained models do not require dihedrals. Additionally, any angles inside a triangle of bond lengths are excluded from the output as they often cause simulation stability issues when used in conjunction with LINCS. :: - - ; comments begin with a semicolon - [ALLA] - C1 C2 - C2 C3 - C3 C4 - C4 C5 - C5 O5 - O5 C1 - - C1 C2 C3 - C2 C3 C4 - C3 C4 C5 - C4 C5 O5 - C5 O5 C1 - O5 C1 C2 - - C1 C2 C3 C4 - C2 C3 C4 C5 - C3 C4 C5 O5 - C4 C5 O5 C1 - C5 O5 C1 C2 - O5 C1 C2 C3 - - -Advanced Usage --------------- - -Modes -~~~~~ - -PyCGTOOL performs several other functions which may be useful in the testing and use of coarse-grained models. - -Mapping Only -............ - -Mapping-only mode simply converts an input atomistic coordinate file into its coarse-grained representation. -For full detail see: :doc:`mapping-only`. - -This mode may be invoked by:: - - pycgtool.py -g -m - - -Measure Only -............ - -Measure-only mode may be used to aid in the testing of a coarse-grained model by making measurements of bonds from a true coarse-grained simulation trajectory. -These bond measurements may be compared directly to those collected from the pseudo-coarse-grained trajectory used to generate the model. -This mode may be invoked by:: - - pycgtool.py -g -x -b - - -Advanced Options -~~~~~~~~~~~~~~~~ -By passing the flag ``--advanced`` to PyCGTOOL several advanced options are accessible. The arrow keys may be used to navigate through the menu. Enter selects an option to be edited, or if the option is boolean toggles it. Once you have edited an option press enter again. When all options are satisfactory, press q to proceed. - -================== ========================================== ======================= -Option Description Values -================== ========================================== ======================= -output_name Base name of output files **out**, any string -output Coordinate output format **gro** -output_xtc Should a pseudo-CG XTC be created **False**, True -map_only Run in mapping-only mode **False**, True -map_center Mapping method **geom**, mass -constr_threshold Convert stiff bonds to constraints over **100000**, any number -dump_measurements Whether to output bond measurements **False**, True -dump_n_values How many measurements to output **10000**, any number -output_forcefield Output a GROMACS forcefield directory? **False**, True -temperature Temperature of reference simulation **310**, any number -default_fc Use default MARTINI force constants? **False**, True -generate_angles Generate angles from bonds **True**, False -generate_dihedrals Generate dihedrals from bonds **False**, True -================== ========================================== ======================= - -Indexes -======= - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - diff --git a/doc/source/modules.rst b/doc/source/modules.rst deleted file mode 100644 index cb57cae..0000000 --- a/doc/source/modules.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool -======== - -.. toctree:: - :maxdepth: 4 - - pycgtool diff --git a/doc/source/pycgtool.bondset.rst b/doc/source/pycgtool.bondset.rst deleted file mode 100644 index 6d1777e..0000000 --- a/doc/source/pycgtool.bondset.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.bondset module -======================= - -.. automodule:: pycgtool.bondset - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.forcefield.rst b/doc/source/pycgtool.forcefield.rst deleted file mode 100644 index a25ef72..0000000 --- a/doc/source/pycgtool.forcefield.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.forcefield module -========================== - -.. automodule:: pycgtool.forcefield - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.frame.rst b/doc/source/pycgtool.frame.rst deleted file mode 100644 index f231e7f..0000000 --- a/doc/source/pycgtool.frame.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.frame module -===================== - -.. automodule:: pycgtool.frame - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.functionalforms.rst b/doc/source/pycgtool.functionalforms.rst deleted file mode 100644 index c69160b..0000000 --- a/doc/source/pycgtool.functionalforms.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.functionalforms module -=============================== - -.. automodule:: pycgtool.functionalforms - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.interface.rst b/doc/source/pycgtool.interface.rst deleted file mode 100644 index a724d24..0000000 --- a/doc/source/pycgtool.interface.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.interface module -========================= - -.. automodule:: pycgtool.interface - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.mapping.rst b/doc/source/pycgtool.mapping.rst deleted file mode 100644 index 7beba67..0000000 --- a/doc/source/pycgtool.mapping.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.mapping module -======================= - -.. automodule:: pycgtool.mapping - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.parsers.cfg.rst b/doc/source/pycgtool.parsers.cfg.rst deleted file mode 100644 index 07faee1..0000000 --- a/doc/source/pycgtool.parsers.cfg.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.parsers.cfg module -=========================== - -.. automodule:: pycgtool.parsers.cfg - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.parsers.rst b/doc/source/pycgtool.parsers.rst deleted file mode 100644 index e1fea8b..0000000 --- a/doc/source/pycgtool.parsers.rst +++ /dev/null @@ -1,17 +0,0 @@ -pycgtool.parsers package -======================== - -Submodules ----------- - -.. toctree:: - - pycgtool.parsers.cfg - -Module contents ---------------- - -.. automodule:: pycgtool.parsers - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.pycgtool.rst b/doc/source/pycgtool.pycgtool.rst deleted file mode 100644 index 1b88183..0000000 --- a/doc/source/pycgtool.pycgtool.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.pycgtool module -======================== - -.. automodule:: pycgtool.pycgtool - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.rst b/doc/source/pycgtool.rst deleted file mode 100644 index 17932f8..0000000 --- a/doc/source/pycgtool.rst +++ /dev/null @@ -1,31 +0,0 @@ -pycgtool package -================ - -Subpackages ------------ - -.. toctree:: - - pycgtool.parsers - -Submodules ----------- - -.. toctree:: - - pycgtool.bondset - pycgtool.forcefield - pycgtool.frame - pycgtool.functionalforms - pycgtool.interface - pycgtool.mapping - pycgtool.pycgtool - pycgtool.util - -Module contents ---------------- - -.. automodule:: pycgtool - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/pycgtool.util.rst b/doc/source/pycgtool.util.rst deleted file mode 100644 index 973651b..0000000 --- a/doc/source/pycgtool.util.rst +++ /dev/null @@ -1,7 +0,0 @@ -pycgtool.util module -==================== - -.. automodule:: pycgtool.util - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/arguments.md b/docs/arguments.md new file mode 100644 index 0000000..3aeec72 --- /dev/null +++ b/docs/arguments.md @@ -0,0 +1,15 @@ +# Full Arguments List + +## Input Files + +`topology` +: Atomistic simulation topology + +`trajectory` +: Atomistic simulation trajectory + +`-m`, `--mapping` +: CG mapping definition file + +`-b`, `--bondset` +: Bond definition file diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..522a3b2 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,68 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +# import os +# import sys +# sys.path.insert(0, os.path.abspath('.')) + + +# -- Project information ----------------------------------------------------- + +project = 'PyCGTOOL' +copyright = '2016, James Graham' +author = 'James Graham' + +# The full version, including alpha/beta/rc tags +release = '2.0.0' + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + 'autoapi.extension', + 'sphinx_rtd_theme', + 'sphinx.ext.viewcode', + 'myst_parser', +] + +source_suffix = ['.rst', '.md'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + +myst_enable_extensions = ['deflist'] + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = 'sphinx_rtd_theme' + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + + +# -- Sphinx AudoAPI options -------------------------------------------------- + +autoapi_type = 'python' +autoapi_dirs = ['../pycgtool'] diff --git a/docs/file-formats.md b/docs/file-formats.md new file mode 100644 index 0000000..4e3c3ce --- /dev/null +++ b/docs/file-formats.md @@ -0,0 +1,94 @@ +# File Formats + +## Mapping Definition File +An example of mapping definition file for the monosaccharide allose taken from `test/data/sugar.map` is shown below. + +Molecule names (as present in the coordinate file) are used as section headers inside square brackets. +Each of the following lines describes a single coarse-grained bead mapping. +The items on a line are: +- the name of the bead +- its MARTINI bead type +- optionally the bead charge +- a list of all the atom names it should contain + +All items on a line are whitespace separated. +Multiple molecules may be specified in their own sections. +It is not recommended to provide a mapping for water since MARTINI water combines four molecules into a single bead which is not possible to map directly. +Note that bead charges in the MARTINI framework are by convention integers and are used only for formally charged functional groups. + +``` +; comments begin with a semicolon +[ALLA] +C1 P3 C1 O1 +C2 P3 C2 O2 +C3 P3 C3 O3 +C4 P3 C4 O4 +C5 P2 C5 C6 O6 +O5 P4 O5 + +[DPPC] +NC3 Q0 1 NC3 +PO4 Qa -1 PO4 +GL1 Na GL1 +GL2 Na GL2 +C1A C1 C1A +C2A C3 C2A +C3A C1 C3A +C4A C1 C4A +C1B C1 C1B +C2B C3 C2B +C3B C1 C3B +C4B C1 C4B +``` + +The Martini force field has introduced in version 3 the use of virtual sites for polycylic compounds or polysaccharides in order to improve numerical stability for highly constrained structures. +Below is an example of how virtual sites can be included in the mapping file for naphthalene (see `/test/data/martini3/naphthalene.map`). +Similar to the previously described mapping syntax, a virtual site is defined with a prefix of ``@v`` as follows `@v [name] [type] [charge] [constructing beads]`. +The constructing beads refer to a list of space delimited coarse grained bead names from which the position of the virtual site will be calculated. +Currently virtual sites can be constructed from either the center of geometry or mass of the constructing sites via the `--virtual-map-center` flag. + +``` +[ NAPH ] +R1 TC4 C8 H8 C9 H9 +R2 TC4 C6 H6 C7 H7 +@v R3 TC4 R1 R2 R4 R5 +R4 TC4 C1 H1 C2 H2 +R5 TC4 C3 H3 C4 H4 +``` + +## Bond Definition File +An example bond definition file for the monosaccharide allose taken from `test/data/sugar.bnd` is shown below. + +As in the mapping definition file, molecule names are used as section headers inside square brackets. +The following lines define bonds lengths, angles and dihedrals between coarse-grained beads. +Each line is a list of bead names, using the names defined in the mapping file. +Two bead names on a line defines a bond length, three defines an angle, and four defines a dihedral. + +If no angles are defined for a molecule, PyCGTOOL will construct all angles from the list of bonds. +This may also be enabled for dihedrals via the `--generate-dihedrals` flag, but is not recommended as in most cases coarse-grained models do not require dihedrals. +Additionally, any angles inside a triangle of bond lengths are excluded from the output as they often cause simulation stability issues when used in conjunction with LINCS. + +``` +; comments begin with a semicolon +[ALLA] +C1 C2 +C2 C3 +C3 C4 +C4 C5 +C5 O5 +O5 C1 + +C1 C2 C3 +C2 C3 C4 +C3 C4 C5 +C4 C5 O5 +C5 O5 C1 +O5 C1 C2 + +C1 C2 C3 C4 +C2 C3 C4 C5 +C3 C4 C5 O5 +C4 C5 O5 C1 +C5 O5 C1 C2 +O5 C1 C2 C3 +``` diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..3938516 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,17 @@ + +# PyCGTOOL Documentation + +```{toctree} +:maxdepth: 2 +self +file-formats +tutorial +mapping-only +arguments +autoapi/index +``` + +```{include} ../README.md +:relative-docs: docs/ +:relative-images: +``` diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..2119f51 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/doc/source/mapping-only.rst b/docs/mapping-only.md similarity index 51% rename from doc/source/mapping-only.rst rename to docs/mapping-only.md index 976ae60..1abffb5 100644 --- a/doc/source/mapping-only.rst +++ b/docs/mapping-only.md @@ -1,5 +1,4 @@ -Mapping Only Mode -================= +# Mapping Only Mode PyCGTOOL may be used in mapping only mode to simply convert an all-atom (AA) coordinate file into its coarse-grained (CG) representation. In this respect it functions similarly to the MARTINI tool `Martinize`. @@ -9,14 +8,16 @@ The main uses of the functionality are: - Use a pre-equilibrated AA coordinate file as the starting point for a CG simulation In order to perform the AA to CG mapping, a PyCGTOOL mapping file is required. -For guidance on the creation of this file see the full :doc:`tutorial`. +For guidance on the creation of this file see the full [tutorial](tutorial). -To perform a mapping from a single snapshot `.gro` file use the command:: +To perform a mapping from a single snapshot file (e.g. PDB, GRO, etc.) use the command: - pycgtool.py -g -m +``` +pycgtool -m +``` -To perform a mapping of a complete `.xtc` trajectory use the command:: +To perform a mapping of a complete trajectory (e.g. XTC, DCD, etc.) use the command: - pycgtool.py -g -x -m - -But note that mapping an entire trajectory requires that the optional dependency `MDTraj` is installed. +``` +pycgtool -m +``` diff --git a/doc/source/tutorial.rst b/docs/tutorial.md similarity index 59% rename from doc/source/tutorial.rst rename to docs/tutorial.md index dc7972b..a0b5c61 100644 --- a/doc/source/tutorial.rst +++ b/docs/tutorial.md @@ -1,22 +1,20 @@ -PyCGTOOL Tutorial -================= +# PyCGTOOL Tutorial This tutorial follows the complete process of parametrising a new molecule within the MARTINI forcefield, covering aspects of mapping design, model generation and model validation. PyCGTOOL is used at multiple stages, showing its use in several different situations. -All files required to follow this tutorial are present in the ``doc/tutorial_files`` directory. +All files required to follow this tutorial are present in the `docs/tutorial_files` directory of the [PyCGTOOL repository](https://github.com/jag1g13/pycgtool). -The molecule chosen as a target for this parametrisation is the :math:`\beta_1` antagonist atenolol. +The molecule chosen as a target for this parametrisation is the beta-receptor antagonist atenolol. +## Atomistic Simulation -Atomistic Simulation --------------------- -The reference simulation for the parametrisation of atenolol was performed using the GROMOS 54A7 united atom forcefield with a topology from the `ATB database `_. +The reference simulation for the parametrisation of atenolol was performed using the GROMOS 54A7 united atom forcefield with a topology from the [ATB database](https://atb.uq.edu.au/molecule.py?molid=23433). A single molecule of atenolol was solvated and equilibrated, before collecting a 50 ns trajectory using the GROMACS molecular dynamics simulator. -A reduced copy of this trajectory is provided in the tutorial files (as ``ref.xtc``, ``ref.gro`` contains the initial structure) since the original is prohibitively large. +A reduced copy of this trajectory is provided in the tutorial files (as `ref.xtc`, `ref.gro` contains the initial structure) since the original is prohibitively large. -Mapping Design --------------- -Designing a suitable mapping from the atomistic to the coarse-grained representation requires some experience and a degree of `chemical intuition`, but the ease with which the mapping may be modified using PyCGTOOL allows the mapping to be iterated much more quickly than if the construction of the CG model were to be performed manually. +## Mapping Design + +Designing a suitable mapping from the atomistic to the coarse-grained representation requires some experience and a degree of 'chemical intuition', but the ease with which the mapping may be modified using PyCGTOOL allows the mapping to be iterated much more quickly than if the construction of the CG model were to be performed manually. The process of designing a mapping involves splitting the molecule into fragments, each of which contains approximately four heavy atoms. Start by finding functional groups such as amides or carboxylates, each of which may become a single bead. @@ -31,120 +29,144 @@ It will probably be the case that there is no obviously best mapping and bond to Once the mapping and bond topology have been determined, they must be put into a format readable by PyCGTOOL. This format is as described in the introduction to PyCGTOOL. The mapping file must contain a molecule header which is the residue name enclosed in square brackets. -Each subsequent line represents a single CG bead and is of the structure (where items in square brackets are optional):: +Each subsequent line represents a single CG bead and is of the structure (where items in square brackets are optional): - [] [ ...] +``` + [] [ ...] +``` -The bonding file has a similar structure with a molecule header followed by lines defining each bond in the format:: +The bonding file has a similar structure with a molecule header followed by lines defining each bond in the format: - +``` + +``` It is not necessary to define angles since PyCGTOOL is able to infer these from the bond network. If only a subset of the possible angles require parameters then they may be listed, preventing automatic enumeration of all possible angles. The mapping used in the paper to describe atenolol (just one of the several possible mappings) is described by the following input files. -``atenolol.map``:: - - [36KB] - N1 P1 N1 C12 C13 C14 - O1 P1 O3 C1 C2 C3 - O2 SP3 O2 C4 - C1 SC3 C5 C6 - C2 SC3 C8 C9 - C3 SC3 C7 C10 - N2 P5 C11 O1 N2 - -``atenolol.bnd``:: - - [36KB] - N1 O1 - O1 O2 - O2 C1 - O2 C2 - C1 C2 - C1 C3 - C2 C3 - C3 N2 - -Model Generation ----------------- +``` +; atenolol.map +[36KB] +N1 P1 N1 C12 C13 C14 +O1 P1 O3 C1 C2 C3 +O2 SP3 O2 C4 +C1 SC3 C5 C6 +C2 SC3 C8 C9 +C3 SC3 C7 C10 +N2 P5 C11 O1 N2 +``` + +``` +; atenolol.bnd +[36KB] +N1 O1 +O1 O2 +O2 C1 +O2 C2 +C1 C2 +C1 C3 +C2 C3 +C3 N2 +``` + +## Model Generation + The process of model generation after having created the mapping and bond definition files is automated by PyCGTOOL. -In the simplest case, a parameter set may be generated simply by passing the four input files to PyCGTOOL:: +In the simplest case, a parameter set may be generated simply by passing the four input files to PyCGTOOL: + +``` +pycgtool ref.gro ref.xtc -m atenolol.map -b atenolol.bnd +``` - pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd +This will create two output files `out.gro`, the mapped CG coordinates, and `out.itp`, the calculated CG model parameters. -This will create two output files ``out.gro``, the mapped CG coordinates, and ``out.itp``, the calculated CG model parameters. +## Running the CG Simulation -Running the CG Simulation -------------------------- Note: These instructions assume the use of GROMACS 5.0 or newer. From this stage the usual preparation of MARTINI/GROMACS simulations applies. -The output coordinates ``out.gro`` must be solvated using the GROMACS tool `gmx solvate` with the options:: +The output coordinates `out.gro` must be solvated using the GROMACS tool `gmx solvate` with the options: - gmx solvate -cp out.gro -cs ../../data/water.gro -o solv.gro -radius 0.21 +``` +gmx solvate -cp out.gro -cs ../../data/water.gro -o solv.gro -radius 0.21 +``` + +When we run this, GROMACS will tell us how many solvent molecules have been added - remember this number! Since MARTINI water cannot be automatically added to the `.top` file, this must be done manually. -A template file, ``template.top``, is provided. -Copy this to ``topol.top`` and add the line "W 251" to the bottom, since 251 should be the number of water molecules added by `gmx solvate`. +A template file, `template.top`, is provided. +Copy this to `topol.top` and add a new line to the bottom with a `W`, a space, then the number of solvent molecules added by `gmx solvate`. -The three stages of simulation: minimisation, equilibration, and production may then be run:: +The three stages of simulation: minimisation, equilibration, and production may then be run: - gmx grompp -f em.mdp -c solv.gro -p topol.top -o em.tpr - gmx mdrun -deffnm em +``` +gmx grompp -f em.mdp -c solv.gro -p topol.top -o em.tpr +gmx mdrun -deffnm em - gmx grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr - gmx mdrun -deffnm npt -v +gmx grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr +gmx mdrun -deffnm npt -v - gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr - gmx mdrun -deffnm md -v +gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr +gmx mdrun -deffnm md -v +``` These simulations should take a few minutes on a modern desktop. -Model Validation ----------------- +## Model Validation + It is recommended to perform validation before using a generated CG model for production simulations, so that we may have confidence in its ability to replicate the behaviour of the molecule being studied. -The methods of validation applied in the PyCGTOOL paper are a comparison of the distribution of bonded term measurements between the CG test simulation and the atomistic reference simulation, and a comparison of the radius of gyration between these two simulations. -Additionally, other methods of validation should be applied relevant to the class of molecule being studied; for instance, validation of membrane lipids should compare the membrane thickness and surface area per lipid to the atomistic reference.o +The methods of validation applied in the [PyCGTOOL paper](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00096) are a comparison of the distribution of bonded term measurements between the CG test simulation and the atomistic reference simulation, and a comparison of the radius of gyration between these two simulations. +Additionally, other methods of validation should be applied relevant to the class of molecule being studied; for instance, validation of membrane lipids should compare the membrane thickness and surface area per lipid to the atomistic reference. To compare the distribution of bonded terms, we must first rerun PyCGTOOL to generate samples of the bonded measurements. -For the atomistic reference simulation, this can be done by running:: +For the atomistic reference simulation, this can be done by running: - pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd --advanced +``` +pycgtool ref.gro ref.xtc -m atenolol.map -b atenolol.bnd --dump-measurements +``` -In the menu, set the advanced option `dump_measurements` to `True` by selecting it with the arrow keys and toggling with the enter key. -Once this option has been set, continue by pressing the q key. -PyCGTOOL will now output a sample of each measured bond length and angle (but since the reference trajectory is short, the target sample size is not met and all values are collected), in the files ``36KB_length.dat`` and ``36KB_angle.dat``. +PyCGTOOL will output a sample of each measured bond length and angle, in the files `36KB_length.dat` and `36KB_angle.dat`. +Since the reference trajectory is short this will give us the measurements from every frame, but for longer trajectories it gives us a sample of 10,000 values to make the analysis quicker. Since we will be collecting samples of the same measurements from the CG simulation, these files should be renamed to, for instance, `ref_length.dat` and `ref_angle.dat`. -Collect the same samples for the CG simulation using:: +Next, we collect the same samples for the CG simulation using: - pycgtool.py -g md.gro -x md.xtc -b atenolol.bnd +``` +pycgtool md.gro md.xtc -b atenolol.bnd +``` -Since we provide a bond file, but not a mapping file, PyCGTOOL will know that this is intended to simply collect bond measurements and will automatically set the `dump_measurements` option to `True`. -Again, the files created will be called ``36KB_length.dat`` and ``36KB_angle.dat``. +Since we provide a bond file, but not a mapping file, PyCGTOOL will know that this is intended to collect bond measurements and will set the `--dump-measurements` option automatically. +Again, the files created will be called `36KB_length.dat` and `36KB_angle.dat`. -These samples were compared in the paper using an R script to generate a series of boxplots, but a simpler Python script is provided which may be used to compare the mean and standard deviations of the samples:: +These samples were compared in the paper using an R script to generate a series of boxplots, but a simpler Python script is provided which may be used to compare the mean and standard deviations of the samples: - ./average_columns.py ref_length.dat 36KB_length.dat - ./average_columns.py ref_angle.dat 36KB_angle.dat +``` +./average_columns.py ref_length.dat 36KB_length.dat +./average_columns.py ref_angle.dat 36KB_angle.dat +``` If the automatically generated parameters provide an accurate representation of the reference structure, the percentage error between the two samples will be small. -Validation of the more general molecular conformation may be performed by comparison of the radius of gyration of the reference and CG models. -This may be performed using the standard GROMACS too `gmx gyrate`:: +Validation of the more general molecular conformation may be performed by comparison of the radius of gyration of the reference and CG models +This may be performed using the standard GROMACS too `gmx gyrate`: - gmx gyrate -f ref.xtc -s ref-for-rgyr.tpr -o ref-gyr.xvg - gmx gyrate -f md.xtc -s md.tpr -o cg-gyr.xvg +``` +gmx gyrate -f ref.xtc -s ref-for-rgyr.tpr -o ref-gyr.xvg +gmx gyrate -f md.xtc -s md.tpr -o cg-gyr.xvg +``` In both cases select the 36KB group as the one on which to perform the calculation. These commands will calculate the radius of gyration for each trajectory frame for both the reference and CG simulations. -The resulting `.xvg` files may be visualised using a graphing program such as `xmgrace` or compared in the same way as the bonded samples, using:: +The resulting `.xvg` files may be visualised using a graphing program such as `xmgrace` or compared in the same way as the bonded samples, using: - ./average_columns.py ref-gyr.xvg cg-gyr.xvg +``` +./average_columns.py ref-gyr.xvg cg-gyr.xvg +``` As before, a small percentage difference in each of the columns suggests good replication of gross conformation. +Note that the first column is the time in picoseconds, so don't worry if that column doesn't match - the other four columns are the total radius of gyration, and components along the X, Y and Z axes respectively. In addition to these simple forms of validation, it is recommended that further validation, relevant to the class of molecule, is performed. In the case of membane lipids, for instance, this may take the form of an assessment of membrane thickness and surface area per lipid. diff --git a/doc/tutorial_files/Makefile b/docs/tutorial_files/Makefile similarity index 78% rename from doc/tutorial_files/Makefile rename to docs/tutorial_files/Makefile index 35bd7f9..543529a 100644 --- a/doc/tutorial_files/Makefile +++ b/docs/tutorial_files/Makefile @@ -1,7 +1,7 @@ all: pycgtool cgprepare em npt md samples rgyr pycgtool: - ../../pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd + pycgtool ref.gro ref.xtc -m atenolol.map -b atenolol.bnd cgprepare: gmx solvate -cp out.gro -cs ../../data/water.gro -o solv.gro -radius 0.21 @@ -21,10 +21,10 @@ md: gmx mdrun -deffnm md -v samples: - ../../pycgtool.py -g ref.gro -x ref.xtc -m atenolol.map -b atenolol.bnd --advanced + pycgtool ref.gro ref.xtc -m atenolol.map -b atenolol.bnd --advanced mv {36KB,ref}_length.dat mv {36KB,ref}_angle.dat - ../../pycgtool.py -g md.gro -x md.xtc -b atenolol.bnd + pycgtool md.gro md.xtc -b atenolol.bnd comparesamples: ./average_columns.py ref_length.dat 36KB_length.dat diff --git a/doc/tutorial_files/atenolol.bnd b/docs/tutorial_files/atenolol.bnd similarity index 100% rename from doc/tutorial_files/atenolol.bnd rename to docs/tutorial_files/atenolol.bnd diff --git a/doc/tutorial_files/atenolol.map b/docs/tutorial_files/atenolol.map similarity index 77% rename from doc/tutorial_files/atenolol.map rename to docs/tutorial_files/atenolol.map index c31cd79..57268b0 100644 --- a/doc/tutorial_files/atenolol.map +++ b/docs/tutorial_files/atenolol.map @@ -2,7 +2,7 @@ N1 P1 N1 C12 C13 C14 O1 P1 O3 C1 C2 C3 O2 SP3 O2 C4 -C1 SC2 C5 C6 -C2 SC2 C8 C9 +C1 SC3 C5 C6 +C2 SC3 C8 C9 C3 SC3 C7 C10 N2 P5 C11 O1 N2 diff --git a/doc/tutorial_files/average_columns.py b/docs/tutorial_files/average_columns.py similarity index 89% rename from doc/tutorial_files/average_columns.py rename to docs/tutorial_files/average_columns.py index f96726d..6841ac8 100755 --- a/doc/tutorial_files/average_columns.py +++ b/docs/tutorial_files/average_columns.py @@ -1,46 +1,52 @@ #!/usr/bin/env python3 -""" -Calculate mean and standard deviation of column data using Welford's one pass algorithm -""" +"""Calculate mean and standard deviation of column data using Welford's one pass algorithm.""" import sys import numpy as np np.set_printoptions(formatter={"float": lambda x: "{0:10.3f}".format(x)}) + def average_columns(filename): with open(filename) as f: mean, sdev = None, None nlines = 0 for line in f: - if not line.strip(): + line = line.strip() + if not line: continue + try: cols = np.array(list(map(float, line.split()))) + except ValueError: continue + if mean is None: mean = np.zeros(len(cols)) sdev = np.zeros(len(cols)) + nlines += 1 delta = cols - mean mean += delta / nlines sdev += delta * (cols - mean) - sdev = np.sqrt(sdev / (nlines - 1)) print("File: {0}".format(filename)) print("Mean: {0}".format(mean)) print("Sdev: {0}".format(sdev)) print() + return (mean, sdev) + def compare_files(filename1, filename2): means = (average_columns(filename1)[0], average_columns(filename2)[0]) print("Diff: {0}".format(means[1] - means[0])) print("%Dif: {0}".format(100. * (means[1] - means[0]) / means[0])) + if __name__ == "__main__": if len(sys.argv) == 2: average_columns(sys.argv[1]) diff --git a/doc/tutorial_files/em.mdp b/docs/tutorial_files/em.mdp similarity index 100% rename from doc/tutorial_files/em.mdp rename to docs/tutorial_files/em.mdp diff --git a/doc/tutorial_files/md.mdp b/docs/tutorial_files/md.mdp similarity index 100% rename from doc/tutorial_files/md.mdp rename to docs/tutorial_files/md.mdp diff --git a/doc/tutorial_files/npt.mdp b/docs/tutorial_files/npt.mdp similarity index 100% rename from doc/tutorial_files/npt.mdp rename to docs/tutorial_files/npt.mdp diff --git a/doc/tutorial_files/ref-for-rgyr.tpr b/docs/tutorial_files/ref-for-rgyr.tpr similarity index 100% rename from doc/tutorial_files/ref-for-rgyr.tpr rename to docs/tutorial_files/ref-for-rgyr.tpr diff --git a/doc/tutorial_files/ref.gro b/docs/tutorial_files/ref.gro similarity index 100% rename from doc/tutorial_files/ref.gro rename to docs/tutorial_files/ref.gro diff --git a/doc/tutorial_files/ref.xtc b/docs/tutorial_files/ref.xtc similarity index 100% rename from doc/tutorial_files/ref.xtc rename to docs/tutorial_files/ref.xtc diff --git a/doc/tutorial_files/template.top b/docs/tutorial_files/template.top similarity index 100% rename from doc/tutorial_files/template.top rename to docs/tutorial_files/template.top diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..dffbd83 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1797 @@ +[[package]] +name = "alabaster" +version = "0.7.12" +description = "A configurable sidebar-enabled Sphinx theme" +category = "main" +optional = false +python-versions = "*" + +[[package]] +name = "astroid" +version = "2.9.0" +description = "An abstract syntax tree for Python with inference 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from pycgtool.functionalforms import FunctionalForms -except SyntaxError: - raise RuntimeError("PyCGTOOL requires Python 3.2 or greater") - -if __name__ == "__main__": - parser = argparse.ArgumentParser(description="Perform coarse-grain mapping of atomistic trajectory") - input_files = parser.add_argument_group("Input files") - input_files.add_argument('-g', '--gro', type=str, required=True, help="GROMACS GRO file") - input_files.add_argument('-m', '--map', type=str, help="Mapping file") - input_files.add_argument('-x', '--xtc', type=str, help="GROMACS XTC file") - input_files.add_argument('-b', '--bnd', type=str, help="Bonds file") - input_files.add_argument('-i', '--itp', type=str, help="GROMACS ITP file") - - parser.add_argument('--advanced', default=False, action='store_true', help="Show advanced options menu") - parser.add_argument('--outputxtc', default=False, action='store_true', help="Output a pseudo-CG trajectory") - parser.add_argument('--quiet', default=False, action='store_true', help="Hide progress bars") - input_files.add_argument('--begin', type=int, default=0, help="Frame number to begin") - input_files.add_argument('--end', type=int, default=-1, help="Frame number to end") - - func_forms = FunctionalForms() - - args = parser.parse_args() - config = Options([ - ("output_name", "out"), - ("output", "gro"), - ("output_xtc", args.outputxtc), - ("map_only", not bool(args.bnd)), - ("map_center", "geom"), - ("constr_threshold", 100000), - ("dump_measurements", bool(args.bnd) and not bool(args.map)), - ("dump_n_values", 10000), - ("output_forcefield", False), - ("temperature", 310), - ("default_fc", False), - ("generate_angles", True), - ("generate_dihedrals", False), - ("length_form", "harmonic"), - ("angle_form", "cosharmonic"), - ("dihedral_form", "harmonic") - ], args) - - if not args.map and not args.bnd: - parser.error("One or both of -m and -b is required.") - - if args.advanced: - try: - config.interactive() - except KeyboardInterrupt: - sys.exit(0) - else: - print("Using GRO: {0}".format(args.gro)) - print("Using XTC: {0}".format(args.xtc)) - - if config.map_only: - map_only(args, config) - else: - main(args, config) diff --git a/pycgtool/__main__.py b/pycgtool/__main__.py new file mode 100755 index 0000000..fde9579 --- /dev/null +++ b/pycgtool/__main__.py @@ -0,0 +1,348 @@ +#!/usr/bin/env python3 + +import argparse +import cProfile +import logging +import pathlib +import pkg_resources +import sys +import textwrap +import time +import typing + +from rich.logging import RichHandler + +from pycgtool.frame import Frame +from pycgtool.mapping import Mapping +from pycgtool.bondset import BondSet +from pycgtool.forcefield import ForceField + +PathLike = typing.Union[pathlib.Path, str] + +logger = logging.getLogger(__name__) + + +class ArgumentValidationError(ValueError): + """Exception raised for invalid combinations of command line arguments.""" + + +class PyCGTOOL: + def __init__(self, config): + self.config = config + + self.in_frame = Frame( + topology_file=self.config.topology, + trajectory_file=self.config.trajectory, # May be None + frame_start=self.config.begin, + frame_end=self.config.end, + ) + + self.mapping = None + self.out_frame = self.in_frame + if self.config.mapping: + self.mapping, self.out_frame = self.apply_mapping(self.in_frame) + + if self.out_frame.natoms == 0: + # The following steps won't work with frames containing no atoms + logger.warning( + "Mapped trajectory contains no atoms - check your mapping file is correct!" + ) + return + + self.bondset = None + if self.config.bondset: + self.bondset = BondSet(self.config.bondset, self.config) + self.measure_bonds() + + if self.config.output_xtc: + self.out_frame.save(self.get_output_filepath("xtc")) + + def get_output_filepath(self, ext: PathLike) -> pathlib.Path: + """Get file path for an output file by extension. + + Creates the output directory if missing. + """ + out_dir = pathlib.Path(self.config.out_dir) + out_dir.mkdir(parents=True, exist_ok=True) + return out_dir.joinpath(self.config.output_name + "." + ext) + + def apply_mapping(self, in_frame: Frame) -> typing.Tuple[Mapping, Frame]: + """Map input frame to output using requested mapping file.""" + mapping = Mapping( + self.config.mapping, self.config, itp_filename=self.config.itp + ) + out_frame = mapping.apply(in_frame) + out_frame.save(self.get_output_filepath("gro"), frame_number=0) + + if self.config.backmapper_resname and self.out_frame.n_frames > 1: + try: + self.train_backmapper(self.config.resname) + + except ImportError: + logger.error("MDPlus must be installed to perform backmapping") + + return mapping, out_frame + + def measure_bonds(self) -> None: + """Measure bonds at the end of a run.""" + self.bondset.apply(self.out_frame) + + if self.mapping is not None and self.out_frame.n_frames > 1: + # Only perform Boltzmann Inversion if we have a mapping and a trajectory. + # Otherwise we get infinite force constants. + logger.info("Starting Boltzmann Inversion") + self.bondset.boltzmann_invert() + logger.info("Finished Boltzmann Inversion") + + if self.config.output_forcefield: + logger.info("Writing GROMACS forcefield directory") + out_dir = pathlib.Path(self.config.out_dir) + forcefield = ForceField(self.config.output_name, dir_path=out_dir) + forcefield.write(self.config.output_name, self.mapping, self.bondset) + logger.info("Finished writing GROMACS forcefield directory") + + else: + self.bondset.write_itp( + self.get_output_filepath("itp"), mapping=self.mapping + ) + + if self.config.dump_measurements: + logger.info("Writing bond measurements to file") + self.bondset.dump_values(self.config.dump_n_values, self.config.out_dir) + logger.info("Finished writing bond measurements to file") + + def train_backmapper(self, resname: str): + from mdplus.multiscale import GLIMPS + + sel = f"resname {resname}" + + aa_subset_traj = self.in_frame._trajectory.atom_slice( + self.in_frame._trajectory.topology.select(sel) + ) + cg_subset_traj = self.out_frame._trajectory.atom_slice( + self.out_frame._trajectory.topology.select(sel) + ) + + logger.info("Training backmapper") + # Param x_valence is approximate number of bonds per CG bead + # Values greater than 2 fail for small molecules e.g. sugar test case + backmapper = GLIMPS(x_valence=2) + backmapper.fit(cg_subset_traj.xyz, aa_subset_traj.xyz) + logger.info("Finished training backmapper") + + backmapper.save(self.get_output_filepath("backmapper.pkl")) + + +class BooleanAction(argparse.Action): + """Set up a boolean argparse argument with matching `--no` argument. + + Based on https://thisdataguy.com/2017/07/03/no-options-with-argparse-and-python/ + """ + + def __init__(self, option_strings, dest, nargs=None, **kwargs): + super().__init__(option_strings, dest, nargs=0, **kwargs) + + def __call__(self, parser, namespace, values, option_string=None): + setattr(namespace, self.dest, not option_string.startswith("--no-")) + + +def parse_arguments(arg_list): + # fmt: off + parser = argparse.ArgumentParser( + prog='pycgtool', + formatter_class=argparse.ArgumentDefaultsHelpFormatter, + description="Generate coarse-grained molecular dynamics models from atomistic trajectories." + ) + + parser.add_argument('-v', '--version', action='version', + version=pkg_resources.get_distribution('pycgtool').version) + + # Input files + input_files = parser.add_argument_group("input files") + + input_files.add_argument('topology', type=str, + help="AA simulation topology - e.g. PDB, GRO, etc.") + input_files.add_argument('trajectory', type=str, nargs='?', + help="AA simulation trajectory - e.g. XTC, DCD, etc.") + input_files.add_argument('-m', '--mapping', type=str, + help="Mapping file") + input_files.add_argument('-b', '--bondset', type=str, + help="Bonds file") + input_files.add_argument('-i', '--itp', type=str, + help="GROMACS ITP file") + input_files.add_argument('--begin', type=int, default=0, + help="Trajectory frame number to begin") + input_files.add_argument('--end', type=int, default=None, + help="Trajectory frame number to end") + + # Output files + output_files = parser.add_argument_group("output files") + + output_files.add_argument('--out-dir', default='.', type=str, + help="Directory where output files should be placed") + output_files.add_argument("--output-name", default="out", + help="Base name of output files") + output_files.add_argument('--output-xtc', '--no-output-xtc', default=False, action=BooleanAction, + help="Output a pseudo-CG trajectory?") + output_files.add_argument("--output", default="gro", + help="Coordinate output format") + output_files.add_argument("--output-forcefield", '--no-output-forcefield', default=False, action=BooleanAction, + help="Output GROMACS forefield directory?") + output_files.add_argument("--dump-measurements", '--no-dump-measurements', default=False, action=BooleanAction, + help="Output sample of bond measurements?") + output_files.add_argument("--dump-n-values", type=int, default=10000, + help="Size of sample of measurements to output") + + # Mapping options + mapping_options = parser.add_argument_group("mapping options") + + mapping_options.add_argument("--map-center", default="geom", + choices=["geom", "mass", "first"], + help="Mapping method") + mapping_options.add_argument("--virtual-map-center", default="geom", + choices=["geom", "mass"], + help="Virtual site mapping method") + mapping_options.add_argument("--backmapper-resname", default=None, + help="Residue name for which to train a backmapper") + + # Bond options + bond_options = parser.add_argument_group("bond options") + + bond_options.add_argument("--constr-threshold", type=float, default=100000, + help="Convert bonds with force constants over [value] to constraints") + bond_options.add_argument("--temperature", type=float, default=310, + help="Temperature of reference simulation") + bond_options.add_argument("--default-fc", '--no-default-fc', default=False, action=BooleanAction, + help="Use default MARTINI force constants?") + bond_options.add_argument("--generate-angles", '--no-generate-angles', default=True, action=BooleanAction, + help="Generate angles from bonds?") + bond_options.add_argument("--generate-dihedrals", '--no-generate-dihedrals', default=False, action=BooleanAction, + help="Generate dihedrals from bonds?") + bond_options.add_argument("--length-form", default="Harmonic", + help="Form of bond potential") + bond_options.add_argument("--angle-form", default="CosHarmonic", + help="Form of angle potential") + bond_options.add_argument("--dihedral-form", default="Harmonic", + help="Form of dihedral potential") + + # Run options + run_options = parser.add_argument_group("run options") + + run_options.add_argument('--profile', '--no-profile', default=False, action=BooleanAction, + help="Profile performance?") + run_options.add_argument('--log-level', default='INFO', + choices=('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'), + help="Which log messages should be shown?") + + # Secret options + + secret_options = parser.add_argument_group("secret options") + secret_options.add_argument('--curmudgeon', default=False, action='store_true', + help=argparse.SUPPRESS) + secret_options.add_argument('--cow', default=False, action='store_true', + help=argparse.SUPPRESS) + # fmt: on + + args = parser.parse_args(arg_list) + + try: + args = validate_arguments(args) + + except ArgumentValidationError as exc: + parser.error(exc) + + return args + + +def validate_arguments(args): + """Check that arguments are not contradictory and modify where necessary. + + :param args: Parsed arguments from ArgumentParser + """ + if not args.dump_measurements: + args.dump_measurements = bool(args.bondset) and not bool(args.mapping) + logger.info( + "Argument --dump-measurements has been set because you have provided a bondset but no mapping" + ) + + if not args.mapping and not args.bondset: + raise ArgumentValidationError("One or both of -m and -b is required") + + if args.backmapper_resname: + logger.warning( + "Backmapping is an experimental feature and has not yet been fully validated" + ) + + return args + + +def main(): + start_time = time.time() + args = parse_arguments(sys.argv[1:]) + + if args.curmudgeon: + logging.basicConfig(level=args.log_level) + + else: + logging.basicConfig( + level=args.log_level, + format="%(message)s", + datefmt="[%X]", + handlers=[RichHandler(rich_tracebacks=True)], + ) + + banner = r""" + _____ _____ _____ _______ ____ ____ _ + | __ \ / ____/ ____|__ __/ __ \ / __ \| | + | |__) | _| | | | __ | | | | | | | | | | + | ___/ | | | | | | |_ | | | | | | | | | | | + | | | |_| | |___| |__| | | | | |__| | |__| | |____ + |_| \__, |\_____\_____| |_| \____/ \____/|______| + __/ | + |___/ + """ # noqa + + banner = textwrap.dedent(banner) + if args.cow: + try: + import cowsay + + banner = cowsay.cow("PyCGTOOL") + + except ImportError: + pass + + else: + logger.info( + "[bold blue]%s[/]", textwrap.dedent(banner), extra={"markup": True} + ) + + logger.info(30 * "-") + logger.info("Topology:\t%s", args.topology) + logger.info("Trajectory:\t%s", args.trajectory) + logger.info("Mapping:\t%s", args.mapping) + logger.info("Bondset:\t%s", args.bondset) + logger.info(30 * "-") + + try: + if args.profile: + with cProfile.Profile() as profiler: + pycgtool = PyCGTOOL(args) + + profiler.dump_stats("gprof.out") + + else: + pycgtool = PyCGTOOL(args) + + elapsed_time = time.time() - start_time + logger.info( + "Processed %d frames in %.2f s", pycgtool.out_frame.n_frames, elapsed_time + ) + logger.info("Finished processing - goodbye!") + + except Exception as exc: + logger.exception(exc) + + +if __name__ == "__main__": + main() diff --git a/pycgtool/bondset.py b/pycgtool/bondset.py index e8184db..3a4dca5 100644 --- a/pycgtool/bondset.py +++ b/pycgtool/bondset.py @@ -1,41 +1,47 @@ -""" -Module containing classes to calculate bonded properties from a Frame. +"""Module containing classes to calculate bonded properties from a Frame. BondSet contains a dictionary of lists of Bonds. Each list corresponds to a single molecule. """ import itertools -import math import logging +import math +import pathlib +import typing import numpy as np +import mdtraj - -try: - from tqdm import tqdm -except ImportError: - from .util import tqdm_dummy as tqdm - -from .util import sliding, dist_with_pbc, transpose_and_sample -from .util import extend_graph_chain, backup_file -from .util import vector_len, vector_cross, vector_angle, vector_angle_signed +from .mapping import VirtualMap +from .functionalforms import get_functional_forms from .parsers.cfg import CFG -from .functionalforms import FunctionalForms +from .util import ( + circular_mean, + circular_variance, + extend_graph_chain, + file_write_lines, + sliding, + transpose_and_sample, +) logger = logging.getLogger(__name__) +PathLike = typing.Union[str, pathlib.Path] + class Bond: - """ - Class holding the properties of a single bonded term. + """Class holding the properties of a single bonded term. Bond lengths, angles and dihedrals are all equivalent, distinguished by the number of atoms present. """ - __slots__ = ["atoms", "atom_numbers", "values", "eqm", "fconst", "gromacs_type_id", "_func_form"] - def __init__(self, atoms, atom_numbers=None, func_form=None): - """ - Create a single bond definition. + def __init__( + self, + atoms: typing.Iterable[str], + atom_numbers: typing.Optional[typing.Iterable[int]] = None, + func_form=None, + ): + """Create a single bond definition. :param List[str] atoms: List of atom names defining the bond :param List[int] atom_numbers: List of atom numbers defining the bond @@ -50,32 +56,41 @@ def __init__(self, atoms, atom_numbers=None, func_form=None): self._func_form = func_form self.gromacs_type_id = func_form.gromacs_type_id_by_natoms(len(atoms)) - def __len__(self): - return len(self.atoms) - def __iter__(self): return iter(self.atoms) - def boltzmann_invert(self, temp=310): - """ - Perform Boltzmann Inversion using measured values of bond to calculate equilibrium value and force constant. + def boltzmann_invert(self, temp: float = 310) -> None: + """Perform Boltzmann Inversion using measured values of bond to calculate equilibrium value and force constant. :param temp: Temperature at which the simulation was performed """ - if not self.values: - raise ValueError("No bonds were measured between atoms {0}".format(self.atoms)) + if len(self.values) == 0: + raise ValueError( + "No bonds were measured between beads {0}".format(self.atoms) + ) - values = np.array(self.values) + values = self.values + if not isinstance(self.values, np.ndarray): + values = np.array(self.values) with np.errstate(divide="raise"): self.eqm = self._func_form.eqm(values, temp) + + # TODO: consider moving this correction to the functional form + # If dihedral, get value to shift cosine function by, NOT equilibrium value + if len(self.atoms) == 4: + two_pi = 2 * np.pi + self.eqm -= np.pi + self.eqm = ((self.eqm + np.pi) % two_pi) - np.pi + try: self.fconst = self._func_form.fconst(values, temp) + except FloatingPointError: # Happens when variance is 0, i.e. we only have one value - self.fconst = float("inf") + self.fconst = math.inf - def __repr__(self): + def __repr__(self) -> str: try: return "".format( ", ".join(self.atoms), self.eqm, self.fconst @@ -85,56 +100,69 @@ def __repr__(self): class BondSet: - """ - Class used to perform bond measurements in a Frame. + """Class used to perform bond measurements in a Frame. - BondSet contains a dictionary of lists of Bonds. Each list corresponds to a single molecule. + BondSet contains a dictionary of lists of Bonds. Each list corresponds to a single molecule. """ - def __init__(self, filename, options): - """ - Read in bonds from a file. - :param filename: File to read - :return: Instance of BondSet - """ - self._molecules = {} - - self._fconst_constr_threshold = options.constr_threshold + def _get_default_func_forms(self, options): try: - self._temperature = options.temperature - except AttributeError: - self._temperature = 310. + default_fc = options.default_fc - try: - self._default_fc = options.default_fc except AttributeError: - self._default_fc = False - - # Setup default functional forms - functional_forms = FunctionalForms() - if self._default_fc: - default_forms = ["MartiniDefaultLength", "MartiniDefaultAngle", "MartiniDefaultDihedral"] + default_fc = False + + if default_fc: + default_forms = [ + "MartiniDefaultLength", + "MartiniDefaultAngle", + "MartiniDefaultDihedral", + ] else: default_forms = ["Harmonic", "CosHarmonic", "Harmonic"] - self._functional_forms = [None, None] - self._functional_forms.extend(map(lambda x: functional_forms[x], default_forms)) + + functional_forms_map = get_functional_forms() + + functional_forms = [None, None] + functional_forms.extend( + [functional_forms_map[ff].value for ff in default_forms] + ) try: - self._functional_forms[2] = functional_forms[options.length_form] + functional_forms[2] = functional_forms_map[options.length_form].value except AttributeError: pass try: - self._functional_forms[3] = functional_forms[options.angle_form] + functional_forms[3] = functional_forms_map[options.angle_form].value except AttributeError: pass try: - self._functional_forms[4] = functional_forms[options.dihedral_form] + functional_forms[4] = functional_forms_map[options.dihedral_form].value except AttributeError: pass + return functional_forms + + def __init__(self, filename: PathLike, options): + """Read in bonds from a file. + + :param filename: File to read + :return: Instance of BondSet + """ + self._molecules = {} + + self._fconst_constr_threshold = options.constr_threshold + + try: + self._temperature = options.temperature + except AttributeError: + self._temperature = 310.0 + + self._functional_forms = self._get_default_func_forms(options) + with CFG(filename) as cfg: for mol_name, mol_section in cfg.items(): self._molecules[mol_name] = [] @@ -142,15 +170,27 @@ def __init__(self, filename, options): angles_defined = False for atomlist in mol_section: - try: - # TODO consider best way to override default func form - # On per bond, or per type basis - func_form = functional_forms[atomlist[-1]] - except AttributeError: - func_form = self._functional_forms[len(atomlist)] + is_angle_or_dihedral = len(atomlist) > 2 + mean_function = ( + circular_mean if is_angle_or_dihedral else np.nanmean + ) + variance_function = ( + circular_variance if is_angle_or_dihedral else np.nanvar + ) + + # Construct instance of Boltzmann Inversion function and + # inject dependencies for mean and variance functions + # TODO: Should we allow overriding functional forms per bond? + func_form = self._functional_forms[len(atomlist)]( + mean_function, variance_function + ) if {x for x in atomlist if atomlist.count(x) > 1}: - raise ValueError("Defined bond '{0}' contains duplicate atoms".format(atomlist)) + raise ValueError( + "Defined bond '{0}' contains duplicate atoms".format( + atomlist + ) + ) mol_bonds.append(Bond(atoms=atomlist, func_form=func_form)) if len(atomlist) > 2: @@ -161,16 +201,29 @@ def __init__(self, filename, options): if options.generate_angles: for atomlist in angles: - mol_bonds.append(Bond(atoms=atomlist, func_form=self._functional_forms[3])) + mol_bonds.append( + Bond( + atoms=atomlist, + func_form=self._functional_forms[3]( + circular_mean, circular_variance + ), + ) + ) if options.generate_dihedrals: for atomlist in dihedrals: - mol_bonds.append(Bond(atoms=atomlist, func_form=self._functional_forms[4])) + mol_bonds.append( + Bond( + atoms=atomlist, + func_form=self._functional_forms[4]( + circular_mean, circular_variance + ), + ) + ) @staticmethod def _create_angles(mol_bonds): - """ - Create angles and dihedrals from bonded topology. + """Create angles and dihedrals from bonded topology. :param mol_bonds: List of bonds within a molecule to generate angles for :return: List of angle and dihedral bond name tuples @@ -180,9 +233,30 @@ def _create_angles(mol_bonds): dihedrals = extend_graph_chain(angles, bonds) return angles, dihedrals - def get_bond_lengths(self, mol, with_constr=False): + def get_bonds( + self, + mol: str, + natoms: int, + select: typing.Callable[[Bond], bool] = lambda x: True, + ) -> typing.List[Bond]: + """Return list of bonds from molecule containing natoms atoms. + + :param str mol: Molecule name + :param int natoms: Number of atoms in bond, i.e. 2 for bond length, 3 for angle, 4 for dihedral + :param function select: Optional lambda, return only bonds for which this is True + :return List[Bond]: List of bonds """ - Return list of all bond lengths in molecule. May include constraints. + if natoms == -1: + return [bond for bond in self._molecules[mol] if select(bond)] + + return [ + bond + for bond in self._molecules[mol] + if len(bond.atoms) == natoms and select(bond) + ] + + def get_bond_lengths(self, mol, with_constr=False): + """Return list of all bond lengths in molecule. May include constraints. :param mol: Molecule name to return bonds for :param with_constr: Include constraints? @@ -190,21 +264,27 @@ def get_bond_lengths(self, mol, with_constr=False): """ if with_constr: return [bond for bond in self._molecules[mol] if len(bond.atoms) == 2] - else: - return [bond for bond in self._molecules[mol] if len(bond.atoms) == 2 and bond.fconst < self._fconst_constr_threshold] + + return [ + bond + for bond in self._molecules[mol] + if len(bond.atoms) == 2 and bond.fconst < self._fconst_constr_threshold + ] def get_bond_length_constraints(self, mol): - """ - Return list of all bond length constraints in molecule. + """Return list of all bond length constraints in molecule. :param mol: Molecule name to return bonds for :return: List of bonds """ - return [bond for bond in self._molecules[mol] if len(bond.atoms) == 2 and bond.fconst >= self._fconst_constr_threshold] + return [ + bond + for bond in self._molecules[mol] + if len(bond.atoms) == 2 and bond.fconst >= self._fconst_constr_threshold + ] def get_bond_angles(self, mol, exclude_triangle=True): - """ - Return list of all bond angles in molecule. + """Return list of all bond angles in molecule. :param mol: Molecule name to return bonds for :param exclude_triangle: Exclude angles that are part of a triangle? @@ -213,12 +293,18 @@ def get_bond_angles(self, mol, exclude_triangle=True): angles = [bond for bond in self._molecules[mol] if len(bond.atoms) == 3] if exclude_triangle: - edges = [tuple(bond.atoms) for bond in self.get_bond_lengths(mol, with_constr=True)] + edges = [ + tuple(bond.atoms) + for bond in self.get_bond_lengths(mol, with_constr=True) + ] def is_triangle(atoms): triangle_edges = 0 for j in range(3): - if (atoms[j - 1], atoms[j]) in edges or (atoms[j], atoms[j - 1]) in edges: + if (atoms[j - 1], atoms[j]) in edges or ( + atoms[j], + atoms[j - 1], + ) in edges: triangle_edges += 1 return triangle_edges >= 3 @@ -227,17 +313,22 @@ def is_triangle(atoms): return angles def get_bond_dihedrals(self, mol): - """ - Return list of all bond dihedrals in molecule. + """Return list of all bond dihedrals in molecule. :param mol: Molecule name to return bonds for :return: List of bonds """ return [bond for bond in self._molecules[mol] if len(bond.atoms) == 4] - def _populate_atom_numbers(self, mapping): + def get_virtual_beads(self, mapping): + """Return list of all virtual beads in molecule + :param mapping: + :return: list of virtual beads """ - Add atom numbers to all bonds. + return [bead for bead in mapping if isinstance(bead, VirtualMap)] + + def _populate_atom_numbers(self, mapping): + """Add atom numbers to all bonds. Uses previously defined atom names. @@ -254,168 +345,258 @@ def _populate_atom_numbers(self, mapping): for bond in self._molecules[mol]: # TODO this causes issue #8 try: - bond.atom_numbers = [index.index(atom.lstrip("+-")) for atom in bond.atoms] + bond.atom_numbers = [ + index.index(atom.lstrip("+-")) for atom in bond.atoms + ] except ValueError as e: - missing = [atom for atom in bond.atoms if atom.lstrip("+-") not in index] - e.args = ("Bead(s) {0} do(es) not exist in residue {1}".format(missing, mol),) + missing = [ + atom for atom in bond.atoms if atom.lstrip("+-") not in index + ] + e.args = ( + "Bead(s) {0} do(es) not exist in residue {1}".format( + missing, mol + ), + ) raise def write_itp(self, filename, mapping): - """ - Output a GROMACS .itp file containing atoms/beads and bonded terms. + """Output a GROMACS .itp file containing atoms/beads and bonded terms. :param filename: Name of output file :param mapping: AA->CG Mapping from which to collect bead properties """ self._populate_atom_numbers(mapping) - backup_file(filename) - - def write_bond_angle_dih(bonds, section_header, itp, print_fconst=True, multiplicity=None, rad2deg=False): + file_write_lines(filename, self.itp_text(mapping)) + + def itp_text(self, mapping): + atom_template = { + "nomass": "{0:4d} {1:4s} {2:4d} {3:4s} {4:4s} {5:4d} {6:8.3f}", + "mass": "{0:4d} {1:4s} {2:4d} {3:4s} {4:4s} {5:4d} {6:8.3f} {7:8.3f}", + } + + def write_bond_angle_dih( + bonds, section_header, print_fconst=True, multiplicity=None, rad2deg=False + ): + ret_lines = [] if bonds: - print("\n[ {0:s} ]".format(section_header), file=itp) + ret_lines.append("\n[ {0:s} ]".format(section_header)) for bond in bonds: - line = " ".join(["{0:4d}".format(atnum + 1) for atnum in bond.atom_numbers]) + line = " ".join( + ["{0:4d}".format(atnum + 1) for atnum in bond.atom_numbers] + ) eqm = math.degrees(bond.eqm) if rad2deg else bond.eqm line += " {0:4d} {1:12.5f}".format(bond.gromacs_type_id, eqm) if print_fconst: line += " {0:12.5f}".format(bond.fconst) if multiplicity is not None: line += " {0:4d}".format(multiplicity) - print(line, file=itp) - - with open(filename, "w") as itp: - header = ("; \n" - "; Topology prepared automatically using PyCGTOOL \n" - "; James Graham 2016 \n" - "; University of Southampton \n" - "; https://github.com/jag1g13/pycgtool \n" - ";") - print(header, file=itp) - - # Print molecule - not_calc = " Parameters have not been calculated." - for mol in self._molecules: - if mol not in mapping: - logger.warning("Molecule '{0}' present in bonding file, but not in mapping.".format(mol) + not_calc) - continue - if not all((bond.fconst is not None for bond in self._molecules[mol])): - logger.warning("Molecule '{0}' has no measured bond values.".format(mol) + not_calc) - continue - - print("\n[ moleculetype ]", file=itp) - print("{0:4s} {1:4d}".format(mol, 1), file=itp) - - print("\n[ atoms ]", file=itp) - for i, bead in enumerate(mapping[mol]): - # atnum type resnum resname atname c-group charge (mass) - print("{0:4d} {1:4s} {2:4d} {3:4s} {4:4s} {5:4d} {6:8.3f}".format( - i + 1, bead.type, 1, mol, bead.name, i + 1, bead.charge - ), file=itp) - - write_bond_angle_dih(self.get_bond_lengths(mol), "bonds", itp) - write_bond_angle_dih(self.get_bond_angles(mol), "angles", itp, rad2deg=True) - write_bond_angle_dih(self.get_bond_dihedrals(mol), "dihedrals", itp, multiplicity=1, rad2deg=True) - write_bond_angle_dih(self.get_bond_length_constraints(mol), "constraints", itp, print_fconst=False) + ret_lines.append(line) - def apply(self, frame): - """ - Calculate bond lengths/angles for a given Frame and store into Bonds. + return ret_lines - :param frame: Frame from which to calculate values - """ - def calc_length(atoms): - vec = dist_with_pbc(atoms[0].coords, atoms[1].coords, frame.box) - return vector_len(vec) + ret_lines = [ + ";", + "; Topology prepared automatically using PyCGTOOL", + "; James Graham 2016", + "; University of Southampton", + "; https://github.com/jag1g13/pycgtool", + ";", + ] # fmt: skip - def calc_angle(atoms): - veca = dist_with_pbc(atoms[0].coords, atoms[1].coords, frame.box) - vecb = dist_with_pbc(atoms[1].coords, atoms[2].coords, frame.box) - return math.pi - vector_angle(veca, vecb) - - def calc_dihedral(atoms): - veca = dist_with_pbc(atoms[0].coords, atoms[1].coords, frame.box) - vecb = dist_with_pbc(atoms[1].coords, atoms[2].coords, frame.box) - vecc = dist_with_pbc(atoms[2].coords, atoms[3].coords, frame.box) - - c1 = vector_cross(veca, vecb) - c2 = vector_cross(vecb, vecc) - - return vector_angle_signed(c1, c2, vecb) - - calc = {2: calc_length, - 3: calc_angle, - 4: calc_dihedral} + # Print molecule + for mol in self._molecules: + if mol not in mapping: + logger.warning( + ( + "Molecule '%s' present in bonding file, but not in mapping. " + "Parameters have not been calculated." + ), + mol, + ) + continue - for prev_res, res, next_res in sliding(frame): - try: - mol_meas = self._molecules[res.name] - except KeyError: - # Bonds have not been specified for molecule - probably water - ignore this residue + if not all(bond.fconst is not None for bond in self._molecules[mol]): + logger.warning( + ( + "Molecule '%s' has no measured bond values. " + "Parameters have not been calculated." + ), + mol, + ) continue - adj_res = {"-": prev_res, - "+": next_res} + ret_lines.append("\n[ moleculetype ]") + ret_lines.append("{0:4s} {1:4d}".format(mol, 1)) + + ret_lines.append("\n[ atoms ]") + + for i, bead in enumerate(mapping[mol], start=1): + # atnum type resnum resname atname c-group charge (mass) + if isinstance(bead, VirtualMap): + ret_lines.append( + atom_template["mass"].format( + i, bead.type, 1, mol, bead.name, i, bead.charge, bead.mass + ) + ) + else: + ret_lines.append( + atom_template["nomass"].format( + i, bead.type, 1, mol, bead.name, i, bead.charge + ) + ) + + virtual_beads = self.get_virtual_beads(mapping[mol]) + if len(virtual_beads) != 0: + ret_lines.append("\n[ virtual_sitesn ]") + excl_lines = [ + "\n[ exclusions ]" + ] # Exclusions section for virtual sites + + for vbead in virtual_beads: + cg_ids = sorted( + [ + bead.num + 1 + for bead in mapping[mol] + if bead.name in vbead.atoms + ] + ) + cg_ids_string = " ".join(map(str, cg_ids)) + ret_lines.append( + "{0:^6d} {1:^6d} {2}".format( + vbead.num + 1, vbead.gromacs_type_id, cg_ids_string + ) + ) + vsite_exclusions = "{} ".format(vbead.num + 1) + cg_ids_string + excl_lines.append(vsite_exclusions) + + ret_lines.extend(excl_lines) + + ret_lines.extend(write_bond_angle_dih(self.get_bond_lengths(mol), "bonds")) + ret_lines.extend( + write_bond_angle_dih(self.get_bond_angles(mol), "angles", rad2deg=True) + ) + ret_lines.extend( + write_bond_angle_dih( + self.get_bond_dihedrals(mol), + "dihedrals", + multiplicity=1, + rad2deg=True, + ) + ) + ret_lines.extend( + write_bond_angle_dih( + self.get_bond_length_constraints(mol), + "constraints", + print_fconst=False, + ) + ) + + return ret_lines - for bond in mol_meas: - try: - # TODO tidy this - atoms = [adj_res.get(name[0], res)[name.lstrip("-+")] for name in bond.atoms] - val = calc[len(atoms)](atoms) - bond.values.append(val) - except (NotImplementedError, TypeError): - # TypeError is raised when residues on end of chain calc bond to next - pass - except ZeroDivisionError as e: - e.args = ("Zero division in calculation of <{0}>".format(" ".join(bond.atoms)),) - raise e - - def boltzmann_invert(self, progress=False): - """ - Perform Boltzmann Inversion of all bonds to calculate equilibrium value and force constant. + def apply(self, frame): + """Calculate bond lengths/angles for all trajectory frames with a Frame instance and store into Bonds. - :param progress: Display a progress bar using tqdm if available + :param frame: Frame from which to calculate values """ - bond_iter = itertools.chain(*self._molecules.values()) - bond_iter_wrap = bond_iter - if progress: - total = sum(map(len, self._molecules.values())) - bond_iter_wrap = tqdm(bond_iter, total=total, ncols=80) - - for bond in bond_iter_wrap: + calc = { + 2: mdtraj.compute_distances, + 3: mdtraj.compute_angles, + 4: mdtraj.compute_dihedrals, + } + + for mol_name, mol_bonds in self._molecules.items(): + for bond in mol_bonds: + bond_indices = [] + + for prev_residue, residue, next_residue in sliding(frame.residues): + adj_res = {"-": prev_residue, "+": next_residue} + + # Need access to adjacent residues, so can't just iterate over these directly + if residue.name == mol_name: + try: + bond_indices.append( + [ + adj_res.get(atom_name[0], residue) + .atom(atom_name.lstrip("-+")) + .index + for atom_name in bond.atoms + ] + ) + + except AttributeError: + # AttributeError is raised when residues on end of chain calc bond to next + pass + + vals = calc[len(bond.atoms)](frame._trajectory, bond_indices) + bond.values = vals.flatten() + + def boltzmann_invert(self) -> None: + """Perform Boltzmann Inversion of all bonds to calculate equilibrium value and force constant.""" + for bond in itertools.chain(*self._molecules.values()): try: bond.boltzmann_invert(temp=self._temperature) except ValueError: pass - # TODO add test - def dump_values(self, target_number=10000): + @staticmethod + def _get_lines_for_bond_dump( + bonds, target_number: typing.Optional[int] = None, rad2deg: bool = False + ) -> typing.List[str]: + """Return a dump of bond measurements as a list of lines of text. + + :param bonds: Iterable of bonds + :param int target_number: Sample size of bonds to dump - None will dump all bonds + :param bool rad2deg: Should bond measurements be converted from radians to degrees? + :return List[str]: Lines of bond measurements dump """ - Output measured bond values to files for length, angles and dihedrals. - - :param target_number: Approx number of sample measurements to output. If None, all samples will be output + ret_lines = [] + for row in transpose_and_sample( + (bond.values for bond in bonds), n=target_number + ): + if rad2deg: + row = [math.degrees(val) for val in row] + + ret_lines.append((len(row) * "{:12.5f}").format(*row)) + return ret_lines + + def dump_values( + self, + target_number: int = 10000, + output_dir: typing.Optional[typing.Union[pathlib.Path, str]] = None, + ) -> None: + """Output measured bond values to files for length, angles and dihedrals. + + :param int target_number: Approx number of sample measurements to output. If None, all samples will be output. + :param output_dir: Directory to write output files to. """ + if output_dir is None: + output_dir = "." - def write_bonds_to_file(bonds, filename, rad2deg=False): - with open(filename, "w") as f: - for row in transpose_and_sample((bond.values for bond in bonds), n=target_number): - if rad2deg: - row = [math.degrees(val) for val in row] - print((len(row) * "{:12.5f}").format(*row), file=f) + # Cast to Path type + output_dir = pathlib.Path(output_dir) for mol in self._molecules: if mol == "SOL": continue + bonds = self.get_bond_lengths(mol, with_constr=True) if bonds: - write_bonds_to_file(bonds, "{0}_length.dat".format(mol)) + lines = BondSet._get_lines_for_bond_dump(bonds, target_number) + file_write_lines(output_dir.joinpath(f"{mol}_length.dat"), lines) bonds = self.get_bond_angles(mol) if bonds: - write_bonds_to_file(bonds, "{0}_angle.dat".format(mol), rad2deg=True) + lines = BondSet._get_lines_for_bond_dump( + bonds, target_number, rad2deg=True + ) + file_write_lines(output_dir.joinpath(f"{mol}_angle.dat"), lines) bonds = self.get_bond_dihedrals(mol) if bonds: - write_bonds_to_file(bonds, "{0}_dihedral.dat".format(mol), rad2deg=True) + lines = BondSet._get_lines_for_bond_dump( + bonds, target_number, rad2deg=True + ) + file_write_lines(output_dir.joinpath(f"{mol}_dihedral.dat"), lines) def __len__(self): return len(self._molecules) diff --git a/data/martini_v2.2.itp b/pycgtool/data/martini_v2.2.itp similarity index 100% rename from data/martini_v2.2.itp rename to pycgtool/data/martini_v2.2.itp diff --git a/data/w.itp b/pycgtool/data/w.itp similarity index 100% rename from data/w.itp rename to pycgtool/data/w.itp diff --git a/data/water.gro b/pycgtool/data/water.gro similarity index 100% rename from data/water.gro rename to pycgtool/data/water.gro diff --git a/data/watermodels.dat b/pycgtool/data/watermodels.dat similarity index 100% rename from data/watermodels.dat rename to pycgtool/data/watermodels.dat diff --git a/pycgtool/forcefield.py b/pycgtool/forcefield.py index 26d8a0f..8fb6339 100644 --- a/pycgtool/forcefield.py +++ b/pycgtool/forcefield.py @@ -3,149 +3,210 @@ """ import os +import pathlib import shutil -import functools +import typing -from .util import dir_up -from .parsers import ITP +from .parsers import CFG +from .util import any_starts_with, backup_file, file_write_lines + +PathLike = typing.Union[pathlib.Path, str] + + +def copy_files( + src_dir: pathlib.Path, dest_dir: pathlib.Path, files: typing.Iterable[str] +) -> None: + """Copy files from one directory to another.""" + for f in files: + src_path = src_dir.joinpath(f) + dest_path = dest_dir.joinpath(f) + shutil.copyfile(str(src_path), str(dest_path)) class ForceField: """ Class used to output a GROMACS .ff forcefield """ - def __init__(self, name): + + def __init__(self, name: str, dir_path: PathLike = pathlib.Path(".")): """ Open a named forcefield directory. If it does not exist it is created. - :param name: Forcefield name to open/create + :param str name: Forcefield name to open/create """ - self.dirname = "ff{0}.ff".format(name) - os.makedirs(self.dirname, exist_ok=True) + self.directory = pathlib.Path(dir_path).joinpath(f"ff{name}.ff") + backup_file(self.directory) + self.directory.mkdir(parents=True, exist_ok=True) - with open(os.path.join(self.dirname, "forcefield.itp"), "w") as itp: - print("#define _FF_PYCGTOOL_{0}".format(name), file=itp) + with open(self.directory.joinpath("forcefield.itp"), "w") as itp: + print(f"#define _FF_PYCGTOOL_{name}", file=itp) print('#include "martini_v2.2.itp"', file=itp) - dist_dat_dir = os.path.join(dir_up(os.path.realpath(__file__), 2), "data") - # Copy main MARTINI itp - martini_itp = os.path.join(dist_dat_dir, "martini_v2.2.itp") - shutil.copyfile(martini_itp, os.path.join(self.dirname, "martini_v2.2.itp")) - # Copy water models - shutil.copyfile(os.path.join(dist_dat_dir, "watermodels.dat"), - os.path.join(self.dirname, "watermodels.dat")) - shutil.copyfile(os.path.join(dist_dat_dir, "w.itp"), - os.path.join(self.dirname, "w.itp")) + data_dir = pathlib.Path(__file__).parent.joinpath("data") + + # Copy MARTINI files + copy_files( + data_dir, + self.directory, + [ + "martini_v2.2.itp", + "watermodels.dat", + "w.itp", + ], + ) # Create atomtypes.atp required for correct masses with pdb2gmx - atomtypes_atp = os.path.join(self.dirname, "atomtypes.atp") - with ITP(martini_itp) as itp, open(atomtypes_atp, 'w') as atomtypes: + atomtypes_atp = os.path.join(self.directory, "atomtypes.atp") + with CFG(data_dir.joinpath("martini_v2.2.itp")) as itp, open( + atomtypes_atp, "w" + ) as atomtypes: for toks in itp["atomtypes"]: print(" ".join(toks), file=atomtypes) - with open(os.path.join(self.dirname, "forcefield.doc"), "w") as doc: - print("PyCGTOOL produced MARTINI force field - {0}".format(name), file=doc) + with open(self.directory.joinpath("forcefield.doc"), "w") as doc: + print(f"PyCGTOOL produced MARTINI force field - {name}", file=doc) - def write(self, filename, mapping, bonds): - nterms, cterms, bothterms = self._write_rtp(filename, mapping, bonds) - self._write_r2b(filename, nterms, cterms, bothterms) + def write(self, filename: str, mapping, bonds): + """ + Write RTP and R2B files for this forcefield. - def _write_rtp(self, filename, mapping, bonds): + :param str filename: Filename prefix to use for both files + :param Mapping mapping: CG Mapping object + :param Iterable[Bond] bonds: CG Bonds object """ - Write a GROMACS .rtp file. + lines, nterms, cterms = ForceField.write_rtp(mapping, bonds) + file_write_lines(self.directory.joinpath(f"{filename}.rtp"), lines) + + lines = ForceField.write_r2b(nterms, cterms) + file_write_lines(self.directory.joinpath(f"{filename}.r2b"), lines) + + @staticmethod + def bond_section(bonds, section_header, multiplicity=None): + """ + Populate an RTP bond/angle/dihedral section. + + :param iterable[Bond] bonds: Iterable of bonds to add to RTP + :param str section_header: RTP section header i.e. "bonds"/"angles"/"dihedrals" + :param int multiplicity: Multiplicity of dihedral, default is None + :return List[str]: Lines to add to RTP file + """ + ret_lines = [] + if bonds: + ret_lines.append(" [ {0:s} ]".format(section_header)) + for bond in bonds: + line = " " + " ".join(["{0:>4s}".format(atom) for atom in bond.atoms]) + line += " {0:12.5f} {1:12.5f}".format(bond.eqm, bond.fconst) + if multiplicity is not None: + line += " {0:4d}".format(multiplicity) + ret_lines.append(line) + return ret_lines + + @staticmethod + def needs_terminal_entries(mol_name, bondset): + bonds = bondset.get_bonds(mol_name, natoms=-1) + return any_starts_with(bonds, "-"), any_starts_with(bonds, "+") + + @staticmethod + def write_rtp(mapping, bonds): + """ + Return lines of a GROMACS RTP file. This file defines the residues present in the forcefield and allows pdb2gmx to be used. - :param filename: Name of the .rtp file to create, N.B. .rtp is appended here - :param mapping: AA->CG mapping from which to collect molecules - :param bonds: BondSet from which to collect bonds + :param Mapping mapping: AA->CG mapping from which to collect molecules + :param BondSet bonds: BondSet from which to collect bonds + :return (list[str], set[str], set[str], set[str]): + List of lines for RTP file, + Set of residues requiring N terminal records, + Set of residues requiring C terminal records, """ - def write_bond_angle_dih(bonds, section_header, file, multiplicity=None): - if bonds: - print(" [ {0:s} ]".format(section_header), file=file) - for bond in bonds: - line = " " + " ".join(["{0:>4s}".format(atom) for atom in bond.atoms]) - line += " {0:12.5f} {1:12.5f}".format(bond.eqm, bond.fconst) - if multiplicity is not None: - line += " {0:4d}".format(multiplicity) - print(line, file=file) - - def any_starts_with(iterable, char): - """ - Return True if any atoms of any bonds in molecule start with 'char'. - - i.e. if char='-' or '+' is part of polymer. - - :param iterable: Iterable of bond entries to check - :param char: Char to check each atom name for startswith, in '-+' - :return: True if any atom name in molecule bonds starts with char, else False - """ - recurse = functools.partial(any_starts_with, char=char) - if type(iterable) is str: - return iterable.startswith(char) - else: - return any(map(recurse, iterable)) - - def write_residue(name, rtp, strip=None, prepend=""): - print("[ {0} ]".format(prepend + name), file=rtp) - - print(" [ atoms ]", file=rtp) - for bead in mapping[name]: - # name type charge chg-group - print(" {:>4s} {:>4s} {:3.6f} {:4d}".format( - bead.name, bead.type, bead.charge, 0 - ), file=rtp) - - needs_terminal_entry = [False, False] - - get_bond_functions = [("bonds", functools.partial(bonds.get_bond_lengths, with_constr=True)), - ("angles", bonds.get_bond_angles), - ("dihedrals", bonds.get_bond_dihedrals)] - - for get_bond in get_bond_functions: - bond_tmp = get_bond[1](name) - if strip is not None: - bond_tmp = [bond for bond in bond_tmp if not any_starts_with(bond, strip)] - write_bond_angle_dih(bond_tmp, get_bond[0], rtp, - multiplicity=1 if get_bond[0] == "dihedrals" else None) - needs_terminal_entry[0] |= any_starts_with(bond_tmp, "-") - needs_terminal_entry[1] |= any_starts_with(bond_tmp, "+") - - return needs_terminal_entry + + def write_residue(mol_name, mol_mapping, strip=None, prepend=""): + ret_lines = ["[ {0} ]".format(prepend + mol_name), " [ atoms ]"] + + for bead in mol_mapping: + # name type charge chg-group + ret_lines.append( + " {:>4s} {:>4s} {:3.6f} {:4d}".format( + bead.name, bead.type, bead.charge, 0 + ) + ) + + for natoms, (section, multiplicity) in enumerate( + (("bonds", None), ("angles", None), ("dihedrals", 1)), start=2 + ): + if strip is None: + bond_list = bonds.get_bonds(mol_name, natoms) + else: + bond_list = bonds.get_bonds( + mol_name, + natoms, + select=lambda bond: not any_starts_with(bond, strip), + ) + + ret_lines.extend( + ForceField.bond_section(bond_list, section, multiplicity) + ) + + return ret_lines n_terms = set() c_terms = set() - both_terms = set() - with open(os.path.join(self.dirname, filename + ".rtp"), "w") as rtp: - print("[ bondedtypes ]", file=rtp) - print(("{:4d}" * 8).format(1, 1, 1, 1, 1, 1, 0, 0), file=rtp) + rtp_lines = ["[ bondedtypes ]", ("{:4d}" * 8).format(1, 1, 1, 1, 1, 1, 0, 0)] + + for mol_name, mol_mapping in mapping.items(): + try: + rtp_lines.extend(write_residue(mol_name, mol_mapping)) + except KeyError: + continue - for mol in mapping: - # Skip molecules not listed in bonds - if mol not in bonds: - continue + needs_terminal_entry = ForceField.needs_terminal_entries(mol_name, bonds) - needs_terminal_entry = write_residue(mol, rtp) + if needs_terminal_entry[0]: + rtp_lines.extend( + write_residue(mol_name, mol_mapping, strip="-", prepend="N") + ) + n_terms.add(mol_name) + + if needs_terminal_entry[1]: + rtp_lines.extend( + write_residue(mol_name, mol_mapping, strip="+", prepend="C") + ) + c_terms.add(mol_name) if needs_terminal_entry[0]: - write_residue(mol, rtp, strip="-", prepend="N") - n_terms.add(mol) - if needs_terminal_entry[1]: - write_residue(mol, rtp, strip="+", prepend="C") - c_terms.add(mol) - if all(needs_terminal_entry): - write_residue(mol, rtp, strip=("-", "+"), prepend="2") - both_terms.add(mol) - - return n_terms, c_terms, both_terms - - def _write_r2b(self, filename, n_terms, c_terms, both_terms): - with open(os.path.join(self.dirname, filename + ".r2b"), "w") as r2b: - print("; rtp residue to rtp building block table", file=r2b) - print("; main N-ter C-ter 2-ter", file=r2b) - - for resname in set.union(n_terms, c_terms, both_terms): - nter_str = ("N" + resname) if resname in n_terms else "-" - cter_str = ("C" + resname) if resname in c_terms else "-" - both_ter_str = ("2" + resname) if resname in both_terms else "-" - print("{0:5s} {0:5s} {1:5s} {2:5s} {3:5s}".format(resname, nter_str, cter_str, both_ter_str), file=r2b) + rtp_lines.extend( + write_residue( + mol_name, mol_mapping, strip=("-", "+"), prepend="2" + ) + ) + + return rtp_lines, n_terms, c_terms + + @staticmethod + def write_r2b(n_terms, c_terms): + """ + Return lines of a GROMACS R2B file. + + This file defines names used for chain terminal records for PDB2GMX. + + :param Iterable[str] n_terms: Set of molecule names requiring N terminal records + :param Iterable[str] c_terms: Set of molecule names requiring C terminal records + :return List[str]: Lines of R2B file + """ + ret_lines = [ + "; rtp residue to rtp building block table", + "; main N-ter C-ter 2-ter", + ] + + for resname in sorted(n_terms | c_terms): + nter_str = ("N" + resname) if resname in n_terms else "-" + cter_str = ("C" + resname) if resname in c_terms else "-" + both_ter_str = ("2" + resname) if resname in (n_terms & c_terms) else "-" + ret_lines.append( + "{0:5s} {0:5s} {1:5s} {2:5s} {3:5s}".format( + resname, nter_str, cter_str, both_ter_str + ) + ) + + return ret_lines diff --git a/pycgtool/frame.py b/pycgtool/frame.py index 6790528..b4f7ae2 100644 --- a/pycgtool/frame.py +++ b/pycgtool/frame.py @@ -1,296 +1,272 @@ -""" -This module contains classes for storing atomic data. +"""This module contains classes for storing atomic data. The Frame class may contain multiple Residues which may each contain multiple Atoms. Both Frame and Residue are iterable. Residue is indexable with either atom numbers or names. """ import logging +import pathlib +import typing +import mdtraj import numpy as np -from .util import backup_file -from .parsers.cfg import CFG +from . import util logger = logging.getLogger(__name__) np.seterr(all="raise") - -# Create FileNotFoundError if using older version of Python -try: - try: - raise FileNotFoundError - except FileNotFoundError: - pass -except NameError: - class FileNotFoundError(OSError): - pass +PathLike = typing.Union[pathlib.Path, str] -class Atom: - """ - Hold data for a single atom - """ - __slots__ = ["name", "num", "type", "mass", "charge", "coords"] +class UnsupportedFormatException(Exception): + """Exception raised when a topology/trajectory format cannot be parsed.""" - def __init__(self, name, num, type=None, mass=None, charge=None, coords=None): - """ - Create an atom. - - :param str name: The name of the atom - :param int num: The atom number - :param str type: The atom type - :param float mass: The mass of the atom - :param float charge: The charge of the atom - :param coords: The coordinates of the atom - """ - self.name = name - self.num = num - self.type = type - self.mass = mass - self.charge = charge - self.coords = coords - - def __repr__(self): - return "Atom #{0} {1} type: {2} mass: {3} charge: {4}".format( - self.num, self.name, self.type, self.mass, self.charge - ) + def __init__(self, msg=None): + if msg is None: + msg = "Topology/Trajectory format not supported by this reader" + super(UnsupportedFormatException, self).__init__(msg) - def add_missing_data(self, other): - assert self.name == other.name - assert self.num == other.num - for attr in ("type", "mass", "charge", "coords"): - if getattr(self, attr) is None: - setattr(self, attr, getattr(other, attr)) +class NonMatchingSystemError(ValueError): + """Exception raised when topology and trajectory do not match.""" + def __init__(self, msg=None): + if msg is None: + msg = "Number of atoms does not match between topology and trajectory files" + super(NonMatchingSystemError, self).__init__(msg) -class Residue: - """ - Hold data for a residue - list of atoms - """ - __slots__ = ["name", "num", "atoms", "name_to_num"] - def __init__(self, name=None, num=None): - self.atoms = [] - self.name = name - self.num = num - self.name_to_num = {} +def load_traj(filepath: PathLike, **kwargs) -> mdtraj.Trajectory: + """Load a trajectory, if a PDB fails with zero box volume disable volume check and try again.""" + filepath = pathlib.Path(filepath) - def __iter__(self): - return iter(self.atoms) + if filepath.suffix.lower() == ".pdb": + # PDBs have a couple of things that can go wrong - we handle these here... + kwargs.pop("top", None) # Can't specify a topology for `load_pdb` - def __getitem__(self, item): try: - return self.atoms[self.name_to_num[item]] - except KeyError: - pass + return mdtraj.load_pdb(str(filepath), **kwargs) - try: - return self.atoms[item] - except TypeError as e: - e.args = ("Atom {0} does not exist in residue {1}".format(item, self.name),) - raise - - def __len__(self): - return len(self.atoms) + except FloatingPointError: + # PDB file loading checks density using the simulation box + # This can fail if the box volume is zero + trajectory = mdtraj.load_pdb(str(filepath), no_boxchk=True, **kwargs) + logger.warning( + "Unitcell has zero volume - periodic boundaries will not be accounted for. " + "If the molecule is split by a periodic boundary, results will be incorrect." + ) - def add_atom(self, atom): - """ - Add an Atom to this Residue and store location in index + return trajectory - :param atom: Atom to add to Residue - :return: None - """ - self.atoms.append(atom) - self.name_to_num[atom.name] = len(self.atoms) - 1 + return mdtraj.load(str(filepath), **kwargs) class Frame: - """ - Hold Atom data separated into Residues - """ - def __init__(self, gro=None, xtc=None, itp=None, frame_start=0, xtc_reader=None): + """Load and store data from a simulation trajectory.""" + + def __init__( + self, + topology_file: typing.Optional[PathLike] = None, + trajectory_file: typing.Optional[PathLike] = None, + frame_start: int = 0, + frame_end: typing.Optional[int] = None, + ): + """Load a simulation trajectory. + + :param topology_file: File containing system topology + :param trajectory_file: File containing simulation trajectory + :param frame_start: First frame of trajectory to use + :param frame_end: Last frame of trajectory to use """ - Return Frame instance having read Residues and Atoms from GRO if provided + if topology_file is not None: + try: + logging.info("Loading topology file") + self._trajectory = load_traj(topology_file) + self._topology = self._trajectory.topology + logging.info("Finished loading topology file") + + if trajectory_file is not None: + try: + logging.info("Loading trajectory file - this may take a while") + self._trajectory = load_traj( + trajectory_file, top=self._topology + ) + self._trajectory = self._slice_trajectory( + frame_start, frame_end + ) + logging.info( + "Finished loading trajectory file - loaded %d frames", + self._trajectory.n_frames, + ) + + except ValueError as exc: + raise NonMatchingSystemError from exc + + self._load_trajectory() + + except OSError as exc: + if "no loader" in str(exc) or "format is not supported" in str(exc): + raise UnsupportedFormatException from exc - :param gro: GROMACS GRO file to read initial frame and extract residues - :param xtc: GROMACS XTC file to read subsequent frames - :param itp: GROMACS ITP file to read masses and charges - :return: Frame instance - """ - self.name = "" - self.residues = [] - self.number = frame_start - 1 - self.time = 0 - self.numframes = 0 - self.natoms = 0 - self.box = np.zeros(3, dtype=np.float32) + raise - self._xtc_buffer = None + else: + # No topology - we're probably building a CG frame + self._topology = mdtraj.Topology() - if gro is not None: - from .framereader import get_frame_reader - self._trajreader = get_frame_reader(gro, traj=xtc, frame_start=frame_start, name=xtc_reader) + def _slice_trajectory( + self, frame_start: int = 0, frame_end: typing.Optional[int] = None + ) -> mdtraj.Trajectory: + """Slice input simulation trajectory to a subset of frames. - self._trajreader.initialise_frame(self) + :param frame_start: First frame of trajectory to use + :param frame_end: Last frame of trajectory to use + """ + traj = self._trajectory - if self._trajreader.num_atoms != self.natoms: - raise AssertionError("Number of atoms does not match between gro and xtc files.") - self.numframes += self._trajreader.num_frames + if frame_start != 0: + if frame_end is not None: + traj = traj[frame_start:frame_end] - if itp is not None: - self._parse_itp(itp) + else: + traj = traj[frame_start:] - @classmethod - def instance_from_reader(cls, reader): - """ - Return Frame instance initialised from existing FrameReader object - - :param FrameReader reader: FrameReader object - :return: Frame instance - """ - obj = cls() - obj._trajreader = reader - obj._trajreader.initialise_frame(obj) - return obj - - def __len__(self): - return len(self.residues) - - def __iter__(self): - return iter(self.residues) - - def __getitem__(self, item): - return self.residues[item] - - def __repr__(self): - rep = self.name + "\n" - atoms = [] - for res in self.residues: - for atom in res: - atoms.append(repr(atom)) - rep += "\n".join(atoms) - return rep - - def yield_resname_in(self, container): - for res in self: - if res.name in container: - yield res - - def next_frame(self): - """ - Read next frame from input XTC. + return traj - :return: True if successful else False - """ - result = self._trajreader.read_next(self) - if result: - self.number += 1 - return result + def _load_trajectory(self) -> None: + """Load a trajectory into the frame attributes.""" + # Improve performance by not double indexing repeatedly + traj = self._trajectory - def write_xtc(self, filename): - """ - Write frame to output XTC file. + for atom in self._topology.atoms: + atom.coords = traj.xyz[:, atom.index] - :param filename: XTC filename to write to + # TODO handle non-cubic boxes + try: + self.unitcell_lengths = traj.unitcell_lengths + self.unitcell_angles = traj.unitcell_angles + + except TypeError: + self.unitcell_lengths = None + self.unitcell_angles = None + + self.time = traj.time + + # Cast unitcell vectors to float32 to avoid warning - they're currently float64 + if traj.unitcell_vectors is not None: + traj.unitcell_vectors = traj.unitcell_vectors.astype(np.float32) + + @property + def residues(self): + """Residues in the frame topology.""" + return self._topology.residues + + def residue(self, *args, **kwargs) -> mdtraj.core.topology.Residue: + """Get a residue from the frame topology by name or id.""" + return self._topology.residue(*args, **kwargs) + + @property + def atoms(self): + """Atoms in the frame topology.""" + return self._topology.atoms + + def atom(self, *args, **kwargs) -> mdtraj.core.topology.Atom: + """Get an atom from the frame topology by name or id.""" + return self._topology.atom(*args, **kwargs) + + @property + def natoms(self) -> int: + """Number of atoms in the frame topology.""" + return self._topology.n_atoms + + @property + def n_frames(self) -> int: + """Number of frames in the trajectory.""" + return self._trajectory.n_frames + + def add_residue( + self, + name, + chain: typing.Optional[mdtraj.core.topology.Residue] = None, + **kwargs + ) -> mdtraj.core.topology.Residue: + """Add a residue to the frame topology. + + :param name: Name of residue + :param chain: MDTraj chain of residue + :return: New residue """ - if self._xtc_buffer is None: + if hasattr(self, "_trajectory"): + raise TypeError("Cannot edit residues if a trajectory has been loaded") + + if chain is None: try: - import mdtraj - except ImportError as e: - if "scipy" in repr(e): - e.msg = "XTC output with MDTraj also requires Scipy" - else: - e.msg = "XTC output requires the module MDTraj (and probably Scipy)" - raise + chain = self._topology.chain(0) - backup_file(filename) - self._xtc_buffer = mdtraj.formats.XTCTrajectoryFile(filename, mode="w") + except IndexError: + chain = self._topology.add_chain() - xyz = np.ndarray((1, self.natoms, 3), dtype=np.float32) - i = 0 - for residue in self.residues: - for atom in residue.atoms: - xyz[0][i] = atom.coords - i += 1 + return self._topology.add_residue(name, chain, **kwargs) - time = np.array([self.time], dtype=np.float32) - step = np.array([self.number], dtype=np.int32) + def add_atom( + self, + name: str, + element: typing.Optional[mdtraj.element.Element], + residue: mdtraj.core.topology.Residue, + ) -> mdtraj.core.topology.Atom: + """Add an atom or CG bead to the frame topology. - box = np.zeros((1, 3, 3), dtype=np.float32) - for i in range(3): - box[0][i][i] = self.box[i] + :param name: Name of atom + :param element: MDTraj element of atom + :param residue: MDTraj residue of atom + :return: New atom + """ + if hasattr(self, "_trajectory"): + raise TypeError("Cannot edit atoms if a trajectory has been loaded") + + return self._topology.add_atom(name, element, residue) - self._xtc_buffer.write(xyz, time=time, step=step, box=box) + def save( + self, filename: PathLike, frame_number: typing.Optional[int] = None, **kwargs + ) -> None: + """Write trajctory to file. - def _parse_itp(self, filename): + :param filename: Name of output file + :param frame_number: Which trajectory frame to save - defaults to all """ - Parse a GROMACS ITP file to extract atom charges/masses. + traj = self._trajectory + if frame_number is not None: + traj = traj.slice(frame_number) - Optional but requires that ITP contains only a single residue. + util.backup_file(filename) + traj.save(str(filename), **kwargs) - :param filename: Filename of GROMACS ITP to read - """ - with CFG(filename) as itp: - itpres = Residue(itp["moleculetype"][0][0]) - for line in itp["atoms"]: - atom = Atom(num=int(line[0]) - 1, type=line[1], name=line[4], charge=float(line[6]), mass=float(line[7])) - itpres.add_atom(atom) - - for res in self.residues: - if res.name == itpres.name: - for atom, itpatom in zip(res, itpres): - atom.add_missing_data(itpatom) - - def output(self, filename, format="gro"): - """ - Write coordinates from Frame to file. + def build_trajectory(self) -> None: + """Build an MDTraj trajectory from atom coordinates and the values stored as attributes on this frame.""" + xyz = np.array([atom.coords for atom in self._topology.atoms], dtype=np.float32) - :param filename: Name of file to write to - :param format: Format to write e.g. 'gro', 'lammps' - """ - outputs = {"gro": self._output_gro, - "lammps": self._output_lammps_data} + # We currently have axes: 0 - each atom, 1 - timestep, 2 - xyz coords + # Need to convert to axes: 0 - timestep, 1 - each atom, 2 - xyz coords try: - outputs[format](filename) - except KeyError: - print("ERROR: Invalid output format {0}, coordinates will not be output.".format(format)) + xyz = xyz.swapaxes(0, 1) - def _output_lammps_data(self, filename): - """ - Output Frame coordinates in LAMMPS data format. + except np.AxisError: + # No atoms, so make an empty array with the right shape + xyz = np.empty((len(self.time), 0, 3)) - :param filename: Name of DATA file to create - """ - raise NotImplementedError("LAMMPS Data output has not yet been implemented.") + optional_values = { + attr: getattr(self, attr, None) + for attr in {"time", "unitcell_lengths", "unitcell_angles"} + } - def _output_gro(self, filename): - """ - Create a GROMACS GRO file from the data in this Frame + new_trajectory = mdtraj.Trajectory( + xyz, topology=self._topology, **optional_values + ) - :param filename: Name of GRO file to create - """ - backup_file(filename) - - with open(filename, "w") as gro: - print(self.name, file=gro) - print("{0:5d}".format(self.natoms), file=gro) - i = 1 - format_string = "{0:5d}{1:5s}{2:>5s}{3:5d}{4:8.3f}{5:8.3f}{6:8.3f}" - for res in self.residues: - for atom in res: - print(format_string.format(res.num, res.name, - atom.name, i, - *atom.coords), file=gro) - i += 1 - print("{0:10.5f}{1:10.5f}{2:10.5f}".format(*self.box), file=gro) - - def add_residue(self, residue): - """ - Add a Residue to this Frame + if hasattr(self, "_trajectory"): + self._trajectory += new_trajectory - :param residue: Residue to add - """ - self.residues.append(residue) + else: + self._trajectory = new_trajectory diff --git a/pycgtool/framereader.py b/pycgtool/framereader.py deleted file mode 100644 index 337d909..0000000 --- a/pycgtool/framereader.py +++ /dev/null @@ -1,285 +0,0 @@ -""" -This module contains classes for reading trajectories into a Frame instance. - -Multiple readers are defined, allowing different underlying trajectory libraries to be used. -This module is tightly coupled with the frame.py module, so shares a set of unit tests. -""" - -import os -import abc -import itertools -import logging -import collections - -import numpy as np - -from .frame import Atom, Residue -from .util import FixedFormatUnpacker - -logger = logging.getLogger(__name__) - - -class UnsupportedFormatException(Exception): - pass - - -def get_frame_reader(top, traj=None, frame_start=0, name=None): - readers = collections.OrderedDict([ - ("simpletraj", FrameReaderSimpleTraj), - ("mdtraj", FrameReaderMDTraj), - ("mdanalysis", FrameReaderMDAnalysis), - ]) - - try: - return readers[name](top, traj, frame_start) - except KeyError as e: - if name is not None: - e.args = ("Frame reader '{0}' is not a valid option.".format(name),) - raise - for name, reader in readers.items(): # Return first reader that accepts given files - try: - return reader(top, traj, frame_start) - except (UnsupportedFormatException, ImportError) as e: - print(e) - continue - raise UnsupportedFormatException("None of the available readers support the trajector format provided, {0} {1}".format(top, traj)) - - -class FrameReader(metaclass=abc.ABCMeta): - def __init__(self, topname, trajname=None, frame_start=0): - self._topname = topname - self._trajname = trajname - self._frame_number = frame_start - - self.num_atoms = 0 - self.num_frames = 0 - - def initialise_frame(self, frame): - self._initialise_frame(frame) - - def read_next(self, frame): - result = self.read_frame_number(self._frame_number, frame) - if result: - self._frame_number += 1 - return result - - def read_frame_number(self, number, frame): - try: - time, coords, box = self._read_frame_number(number) - if box is None: - box = np.zeros(3) - frame.time = time - frame.box = box - - for atom, coord_line in zip(itertools.chain.from_iterable(frame.residues), coords): - atom.coords = coord_line - - except (IndexError, AttributeError): - # IndexError - run out of xtc frames - # AttributeError - we didn't provide an xtc - return False - return True - - @abc.abstractmethod - def _initialise_frame(self, frame): - pass - - @abc.abstractmethod - def _read_frame_number(self, number): - pass - - -class FrameReaderSimpleTraj(FrameReader): - def __init__(self, topname, trajname=None, frame_start=0): - """ - Open input XTC file from which to read coordinates using simpletraj library. - - :param topname: MD topology file - not used - :param trajname: MD trajectory file to read subsequent frames - :param frame_start: Frame number to start on, default 0 - """ - FrameReader.__init__(self, topname, trajname, frame_start) - - with open(self._topname) as gro: - gro.readline() - try: - self.num_atoms = int(gro.readline()) - except ValueError as e: - raise UnsupportedFormatException from e - - from simpletraj import trajectory - - if trajname is not None: - try: - self._traj = trajectory.get_trajectory(trajname) - except OSError as e: - if not os.path.isfile(trajname): - raise FileNotFoundError(trajname) from e - e.args = ("Error opening file '{0}'".format(trajname),) - raise - except Exception as e: - if "extension" in repr(e) and "not supported" in repr(e): - raise UnsupportedFormatException from e - raise - - if self._traj.numatoms != self.num_atoms: - raise UnsupportedFormatException - self.num_frames = self._traj.numframes - - def _initialise_frame(self, frame): - """ - Parse a GROMACS GRO file and create Residues/Atoms - Required before reading coordinates from XTC file - - :param frame: Frame instance to initialise from GRO file - """ - with open(self._topname) as gro: - frame.name = gro.readline().strip() - try: - self.num_atoms = int(gro.readline()) - except ValueError as e: - raise UnsupportedFormatException from e - - frame.natoms = self.num_atoms - resnum_last = None - atnum = 0 - - unpacker = FixedFormatUnpacker("I5,2A5,5X,3F8", - FixedFormatUnpacker.FormatStyle.Fortran) - - for _ in range(self.num_atoms): - resnum, resname, atomname, *coords = unpacker.unpack(gro.readline()) - coords = np.array(coords, dtype=np.float32) - - if resnum != resnum_last: - frame.residues.append(Residue(name=resname, - num=resnum)) - resnum_last = resnum - atnum = 0 - - atom = Atom(name=atomname, num=atnum, coords=coords) - frame.residues[-1].add_atom(atom) - atnum += 1 - - frame.box = np.array([float(x) for x in gro.readline().split()[0:3]], dtype=np.float32) - - def _read_frame_number(self, number): - """ - Read next frame from XTC using simpletraj library. - """ - self._traj.get_frame(number) - # SimpleTraj uses Angstrom, we want nanometers - xyz = self._traj.x / 10 - box = np.diag(self._traj.box)[0:3] / 10 - - return self._traj.time, xyz, box - - -class FrameReaderMDTraj(FrameReader): - def __init__(self, topname, trajname=None, frame_start=0): - """ - Open input XTC file from which to read coordinates using mdtraj library. - - :param topname: GROMACS GRO file from which to read topology - :param trajname: GROMACS XTC file to read subsequent frames - """ - FrameReader.__init__(self, topname, trajname, frame_start) - - try: - import mdtraj - except ImportError as e: - if "scipy" in repr(e): - e.msg = "The MDTraj FrameReader also requires Scipy" - else: - e.msg = "The MDTraj FrameReader requires the module MDTraj (and probably Scipy)" - raise - logger.warning("WARNING: Using MDTraj which renames solvent molecules") - - try: - if trajname is None: - self._traj = mdtraj.load(topname) - else: - self._traj = mdtraj.load(trajname, top=topname) - except OSError as e: - if not os.path.isfile(topname): - raise FileNotFoundError(topname) from e - if trajname is not None and not os.path.isfile(trajname): - raise FileNotFoundError(trajname) from e - if "no loader for filename" in repr(e): - raise UnsupportedFormatException from e - e.args = ("Error opening file '{0}' or '{1}'".format(topname, trajname),) - raise - - self.num_atoms = self._traj.n_atoms - self.num_frames = self._traj.n_frames - - def _initialise_frame(self, frame): - """ - Parse a GROMACS GRO file and create Residues/Atoms - Required before reading coordinates from XTC file - - :param frame: Frame instance to initialise from GRO file - """ - import mdtraj - top = mdtraj.load(self._topname) - - frame.name = "" - self.num_atoms = top.n_atoms - frame.natoms = top.n_atoms - - frame.residues = [Residue(name=res.name, num=res.resSeq) for res in top.topology.residues] - - for atom in top.topology.atoms: - new_atom = Atom(name=atom.name, num=atom.serial, - coords=top.xyz[0][atom.index]) - frame.residues[atom.residue.index].add_atom(new_atom) - - frame.box = top.unitcell_lengths[0] - - def _read_frame_number(self, number): - """ - Read next frame from XTC using mdtraj library. - """ - try: - return self._traj.time[number], self._traj.xyz[number], self._traj.unitcell_lengths[number] - except TypeError: - return self._traj.time[number], self._traj.xyz[number], None - - -class FrameReaderMDAnalysis(FrameReader): - def __init__(self, topname, trajname=None, frame_start=0): - import MDAnalysis - - super().__init__(topname, trajname, frame_start) - - try: - if trajname is None: - self._traj = MDAnalysis.Universe(topname) - else: - self._traj = MDAnalysis.Universe(topname, trajname) - except ValueError as e: - if "isn't a valid topology format" in repr(e): - raise UnsupportedFormatException from e - raise - - self.num_atoms = self._traj.atoms.n_atoms - self.num_frames = self._traj.trajectory.n_frames - - def _initialise_frame(self, frame): - frame.name = "" - frame.natoms = self.num_atoms - - import MDAnalysis - topol = MDAnalysis.Universe(self._topname) - frame.box = topol.dimensions[0:3] / 10. - - for res in topol.residues: - residue = Residue(name=res.resname, num=res.resnum) - for atom in res.atoms: - residue.add_atom(Atom(name=atom.name, num=atom.id, coords=atom.position / 10.)) - frame.residues.append(residue) - - def _read_frame_number(self, number): - traj_frame = self._traj.trajectory[number] - return traj_frame.time, traj_frame.positions / 10., traj_frame.dimensions[0:3] / 10. - diff --git a/pycgtool/functionalforms.py b/pycgtool/functionalforms.py index 7c35f78..f237fe9 100644 --- a/pycgtool/functionalforms.py +++ b/pycgtool/functionalforms.py @@ -1,76 +1,61 @@ +"""Utilities for describing the functional forms of bonded potentials being calculated. + +See http://manual.gromacs.org/documentation/current/reference-manual/functions/bonded-interactions.html +and http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#tab-topfile2 + +The links above list the bonded potentials available for use in GROMACS force fields. +These can be implemented as functional forms in PyCGTOOL by subclassing :class:`FunctionalForm`. +""" import abc +import enum import math +import typing import numpy as np -from pycgtool.util import SimpleEnum +def get_functional_forms() -> enum.Enum: + """Get enum of known functional forms.""" + enum_dict = {} + for subclass in FunctionalForm.__subclasses__(): + name = subclass.__name__ + enum_dict[name] = subclass -class FunctionalForms(object): - """ - Class holding list of all defined functional forms for Boltzmann Inversion. - - Creating an instance causes the Enum of functional forms to be updated with - all new subclasses of FunctionalForm. These may then be accessed by name, - either as attributes or using square brackets. - """ - FormsEnum = SimpleEnum.enum("FormsEnum") - - @classmethod - def _refresh(cls): - """ - Update the functional forms Enum to include all new subclasses of FunctionalForm. - """ - enum_dict = cls.FormsEnum.as_dict() - for subclass in FunctionalForm.__subclasses__(): - name = subclass.__name__ - if name not in cls.FormsEnum: - enum_dict[name] = subclass() + return enum.Enum("FunctionalForms", enum_dict) - cls.FormsEnum = SimpleEnum.enum_from_dict("FormsEnum", enum_dict) - def __init__(self, **kwargs): - self._kwargs = kwargs - type(self)._refresh() +class FunctionalForm(metaclass=abc.ABCMeta): + """Parent class of any functional form used in Boltzmann Inversion to convert variance to a force constant.""" - def __getattr__(self, item): - return type(self).FormsEnum[item].value - - def __getitem__(self, item): - return getattr(self, item) - - def __repr__(self): - return "".format(len(self)) - - def __len__(self): - return len(type(self).FormsEnum) - - def __contains__(self, item): - return item in type(self).FormsEnum + def __init__( + self, + mean_func: typing.Callable = np.nanmean, + variance_func: typing.Callable = np.nanvar, + ): + """Inject functions for calculating the mean and variance into the Boltzmann Inversion equations. + :param mean_func: Function to calculate the mean - default is np.nanmean + :param variance_func: Function to calculate the variance - default is np.nanvar + """ + self._mean_func = mean_func + self._variance_func = variance_func -class FunctionalForm(object, metaclass=abc.ABCMeta): - """ - Parent class of any functional form used in Boltzmann Inversion to convert variance to a force constant. + def eqm( + self, values: typing.Iterable[float], temp: float + ) -> float: # pylint: disable=unused-argument + """Calculate equilibrium value. - New functional forms must define a static __call__ method. - """ - @staticmethod - def eqm(values, temp): - """ - Calculate equilibrium value. May be overridden by functional forms. :param values: Measured internal coordinate values from which to calculate equilibrium value :param temp: Temperature of simulation :return: Calculated equilibrium value """ - return np.nanmean(values) + return self._mean_func(values) - @abc.abstractstaticmethod - def fconst(values, temp): - """ - Calculate force constant. + @abc.abstractmethod + def fconst(self, values: typing.Iterable[float], temp: float) -> float: + """Calculate force constant. Abstract static method to be defined by all functional forms. :param values: Measured internal coordinate values from which to calculate force constant @@ -80,68 +65,84 @@ def fconst(values, temp): raise NotImplementedError @abc.abstractproperty - def gromacs_type_ids(self): - """ - Return tuple of GROMACS potential type ids when used as length, angle, dihedral. - + def gromacs_type_ids(self) -> typing.Tuple[int]: + """Return tuple of GROMACS potential type ids when used as length, angle, dihedral. + :return tuple[int]: Tuple of GROMACS potential type ids """ raise NotImplementedError @classmethod - def gromacs_type_id_by_natoms(cls, natoms): - """ - Return the GROMACS potential type id for this functional form when used with natoms. - - :param int natoms: - :return int: GROMACS potential type id + def gromacs_type_id_by_natoms(cls, natoms: int) -> int: + """Return the GROMACS potential type id for this functional form when used with natoms. + + :param int natoms: Number of atoms in bond + :return int: GROMACS potential type id """ tipe = cls.gromacs_type_ids[natoms - 2] if tipe is None: - raise TypeError("The functional form {0} does not have a defined GROMACS potential type when used with {1} atoms.".format(cls.__name__, natoms)) + raise TypeError( + f"The functional form {cls.__name__} does not have a defined GROMACS " + f"potential type when used with {natoms} atoms." + ) + return tipe class Harmonic(FunctionalForm): - gromacs_type_ids = (1, 1, 1) # Consider whether to use improper (type 2) instead, it is actually harmonic + """Simple harmonic potential. + + See http://manual.gromacs.org/documentation/current/reference-manual/functions/bonded-interactions.html#harmonic-potential # noqa + """ - @staticmethod - def fconst(values, temp): - rt = 8.314 * temp / 1000. - var = np.nanvar(values) + # TODO: Consider whether to use improper (type 2) instead, it is actually harmonic + gromacs_type_ids = (1, 1, 1) + + def fconst(self, values: typing.Iterable[float], temp: float) -> float: + rt = 8.314 * temp / 1000.0 # pylint: disable=invalid-name + var = self._variance_func(values) return rt / var class CosHarmonic(FunctionalForm): + """Cosine based angle potential. + + See http://manual.gromacs.org/documentation/current/reference-manual/functions/bonded-interactions.html#cosine-based-angle-potential # noqa + + Uses the transformation in eqn 20 of the above source. + """ + gromacs_type_ids = (None, 2, None) - @staticmethod - def fconst(values, temp): - rt = 8.314 * temp / 1000. - mean = CosHarmonic.eqm(values, temp) - var = np.nanvar(values) - return rt / (math.sin(mean)**2 * var) + def fconst(self, values: typing.Iterable[float], temp: float) -> float: + rt = 8.314 * temp / 1000.0 # pylint: disable=invalid-name + mean = self.eqm(values, temp) + var = self._variance_func(values) + return rt / (math.sin(mean) ** 2 * var) class MartiniDefaultLength(FunctionalForm): + """Dummy functional form which returns a fixed force constant.""" + gromacs_type_ids = (1, None, None) - @staticmethod - def fconst(values, temp): - return 1250. + def fconst(self, values: typing.Iterable[float], temp: float) -> float: + return 1250.0 class MartiniDefaultAngle(FunctionalForm): + """Dummy functional form which returns a fixed force constant.""" + gromacs_type_ids = (None, 2, None) - @staticmethod - def fconst(values, temp): - return 25. + def fconst(self, values: typing.Iterable[float], temp: float) -> float: + return 25.0 class MartiniDefaultDihedral(FunctionalForm): + """Dummy functional form which returns a fixed force constant.""" + gromacs_type_ids = (None, None, 1) - @staticmethod - def fconst(values, temp): - return 50. + def fconst(self, values: typing.Iterable[float], temp: float) -> float: + return 50.0 diff --git a/pycgtool/interface.py b/pycgtool/interface.py deleted file mode 100644 index d61f5f9..0000000 --- a/pycgtool/interface.py +++ /dev/null @@ -1,310 +0,0 @@ -""" -This module contains classes for interaction at the terminal. -""" -import collections -import curses -import curses.textpad -import time - - -class Options: - """ - Class to hold program options not specified at the initial command line. - - Values can be queried by indexing as a dictionary or by attribute. Iterable. - """ - def __init__(self, default, args=None): - """ - Create Options instance from iterable of keys and default values. - - :param default: Iterable of key, default value pairs (e.g. list of tuples) - :param args: Optional program arguments from Argparse, will be displayed in interactive mode - """ - self._dict = collections.OrderedDict() - for key, val in default: - try: - val = val.lower() - except AttributeError: - pass - - self._dict[key.lower()] = (val, type(val)) - - # Allow to carry options from argparse - self.args = args - - def __getattr__(self, attr): - return self._dict[attr.lower()][0] - - def __repr__(self): - res = "[" + ", ".join((str((key, val[0])) for key, val in self._dict.items())) + "]" - return res - - def __iter__(self): - return iter(((key, val[0]) for key, val in self._dict.items())) - - def __len__(self): - return len(self._dict) - - def __getitem__(self, item): - try: - return self._dict[item] - except KeyError: - try: - opt = list(self._dict.keys())[item] - return self._dict[opt][0] - except TypeError: - raise TypeError("Must access Options using either a string or an integer") - - def set(self, opt, val): - """ - Set an argument by name. - - :param opt: Option to set - :param val: Value to set option to - """ - opt = opt.lower() - try: - val = val.lower() - except AttributeError: - pass - _type = self._dict[opt][1] - - if _type is not type(val): - if _type is bool: - self._dict[opt] = (_truthy(val), bool) - else: - self._dict[opt] = (_type(val), _type) - else: - self._dict[opt] = (val, _type) - - def _set_by_num(self, opt_num, val): - """ - Set an argument if only its position in sequence is known. - For use in Options._inter. - - :param opt_num: Sequence number of option to set - :param val: Value to set option to - """ - opt = list(self._dict.keys())[opt_num] - self.set(opt, val) - - def toggle_boolean(self, opt): - """ - Toggle a boolean argument by name. - - :param opt: Option to toggle - """ - entry = self._dict[opt] - if entry[1] is bool: - self._dict[opt] = (not entry[0], entry[1]) - else: - raise TypeError("Only boolean options can be toggled") - - def _toggle_boolean_by_num(self, opt_num): - """ - Toggle a boolean argument if only its position in sequence is known. - For use in Options._inter. - - :param opt_num: Sequence number of option to toggle - """ - opt = list(self._dict.keys())[opt_num] - self.toggle_boolean(opt) - - def interactive(self): - """ - Read options in interactive terminal mode using curses. - """ - curses.wrapper(self._inter) - - def _inter(self, stdscr): - """ - Read options in interactive terminal mode using curses. - - :param stdscr: Curses window to use as interface - """ - stdscr.clear() - if self.args is not None: - stdscr.addstr(1, 1, "Using GRO: {0}".format(self.args.gro)) - stdscr.addstr(2, 1, "Using XTC: {0}".format(self.args.xtc)) - stdscr.addstr(4, 1, "Press q to proceed") - stdscr.box() - stdscr.refresh() - - nrows = len(self) - - errscr = stdscr.derwin(3, curses.COLS - 3, nrows + 8, 1) - errscr.border() - - window_config = stdscr.derwin(nrows + 2, curses.COLS - 3, 5, 1) - window_config.box() - window_config.refresh() - window_keys = window_config.derwin(nrows, 20, 1, 0) - window_config.vline(1, 18, curses.ACS_VLINE, nrows) - window_vals = window_config.derwin(nrows, curses.COLS - 24, 1, 20) - text_edit_wins = [] - text_inputs = [] - - for i, (key, value) in enumerate(self): - window_keys.addstr(i, 0, key) - try: - text_edit_wins.append(window_vals.derwin(1, 30, i, 0)) - except curses.error as e: - raise RuntimeError("Your terminal is too small to fit the interface, please expand it") from e - text_edit_wins[-1].addstr(0, 0, str(value)) - text_inputs.append(curses.textpad.Textbox(text_edit_wins[-1])) - - stdscr.refresh() - window_keys.refresh() - for window in text_edit_wins: - window.refresh() - - pos = 0 - move = {"KEY_UP": lambda x: (x - 1) % nrows, - "KEY_DOWN": lambda x: (x + 1) % nrows, - "KEY_LEFT": lambda x: x, - "KEY_RIGHT": lambda x: x} - - while True: - key = text_edit_wins[pos].getkey(0, 0) - errscr.erase() - if key in move: - pos = move[key](pos) - if key == "\n": - if type(self[pos]) is bool: - self._toggle_boolean_by_num(pos) - else: - val = text_inputs[pos].edit().strip() - try: - self._set_by_num(pos, val) - except ValueError: - errscr.addstr(0, 0, "Invalid value '{0}' for option".format(val)) - errscr.addstr(1, 0, "Value has been reset".format(val)) - - text_edit_wins[pos].erase() - text_edit_wins[pos].addstr(0, 0, str(self[pos])) - text_edit_wins[pos].refresh() - - errscr.refresh() - if key == "q": - break - - -def _truthy(string): - """ - Evaluate a string as True or False in the natural way. - - :param string: String to evaluate - :return: True or False - """ - truthy_strings = ("yes", "y", "on", "true", "t", "1") - falsey_strings = ("no", "n", "off", "false", "f", "0") - - string = string.lower().strip() - if string in truthy_strings: - return True - elif string in falsey_strings: - return False - else: - raise ValueError("Value '{0}' could not be converted to boolean".format(string)) - - -class Progress: - """ - Display a progress bar during the main loop of a program. - """ - - def __init__(self, maxits, length=20, dowhile=None, quiet=False): - """ - Return progress bar instance to handle printing of a progress bar within loops. - - :param maxits: Expected number of iterations - :param length: Length of progress bar in characters - :param dowhile: Function to call after each iteration, stops if False - :param quiet: Skip printing of progress bar - for testing - """ - self._maxits = maxits - self._length = length - self._dowhile = dowhile - self._quiet = quiet - self._its = -1 - self._start_time = time.perf_counter() - - def __len__(self): - """ - Maximum iterator length. - - This length will be reached if the iterator is not stopped by a False dowhile condition or KeyboardInterrupt. - - :return: Maximum length of iterator - """ - return self._maxits - self._its - - def __iter__(self): - return self - - def __next__(self): - """ - Allow iteration over Progress while testing dowhile condition. - - Will catch Ctrl-C and return control as if the iterator has been fully consumed. - - :return: Iteration number - """ - self._its += 1 - - try: - if self._dowhile is not None and self._its > 0 and not self._dowhile(): - self._stop() - except KeyboardInterrupt: - print(end="\r") - self._stop() - - if self._its >= self._maxits: - self._stop() - - if not self._quiet: - self._display() - - return self._its - - def run(self): - """ - Iterate through self until stopped by maximum iterations or False condition. - - Use the tqdm library if it is present. - """ - no_tqdm = False - try: - from tqdm import tqdm - except ImportError: - no_tqdm = True - - if self._quiet or no_tqdm: - collections.deque(self, maxlen=0) - - else: - self._quiet = True - collections.deque(tqdm(self, total=len(self)-1, ncols=80), maxlen=0) - self._quiet = False - - return self._its - - @property - def _bar(self): - done = int(self._length * (self._its / self._maxits)) - left = self._length - done - width = len(str(self._maxits)) - return "{0:-{width}} [".format(self._its, width=width) + done * "#" + left * "-" + "] {0}".format(self._maxits) - - def _stop(self): - if not self._quiet: - time_taken = int(time.perf_counter() - self._start_time) - print(self._bar + " took {0}s".format(time_taken)) - raise StopIteration - - def _display(self): - try: - time_remain = int((time.perf_counter() - self._start_time) * ((self._maxits - self._its) / self._its)) - except ZeroDivisionError: - time_remain = "-" - print(self._bar + " {0}s left".format(time_remain), end="\r") diff --git a/pycgtool/mapping.py b/pycgtool/mapping.py index 437103e..a02d3e3 100644 --- a/pycgtool/mapping.py +++ b/pycgtool/mapping.py @@ -5,33 +5,37 @@ Each list corresponds to a single molecule. """ -import numpy as np +import copy import logging -import json -import os +import pathlib +import typing -from .frame import Atom, Residue, Frame -from .parsers.cfg import CFG -from .util import dir_up +import mdtraj +from mdtraj.formats.pdb import PDBTrajectoryFile +import numpy as np -try: - import numba -except ImportError: - from .util import NumbaDummy - numba = NumbaDummy() +from .frame import Frame +from .parsers import CFG, ITP logger = logging.getLogger(__name__) -class BeadMap(Atom): - """ - POD class holding values relating to the AA->CG transformation for a single bead. - """ - __slots__ = ["name", "type", "atoms", "charge", "mass", "weights", "weights_dict"] +PathLike = typing.Union[str, pathlib.Path] - def __init__(self, name, num, type=None, atoms=None, charge=0, mass=0): - """ - Create a single bead mapping. + +class BeadMap: + """Class holding values relating to the AA->CG transformation for a single bead.""" + + def __init__( + self, + name: str, + num: int, + type: str = None, + atoms=None, + charge: float = 0, + mass: float = 0, + ): + """Create a single bead mapping. :param str name: The name of the bead :param int num: The number of the bead @@ -40,16 +44,25 @@ def __init__(self, name, num, type=None, atoms=None, charge=0, mass=0): :param float charge: The net charge on the bead :param float mass: The total bead mass """ - Atom.__init__(self, name, num, type=type, charge=charge, mass=mass) + self.name = name + self.num = num + self.type = type + self.mass = mass + self.charge = charge + self.atoms = atoms # NB: Mass weights are added in Mapping.__init__ if an itp file is provided - self.weights_dict = {"geom": np.array([[1. / len(atoms)] for _ in atoms], dtype=np.float32), - "first": np.array([[1.]] + [[0.] for _ in atoms[1:]], dtype=np.float32)} + self.weights_dict = { + "geom": np.array([1.0 / len(atoms) for _ in atoms], dtype=np.float32), + "first": np.array([1.0] + [0.0 for _ in atoms[1:]], dtype=np.float32), + } self.weights = self.weights_dict["geom"] + def __repr__(self): + return f"BeadMap #{self.num} {self.name} type: {self.type} mass: {self.mass} charge: {self.charge}" + def __iter__(self): - """ - Iterate through the atom names from which the bead is made up. + """Iterate through the atom names from which the bead is made up. :return: Iterator over atoms """ @@ -61,77 +74,247 @@ def __len__(self): def __getitem__(self, item): return self.atoms[item] + def guess_atom_masses(self) -> None: + """Guess masses for the atoms inside this bead.""" + mass_array = np.zeros(len(self.atoms), dtype=np.float32) -class EmptyBeadError(Exception): - """ - Exception used to indicate that none of the required atoms are present. - """ - pass + for i, atom in enumerate(self.atoms): + try: + mass = mdtraj.element.Element.getBySymbol(atom[:2]).mass + + except KeyError: + try: + mass = mdtraj.element.Element.getBySymbol(atom[0]).mass + + except KeyError: + raise RuntimeError( + f"Mass of atom {atom} could not be automatically assigned, " + "map_center=mass is not available." + ) + + mass_array[i] = mass + + self.mass = sum(mass_array) + + if not np.all(mass_array): + raise RuntimeError( + "Some atom masses could not be automatically assigned, " + "map_center=mass is not available" + ) + + mass_array /= self.mass + self.weights_dict["mass"] = mass_array + + +class VirtualMap(BeadMap): + def __init__(self, name, num, type=None, atoms=None, charge=0): + """Create a single bead mapping. + + :param str name: The name of the bead + :param int num: The number of the bead + :param str type: The bead type + :param List[str] atoms: The CG bead names from which the bead position is determined + :param float charge: The net charge on the bead + """ + super().__init__(name, num, type=type, atoms=atoms, charge=charge, mass=0.0) + + self.gromacs_type_id_dict = {"geom": 1, "mass": 2} + self.gromacs_type_id = self.gromacs_type_id_dict["geom"] + + def guess_atom_masses(self) -> None: + """Virtual beads should not define atom masses.""" + return class Mapping: - """ - Class used to perform the AA->CG mapping. + """Class used to perform the AA->CG mapping. Contains a dictionary of lists of BeadMaps. Each list corresponds to a single molecule. """ - def __init__(self, filename, options, itp=None): - """ - Read in the AA->CG mapping from a file. + + def __init__( + self, + filename: PathLike, + options, + itp_filename: typing.Optional[PathLike] = None, + ): + """Read in the AA->CG mapping from a file. :param filename: File from which to read mapping - :return: Instance of Mapping + :param options: Options from command line + :param itp_filename: Optional GROMACS itp file for atom mass / charge """ + self._manual_charges = {} self._mappings = {} self._map_center = options.map_center + self._virtual_map_center = options.virtual_map_center self._masses_are_set = False with CFG(filename) as cfg: - self._manual_charges = {} for mol_name, mol_section in cfg.items(): - self._mappings[mol_name] = [] - self._manual_charges[mol_name] = False - molmap = self._mappings[mol_name] - for i, (name, typ, first, *atoms) in enumerate(mol_section): - charge = 0 - try: - # Allow optional charge in mapping file - charge = float(first) - self._manual_charges[mol_name] = True - except ValueError: - atoms.insert(0, first) - assert atoms, "Bead {0} specification contains no atoms".format(name) - newbead = BeadMap(name, i, type=typ, atoms=atoms, charge=charge) - molmap.append(newbead) - - # TODO this only works with one moleculetype in one itp - extend this - if itp is not None: - with CFG(itp) as itp: - atoms = {} - for toks in itp["atoms"]: - # Store charge and mass - atoms[toks[4]] = (float(toks[6]), float(toks[7])) - - molname = itp["moleculetype"][0][0] - for bead in self._mappings[molname]: - mass_array = np.array([[atoms[atom][1]] for atom in bead], dtype=np.float32) - bead.mass = sum(mass_array) - mass_array /= bead.mass - bead.weights_dict["mass"] = mass_array + mol_map, manual_charges = self._mol_map_from_section(mol_section) - for atom in bead: - if self._manual_charges[molname]: - logger.warning("Charges assigned in mapping for molecule {0}, ignoring itp charges.".format(molname)) - else: - bead.charge += atoms[atom][0] + self._mappings[mol_name] = mol_map + self._manual_charges[mol_name] = manual_charges - self._masses_are_set = True + if itp_filename is not None: + self._load_itp(itp_filename) - if self._map_center == "mass" and not self._masses_are_set: + if ( + self._map_center == "mass" or self._virtual_map_center == "mass" + ) and not self._masses_are_set: self._guess_atom_masses() - for molname, mapping in self._mappings.items(): - for bmap in mapping: - bmap.weights = bmap.weights_dict[self._map_center] + + self._set_bead_weights() + self._rename_atoms() + + def _load_itp(self, itp_filename: str) -> None: + """Load mass and charge of atoms in mapping from a GROMACS itp topology file. + + :param itp_filename: ITP file to read + """ + with ITP(itp_filename) as itp: + for mol_name, mol_map in self._mappings.items(): + try: + itp_mol_entry = itp[mol_name] + manual_charges = self._manual_charges[mol_name] + if manual_charges: + logger.warning( + "Charges assigned in mapping for molecule %s, ignoring itp charges", + mol_name, + ) + + self._itp_section_into_mol_map( + mol_map, itp_mol_entry, manual_charges + ) + + except KeyError: + logger.warning( + "No itp information for molecule %s found in %s", + mol_name, + itp.filename, + ) + + self._masses_are_set = True + + def _set_bead_weights(self) -> None: + """Set bead weights for the mapping center being used.""" + for mol_map in self._mappings.values(): + for bmap in mol_map: + if isinstance(bmap, VirtualMap): + bmap.weights = bmap.weights_dict[self._virtual_map_center] + bmap.gromacs_type_id = bmap.gromacs_type_id_dict[ + self._virtual_map_center + ] + + else: + bmap.weights = bmap.weights_dict[self._map_center] + + @staticmethod + def _itp_section_into_mol_map( + mol_map: typing.List[BeadMap], itp_mol_entry, manual_charges: bool + ) -> None: + atoms = {} + for toks in itp_mol_entry["atoms"]: + # Store charge and mass + atoms[toks[4]] = (float(toks[6]), float(toks[7])) + + for bead in mol_map: + if not isinstance(bead, VirtualMap): + mass_array = np.array([atoms[atom][1] for atom in bead]) + bead.mass = sum(mass_array) + mass_array /= bead.mass + bead.weights_dict["mass"] = mass_array + + if not manual_charges: + for atom in bead: + bead.charge += atoms[atom][0] + + for bead in mol_map: + if isinstance(bead, VirtualMap): + mass_array = np.array( + [real_bead.mass for real_bead in mol_map if real_bead.name in bead] + ) + weights_array = mass_array / sum(mass_array) + bead.weights_dict["mass"] = weights_array + + if not manual_charges: + bead.charge = sum( + [ + real_bead.charge + for real_bead in mol_map + if real_bead.name in bead + ] + ) + + @staticmethod + def _mol_map_from_section(mol_section) -> typing.Tuple[typing.List[BeadMap], bool]: + mol_map = [] + manual_charges = False + + prefix_to_class = {"@v": VirtualMap} + + for i, (name, typ, first, *atoms) in enumerate(mol_section): + bead_class = BeadMap + charge = 0 + + if name.startswith("@"): + try: + bead_class = prefix_to_class[name] + name, typ, first, *atoms = mol_section[i][1:] + + except KeyError as exc: + raise ValueError( + f'Invalid line prefix "{name}" in mapping file' + ) from exc + + try: + # Allow optional charge in mapping file + # Using this even once in a molecule enables it for the whole molecule + charge = float(first) + manual_charges = True + + except ValueError: + # Is an atom name, not a charge + atoms.insert(0, first) + + if not atoms: + raise ValueError(f"Bead {name} specification contains no atoms") + + mol_map.append(bead_class(name, i, type=typ, atoms=atoms, charge=charge)) + + return mol_map, manual_charges + + def _rename_atoms(self) -> None: + """Rename residues and atoms in mapping according to MDTraj conventions. + + This means that users can create mappings using the same names as are + in the input topology file and not have this broken by MDTraj renaming + the residues and atoms. + """ + # We need to use a couple of protected methods from MDTraj here + # pylint: disable=protected-access + + PDBTrajectoryFile._loadNameReplacementTables() + + atom_replacements = {} + for mol_name in list(self._mappings.keys()): + mol_map = copy.deepcopy(self._mappings[mol_name]) + + try: + mol_name = PDBTrajectoryFile._residueNameReplacements[mol_name] + atom_replacements = PDBTrajectoryFile._atomNameReplacements[mol_name] + + except KeyError: + continue + + self._mappings[mol_name] = mol_map + + for bead in mol_map: + bead.atoms = [ + atom_replacements[atom] if atom in atom_replacements else atom + for atom in bead.atoms + ] def __len__(self): return len(self._mappings) @@ -145,141 +328,136 @@ def __getitem__(self, item): def __iter__(self): return iter(self._mappings) - def _guess_atom_masses(self): - """ - Guess atom masses from names - """ - dist_dat_dir = os.path.join(dir_up(os.path.realpath(__file__), 2), "data") - mass_file = os.path.join(dist_dat_dir, "atom_masses.json") - with open(mass_file) as f: - mass_dict = json.load(f) + def items(self): + return self._mappings.items() + def _guess_atom_masses(self) -> None: + """Guess atom masses from their names.""" for mol_mapping in self._mappings.values(): for bead in mol_mapping: - if bead.mass == 0: - mass_array = np.zeros((len(bead.atoms), 1), dtype=np.float32) - for i, atom in enumerate(bead.atoms): - try: - mass = mass_dict[atom[:2]] - except KeyError: - try: - mass = mass_dict[atom[0]] - except KeyError: - msg = "Mass of atom {0} could not be automatically assigned, map_center=mass is not available." - raise RuntimeError(msg.format(atom)) - mass_array[i] = mass - bead.mass = sum(mass_array) - - if not np.all(mass_array): - msg = "Some atom masses could not be automatically assigned, map_center=mass is not available." - raise RuntimeError(msg) - - mass_array /= bead.mass - bead.weights_dict["mass"] = mass_array + if not bead.mass: + bead.guess_atom_masses() + + # Set virtual bead masses + # Do this afterwards as it depends on real atom masses + for bead in mol_mapping: + if isinstance(bead, VirtualMap): + mass_array = np.array( + [ + real_bead.mass + for real_bead in mol_mapping + if real_bead.name in bead + ], + dtype=np.float32, + ) + + weights_array = mass_array / sum(mass_array) + bead.weights_dict["mass"] = weights_array self._masses_are_set = True - def _cg_frame_setup(self, aa_residues, name=None): - """ - Create a new CG Frame and populate beads + def _cg_frame_setup( + self, aa_residues: typing.Iterable[mdtraj.core.topology.Residue] + ): + """Create a new CG Frame and populate beads :param aa_residues: Iterable of atomistic residues to map from - :param name: Name of Frame :return: New CG Frame instance """ - cgframe = Frame() - cgframe.name = name - + logger.info("Initialising output frame") + cg_frame = Frame() missing_mappings = set() - cg_bead_num = 1 - for aares in aa_residues: + for aa_res in aa_residues: try: - molmap = self._mappings[aares.name] - except KeyError: - if aares.name not in missing_mappings: - missing_mappings.add(aares.name) - logger.warning("A mapping has not been provided for '{0}' residues, they will not be mapped.".format(aares.name)) - continue - - cgres = Residue(name=aares.name, num=aares.num) - cgres.atoms = [Atom(bmap.name, bmap.num, type=bmap.type, charge=bmap.charge, mass=bmap.mass, coords=np.zeros(3)) for bmap in molmap] + mol_map = self._mappings[aa_res.name] - for i, (bead, bmap) in enumerate(zip(cgres, molmap)): - cgres.name_to_num[bead.name] = i - bead.charge = bmap.charge - bead.mass = bmap.mass - bead.num = cg_bead_num + except KeyError: + if aa_res.name not in missing_mappings: + missing_mappings.add(aa_res.name) + logger.warning( + "A mapping has not been provided for '%s' residues, they will not be mapped", + aa_res.name, + ) - cg_bead_num += 1 + continue - cgframe.add_residue(cgres) - cgframe.natoms += len(cgres) + cg_res = cg_frame.add_residue(aa_res.name) + for bmap in mol_map: + cg_frame.add_atom(bmap.name, None, cg_res) - return cgframe + logger.info("Finished initialising output frame") + return cg_frame - def apply(self, frame, cgframe=None): - """ - Apply the AA->CG mapping to an atomistic Frame. + def apply(self, frame: Frame, cg_frame: typing.Optional[Frame] = None): + """Apply the AA->CG mapping to an atomistic Frame. :param frame: Frame to which mapping will be applied :param cgframe: CG Frame to remap - optional :return: Frame instance containing the CG frame """ - if cgframe is None: + if cg_frame is None: # Frame needs initialising - cgframe = self._cg_frame_setup(frame.yield_resname_in(self._mappings), frame.name) + cg_frame = self._cg_frame_setup(frame.residues) - cgframe.time = frame.time - cgframe.number = frame.number - cgframe.box = frame.box + cg_frame.time = frame.time + cg_frame.unitcell_lengths = frame.unitcell_lengths + cg_frame.unitcell_angles = frame.unitcell_angles - coord_func = calc_coords_weight if frame.box[0] * frame.box[1] * frame.box[2] else calc_coords_weight_nobox + unitcell_lengths = cg_frame.unitcell_lengths + if not np.all(unitcell_lengths): + unitcell_lengths = None - for aares, cgres in zip(frame.yield_resname_in(self._mappings), cgframe): - molmap = self._mappings[aares.name] + logger.info("Applying AA->CG mapping") + residues_to_map = (res for res in frame.residues if res.name in self._mappings) + for aa_res, cg_res in zip(residues_to_map, cg_frame.residues): + mol_map = self._mappings[aa_res.name] - for i, (bead, bmap) in enumerate(zip(cgres, molmap)): - ref_coords = aares[bmap[0]].coords + for bead, bmap in zip(cg_res.atoms, mol_map): + if isinstance(bmap, VirtualMap): + continue + + ref_coords = aa_res.atom(bmap[0]).coords if len(bmap) == 1: bead.coords = ref_coords - continue - coords = np.asarray([aares[atom].coords for atom in bmap], dtype=np.float32) - bead.coords = coord_func(ref_coords, coords, cgframe.box, bmap.weights) + else: + coords = np.array( + [aa_res.atom(atom).coords for atom in bmap], dtype=np.float32 + ) + bead.coords = calc_coords_weight( + ref_coords, coords, bmap.weights, unitcell_lengths + ) - return cgframe + for bead, bmap in zip(cg_res.atoms, mol_map): + if isinstance(bmap, VirtualMap): + coords = np.array( + [cg_res.atom(atom).coords for atom in bmap], dtype=np.float32 + ) + bead.coords = calc_coords_weight( + coords[0], coords, bmap.weights, unitcell_lengths + ) + cg_frame.build_trajectory() -@numba.jit -def calc_coords_weight(ref_coords, coords, box, weights): - """ - Calculate the coordinates of a single CG bead from weighted component atom coordinates. + logger.info("Finished applying AA->CG mapping") + return cg_frame - :param ref_coords: Coordinates of reference atom, usually first atom in bead - :param coords: Array of coordinates of component atoms - :param box: PBC box vectors - :param weights: Array of atom weights, must sum to 1 - :return: Coordinates of CG bead - """ - vectors = coords - ref_coords - vectors -= box * np.rint(vectors / box) - result = np.sum(weights * vectors, axis=0) - result += ref_coords - return result - -@numba.jit -def calc_coords_weight_nobox(ref_coords, coords, box, weights): - """ - Calculate the coordinates of a single CG bead from weighted component atom coordinates. +def calc_coords_weight(ref_coords, coords, weights, box=None): + """Calculate the coordinates of a single CG bead from weighted component atom coordinates. :param ref_coords: Coordinates of reference atom, usually first atom in bead :param coords: Array of coordinates of component atoms - :param box: PBC box vectors :param weights: Array of atom weights, must sum to 1 + :param box: PBC box vectors :return: Coordinates of CG bead """ vectors = coords - ref_coords - result = np.sum(weights * vectors, axis=0) + if box is not None: + vectors -= box * np.rint(vectors / box) + + # Reshape weights array to match atom positions + weights_t = weights[np.newaxis, np.newaxis].T + result = np.sum(weights_t * vectors, axis=0) result += ref_coords return result diff --git a/pycgtool/parsers/__init__.py b/pycgtool/parsers/__init__.py index e0e5097..a454904 100644 --- a/pycgtool/parsers/__init__.py +++ b/pycgtool/parsers/__init__.py @@ -1,3 +1,4 @@ from .cfg import CFG +from .itp import ITP -ITP = CFG \ No newline at end of file +__all__ = ["CFG", "ITP"] diff --git a/pycgtool/parsers/cfg.py b/pycgtool/parsers/cfg.py index e485b60..060e1a6 100644 --- a/pycgtool/parsers/cfg.py +++ b/pycgtool/parsers/cfg.py @@ -1,77 +1,88 @@ -""" -Module containing classes used to parse custom CFG file format. +"""Module containing classes used to parse custom CFG file format. Format is based upon GROMACS .itp files but does not support nesting of sections. """ -import os import collections +import contextlib +import pathlib +import typing + +PathLike = typing.Union[str, pathlib.Path] class DuplicateSectionError(KeyError): - """ - Exception used to indicate that a section has appeared twice in a file. - """ + """Exception used to indicate that a section has appeared twice in a file.""" + def __init__(self, section, filename): - msg = "Section '{0}' appears twice in file '{1}'.".format(section, filename) - super(DuplicateSectionError, self).__init__(msg) + msg = f"Section '{section}' appears twice in file '{filename}'." + super().__init__(msg) class NoSectionError(KeyError): - """ - Exception used to indicate that a file contains no sections. - """ + """Exception used to indicate that a file contains no sections.""" + def __init__(self, filename): - msg = "File '{0}' contains no '[]' section headers.".format(filename) - super(NoSectionError, self).__init__(msg) + msg = f"File '{filename}' contains no '[]' section headers." + super().__init__(msg) -class CFG(collections.OrderedDict): - """ - Class representing a CFG file. +class CFG(collections.OrderedDict, contextlib.AbstractContextManager): + """Class representing a CFG file using a format similar to a GROMACS .itp file. Contains a dictionary of Sections. """ - __slots__ = ["filename"] - def __init__(self, filename=None): - """ - Parse a config file and extract Sections. + def __init__(self, filepath: typing.Optional[PathLike] = None): + """Parse a config file and extract Sections.""" + super().__init__() + self.filepath = None + + if filepath is not None: + self.filepath = pathlib.Path(filepath) + self._read_file(self.filepath) - :param filename: Name of file to read - :return: Instance of CFG - """ - super(CFG, self).__init__() - self.filename = filename + def _read_line(self, line: str, filepath: pathlib.Path) -> str: + # Strip comments + line = line.split(";")[0].strip() - with open(self.filename) as f: + # Handle include directive + if line.startswith("#include"): + include_file = line.split()[1].strip('"') + other = type(self)(filepath.parent.joinpath(include_file)) + self.update(other) + + return "" # Handle include then treat as empty line + + return line + + def _read_file(self, filepath: pathlib.Path) -> None: + with open(filepath) as cfg_file: curr_section = None - for line in f: - line = line.strip() - if not line or line.startswith(";"): - continue - elif line.startswith("#include"): - cfg2 = CFG(os.path.join(os.path.dirname(self.filename), - line.split()[1])) - self.update(cfg2) + for line in cfg_file: + line = self._read_line(line, filepath) + + if not line: continue - elif line.startswith("["): + if line.startswith("["): curr_section = line.strip("[ ]") + if curr_section in self: - raise DuplicateSectionError(curr_section, self.filename) + raise DuplicateSectionError(curr_section, filepath) + self[curr_section] = [] + continue toks = tuple(line.split()) + try: self[curr_section].append(toks) - except KeyError as e: - raise NoSectionError(self.filename) from e - def __enter__(self): - return self + except KeyError as exc: + raise NoSectionError(filepath) from exc - def __exit__(self, type, value, traceback): + def __exit__(self, exc_type, exc_value, traceback): pass diff --git a/pycgtool/parsers/itp.py b/pycgtool/parsers/itp.py new file mode 100644 index 0000000..15b2a12 --- /dev/null +++ b/pycgtool/parsers/itp.py @@ -0,0 +1,62 @@ +"""Module containing classes used to parse ITP/TOP file format.""" + +import collections +import logging +import pathlib + +from .cfg import CFG, NoSectionError, DuplicateSectionError + +logger = logging.getLogger(__name__) + + +class ITP(CFG): + """Class representing an .itp file. + + Contains a dictionary of sections for every molecule definition. + """ + + def _read_file(self, filepath: pathlib.Path) -> None: + mol_sections = ["atoms", "bonds", "angles", "dihedrals"] + + with open(filepath) as itp_file: + curr_section = None + curr_mol = None + + for line in itp_file: + line = self._read_line(line, filepath) + + if not line: + continue + + if line.startswith("["): + curr_section = line.strip("[ ]") + + if curr_section in mol_sections: # pragma: no cover + # This allows a section to appear twice within a single molecule definition + # It is not clear whether this is allowed by GROMACS but does no harm + self[curr_mol].setdefault(curr_section, []) + + continue # coverage.py cannot detect this branch due to the peephole optimizer + + toks = tuple(line.split()) + + if curr_section == "moleculetype": + curr_mol = toks[0] + + if curr_mol in self: + raise DuplicateSectionError(curr_mol, filepath) + + self[curr_mol] = collections.OrderedDict() + + elif curr_section in mol_sections: + self[curr_mol][curr_section].append(toks) + + elif curr_section is None: + raise NoSectionError(filepath) + + else: + logger.info( + "File '%s' contains unexpected section '%s'", + filepath, + curr_section, + ) diff --git a/pycgtool/pycgtool.py b/pycgtool/pycgtool.py deleted file mode 100755 index dc086aa..0000000 --- a/pycgtool/pycgtool.py +++ /dev/null @@ -1,103 +0,0 @@ -import logging - -from .frame import Frame -from .mapping import Mapping -from .bondset import BondSet -from .forcefield import ForceField -from .interface import Progress - -logger = logging.getLogger(__name__) - - -def main(args, config): - """ - Main function of the program PyCGTOOL. - - Performs the complete AA->CG mapping and outputs a files dependent on given input. - - :param args: Arguments from argparse - :param config: Configuration dictionary - """ - frame = Frame(gro=args.gro, xtc=args.xtc, itp=args.itp, frame_start=args.begin) - - if args.bnd: - logger.info("Bond measurements will be made") - bonds = BondSet(args.bnd, config) - else: - logger.info("Bond measurements will not be made") - - if args.map: - logger.info("Mapping will be performed") - mapping = Mapping(args.map, config, itp=args.itp) - cgframe = mapping.apply(frame) - cgframe.output(config.output_name + ".gro", format=config.output) - else: - logger.info("Mapping will not be performed") - cgframe = frame - - # Only measure bonds from GRO frame if no XTC is provided - # Allows the user to get a topology from a single snapshot - if args.bnd and args.xtc is None: - bonds.apply(cgframe) - - # Main loop - perform mapping and measurement on every frame in XTC - def main_loop(): - nonlocal cgframe - if not frame.next_frame(): - return False - if args.map: - cgframe = mapping.apply(frame, cgframe=cgframe) - if config.output_xtc: - cgframe.write_xtc(config.output_name + ".xtc") - else: - cgframe = frame - if args.bnd: - bonds.apply(cgframe) - return True - - numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin - logger.info("Beginning analysis of {0} frames".format(numframes)) - Progress(numframes, dowhile=main_loop, quiet=args.quiet).run() - - if args.bnd: - if args.map: - logger.info("Beginning Boltzmann inversion") - bonds.boltzmann_invert(progress=(not args.quiet)) - if config.output_forcefield: - logger.info("Creating GROMACS forcefield directory") - ForceField(config.output_name).write(config.output_name, mapping, bonds) - logger.info("GROMACS forcefield directory created") - else: - bonds.write_itp(config.output_name + ".itp", mapping=mapping) - - if config.dump_measurements: - logger.info("Dumping bond measurements to file") - bonds.dump_values(config.dump_n_values) - - -def map_only(args, config): - """ - Perform AA->CG mapping and output coordinate file. - - :param args: Program arguments - :param config: Object containing run options - """ - frame = Frame(gro=args.gro, xtc=args.xtc) - mapping = Mapping(args.map, config) - cgframe = mapping.apply(frame) - cgframe.output(config.output_name + ".gro", format=config.output) - - if args.xtc and (config.output_xtc or args.outputxtc): - # Main loop - perform mapping and measurement on every frame in XTC - def main_loop(): - nonlocal cgframe - if not frame.next_frame(): - return False - cgframe = mapping.apply(frame, cgframe=cgframe) - cgframe.write_xtc(config.output_name + ".xtc") - return True - - numframes = frame.numframes - args.begin if args.end == -1 else args.end - args.begin - logger.info("Beginning analysis of {0} frames".format(numframes)) - its = Progress(numframes, dowhile=main_loop, quiet=args.quiet).run() - diff --git a/pycgtool/util.py b/pycgtool/util.py index ca3a201..7ec74bc 100644 --- a/pycgtool/util.py +++ b/pycgtool/util.py @@ -1,152 +1,56 @@ -""" -This module contains some general purpose utility functions used in PyCGTOOL. -""" +"""This module contains some general purpose utility functions used in PyCGTOOL.""" -import os -import itertools -import random -import math import filecmp +import functools +import itertools import logging -import re - -from collections import namedtuple +import os +import pathlib +import random +import typing +import mdtraj import numpy as np logger = logging.getLogger(__name__) +PathLike = typing.Union[pathlib.Path, str] -class NumbaDummy: - """ - Dummy Numba module - """ - def __getattr__(self, item): - if item == "jit": - return NumbaDummy.jit - return self - - def __getitem__(self, item): - return self - - def __call__(self, *args, **kwargs): - return None - - @staticmethod - def jit(*args, **kwargs): - """ - Dummy version of numba.jit decorator, does nothing - """ - if len(args) == 1 and callable(args[0]): - return args[0] - else: - def wrap(func): - return func - return wrap - -try: - import numba -except ImportError: - # If numba isn't installed, create dummy so we don't get NameErrors - numba = NumbaDummy() - - -@numba.jit(numba.float32[3](numba.float32[3], numba.float32[3])) -def vector_cross(u, v): - """ - Return vector cross product of two 3d vectors as numpy array. - :param u: First 3d vector - :param v: Second 3d vector - :return: Cross product of two vectors as numpy.array - """ - res = np.empty_like(u) - res[0] = u[1] * v[2] - u[2] * v[1] - res[1] = u[2] * v[0] - u[0] * v[2] - res[2] = u[0] * v[1] - u[1] * v[0] - return res +class EmptyIterableError(ValueError): + pass -@numba.jit(numba.float32(numba.float32[3], numba.float32[3])) -def vector_dot(u, v): - """ - Return vector dot product of two 3d vectors. +def circular_mean(values: typing.Iterable[float]) -> float: + """Calculate average of angles on a circle. - :param u: First 3d vector - :param v: Second 3d vector - :return: Dot product of two vectors + See https://en.wikipedia.org/wiki/Mean_of_circular_quantities """ - return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] + if not isinstance(values, np.ndarray): + values = np.array(values) + x = np.cos(values) + y = np.sin(values) + vec = np.array([x, y]).T -@numba.jit(numba.float32(numba.float32[3])) -def vector_len(v): - return math.sqrt(v[0]*v[0] + v[1]*v[1] + v[2]*v[2]) + x_av, y_av = np.nanmean(vec, axis=0) + return np.arctan2(y_av, x_av) -@numba.jit(numba.float32(numba.float32[3], numba.float32[3])) -def vector_angle(a, b): - """ - Calculate the angle between two vectors. - - :param a: First vector - :param b: Second vector - :return: Angle in radians - """ - mag = vector_len(a) * vector_len(b) - if mag == 0: - raise ZeroDivisionError("One or more bonds in angle calculation has length zero") - dot = vector_dot(a, b) / mag - # Previously checked to within 1%, but this prevented numba optimisation - ang = math.acos(max(-1, min(1, dot))) - return ang - - -@numba.jit -def vector_angle_signed(a, b, ref=np.array([0., 0., 1.])): - """ - Calculate the signed angle between two vectors. - - :param a: First vector - :param b: Second vector - :param ref: Optional reference vector, will use global z-axis if not provided - :return: Signed angle in radians - """ - ang = vector_angle(a, b) - signum = math.copysign(1, vector_dot(vector_cross(a, b), ref)) - return ang * signum - - -def tuple_equivalent(tuple1, tuple2): - """ - Check if two node tuples are equivalent. Assumes undirected edges. +def circular_variance(values: typing.Iterable[float]) -> float: + """Calculate variance of angles on a circle. - :param tuple1: First tuple to compare - :param tuple2: Second tuple to compare - :return: True if tuples are equivalent, else False + See https://en.wikipedia.org/wiki/Mean_of_circular_quantities """ - if tuple1 == tuple2: - return True - elif tuple1[::-1] == tuple2: - return True - else: - return False - + if not isinstance(values, np.ndarray): + values = np.array(values) -@numba.jit -def dist_with_pbc(pos1, pos2, box): - """ - Calculate the distance between two points accounting for periodicity. + two_pi = 2 * np.pi + mean = circular_mean(values) - :param pos1: 3d vector position 1 - :param pos2: 3d vector position 2 - :param box: Cubic box vectors - :return: Vector between two points - """ - d = pos2 - pos1 - if box[0] * box[1] * box[2]: - d -= box * np.rint(d / box) - return d + diff = values - mean + diff -= np.rint(diff / two_pi) * two_pi + return np.nanmean(np.square(diff)) def extend_graph_chain(extend, pairs): @@ -171,6 +75,7 @@ def append_if_not_in(lst, item): for pair2 in pairs: if node2 == pair2[0] and pair2[1] not in chain: append_if_not_in(ret, spare + (node1, node2, pair2[1])) + elif node2 == pair2[1] and pair2[0] not in chain: append_if_not_in(ret, spare + (node1, node2, pair2[0])) @@ -179,9 +84,17 @@ def append_if_not_in(lst, item): if node2.startswith("+"): for pair2 in pairs: if node2.strip("+") == pair2[0] and "+" + pair2[1] not in chain: - append_if_not_in(ret, spare + (node1, node2, "+" + pair2[1])) - elif node2.strip("+") == pair2[1] and "+" + pair2[0] not in chain: - append_if_not_in(ret, spare + (node1, node2, "+" + pair2[0])) + append_if_not_in( + ret, spare + (node1, node2, "+" + pair2[1]) + ) + + elif ( + node2.strip("+") == pair2[1] and "+" + pair2[0] not in chain + ): + append_if_not_in( + ret, spare + (node1, node2, "+" + pair2[0]) + ) + except AttributeError: pass @@ -191,33 +104,21 @@ def append_if_not_in(lst, item): return ret -def stat_moments(vals, ignore_nan=True): - """ - Return statistical (population) moments of data provided. - - :param vals: The data for which to calculate moments - :param ignore_nan: Whether to exclude np.nan and infinity from calculation - :return: Tuple of moments - population mean and variance, both zero if input is empty list - """ - if ignore_nan: - vals_tmp = [val for val in vals if np.isfinite(val)] - else: - vals_tmp = vals +def transpose_and_sample( + sequence: typing.Iterable, n: typing.Optional[int] = None +) -> typing.List: + """Transpose a sequence of lists and sample to provide target number of rows. - try: - return np.mean(vals_tmp), np.var(vals_tmp) - except FloatingPointError: - return 0., 0. - - -def transpose_and_sample(sequence, n=None): - """ - Transpose a sequence of lists and sample to provide target number of rows. + Skip rows containing non-finite numbers (e.g. NaN). :param sequence: 2d sequence object to transpose :param n: Number of samples to take """ - rows = list(zip(*sequence)) + + def no_nans(row): + return np.isfinite(row).all() + + rows = list(filter(no_nans, zip(*sequence))) if n is not None and len(rows) > n: rows = random.sample(rows, n) @@ -238,32 +139,31 @@ def dir_up(name, n=1): return name -def backup_file(name): +def backup_file(path: PathLike) -> pathlib.Path: """ Backup a file using the GROMACS backup naming scheme. name -> #name.x# - :param name: File to backup + :param path: Path to file to backup :return: New name of file after backup """ - if not os.path.exists(name): - return None + path = pathlib.Path(path) + new_path = path + counter = 1 - directory, basename = os.path.split(name) - for i in itertools.count(1): - new_base = "#{0}.{1}#".format(basename, i) - new_name = os.path.join(directory, new_base) - if not os.path.exists(new_name): - break + while new_path.exists(): + new_path = path.parent.joinpath(f"#{path.name}.{counter}#") + counter += 1 - os.rename(name, new_name) - logger.warning("Existing file {0} backed up as {1}".format(name, new_name)) - return new_name + if new_path != path: + path.rename(new_path) + logger.warning("Existing file %s backed up as %s", path.name, new_path.name) + return new_path -def sliding(vals): - """ - Yield three values in a sliding window along an iterable. + +def sliding(vals: typing.Iterable): + """Yield three values in a sliding window along an iterable. :param vals: Iterable to iterate over :return: Generator of tuples @@ -275,8 +175,8 @@ def sliding(vals): current = next(it) except StopIteration: - raise ValueError('Iterable contains no items') - + raise EmptyIterableError("Cannot make sliding window over empty iterable") + for nxt in it: yield (prev, current, nxt) prev = current @@ -285,233 +185,169 @@ def sliding(vals): yield (prev, current, None) -def r_squared(ref, fit): - """ - Calculate residual R squared of fitted data against reference data by y values. - :param ref: Reference y values - :param fit: Fitted y values - :return: R squared - """ - y_mean = sum(ref) / len(ref) - ss_res, ss_tot = 0, 0 - for refpy, fitpy in zip(ref, fit): - ss_res += (fitpy - refpy)**2 - ss_tot += (refpy - y_mean)**2 - try: - return 1 - (ss_res / ss_tot) - except ZeroDivisionError: - return 0 - - -def cmp_whitespace_float(ref_filename, test_filename, float_rel_error=0.01): +def cmp_file_whitespace_float(ref_filename, test_filename, rtol=0.01, verbose=False): """ Compare two files ignoring spacing on a line and using a tolerance on floats :param ref_filename: Name of reference file :param test_filename: Name of test file - :param float_rel_error: Acceptable relative error on floating point numbers + :param float rtol: Acceptable relative error on floating point numbers + :param bool verbose: Print failing lines :return: True if files are the same, else False """ - def float_or_string(string): - try: - int(string) - return string - except ValueError: - try: - return float(string) - except ValueError: - return string - if filecmp.cmp(ref_filename, test_filename): return True - with open(ref_filename) as ref_file, open(test_filename) as test_file: - for ref_line, test_line in itertools.zip_longest(ref_file, test_file): - if ref_line is None or test_line is None: - return False - if ref_line == test_line: - continue - - ref_toks = ref_line.split() - test_toks = test_line.split() - if len(ref_toks) != len(test_toks): - return False - for ref_tok, test_tok in zip(map(float_or_string, ref_toks), - map(float_or_string, test_toks)): - if ref_tok != test_tok: - if float == type(ref_tok) and float == type(test_tok): - if abs(ref_tok - test_tok) > ref_tok * float_rel_error: - return False - else: - return False - return True + + with open(ref_filename) as ref, open(test_filename) as test: + ref_lines = ref.readlines() + test_lines = test.readlines() + + return cmp_whitespace_float(ref_lines, test_lines, rtol=rtol, verbose=verbose) + + +def number_or_string(string: str) -> typing.Union[float, int, str]: + """Convert string into an int or float if possible.""" + try: + as_float = float(string) + as_int = int(as_float) + if as_int == as_float: + return as_int + + return as_float + + except ValueError: + return string + + +def cmp_whitespace_float(ref_lines, test_lines, rtol=0.01, verbose=False): + """ + Compare two iterables of lines ignoring spacing on a line and using a tolerance on floats + + :param ref_lines: Iterable of reference lines + :param test_lines: Iterable of test lines + :param float rtol: Acceptable relative error on floating point numbers + :param bool verbose: Print failing lines + :return: True if all lines are the same, else False + """ + diff_lines = [] + for i, (ref_line, test_line) in enumerate( + itertools.zip_longest(ref_lines, test_lines) + ): + # Shortcut trivial comparisons + if ref_line is None or test_line is None: + diff_lines.append((i, ref_line, test_line)) + continue + + if ref_line == test_line: + continue + + ref_toks = ref_line.split() + test_toks = test_line.split() + + # Check for float comparison of tokens on line + for ref_tok, test_tok in itertools.zip_longest( + map(number_or_string, ref_toks), map(number_or_string, test_toks) + ): + if ref_tok != test_tok: + try: + if abs(ref_tok - test_tok) > abs(ref_tok) * rtol: + diff_lines.append((i, ref_line, test_line)) + except TypeError: + diff_lines.append((i, ref_line, test_line)) + + if verbose and diff_lines: + print("Lines fail comparison:") + for i, ref_line, test_line in diff_lines: + print("Line {}".format(i)) + print("Ref: {0}".format(ref_line)) + print("Test: {0}".format(test_line)) + + return len(diff_lines) == 0 -def once_wrapper(func): +def file_write_lines(filename, lines=None, backup=True, append=False): """ - Wrap a function such that it runs only once, subsequent calls are ignored. + Open a file and write lines to it. - :param func: Function to wrap - :return: Wrapped function which will only run once. + :param str filename: Name of file to open + :param iterable[str] lines: Iterable of lines to write + :param bool backup: Should the file be backed up if it exists? Disabled if appending + :param bool append: Should lines be appended to an existing file? """ - called = False - - def wrap(*args, **kwargs): - nonlocal called - if not called: - called = True - return func(*args, **kwargs) - - return wrap - - -class SimpleEnum(object): - class Enum(object): - def __iter__(self): - return iter(self.members) - - def __contains__(self, key): - return key in self.members - - def __len__(self): - return len(self.members) - - def __getitem__(self, key): - return getattr(self, key) - - def as_dict(self): - return {key: getattr(self, key).value for key in self.members} - - class EnumItem(object): - def __init__(self, enum_name, key, value=None): - self.enum_name = enum_name - self.key = key - if value is None: - self.value = key - self._default_value = True - else: - self.value = value - self._default_value = False - - def __repr__(self): - if self._default_value: - return "<{0}: {1}>".format(self.enum_name, self.key) - else: - return "<{0}: {1} - {2}>".format(self.enum_name, self.key, self.value) - - def __hash__(self): - return hash(repr(self)) - - def __eq__(self, other): - """ - Compare enums by key rather than by value. - - :param other: RHS enum - :return: Whether EnumValues are equal by key - """ - if self.enum_name != other.enum_name: - raise TypeError("Cannot compare values from different enums") - return self.key == other.key - - def compare_value(self, other): - """ - Compare enums by value rather than by key. - - :param other: RHS enum - :return: Whether EnumValues are equal by value - """ - if self.enum_name != other.enum_name: - raise TypeError("Cannot compare values from different enums") - return self.value == other.value - - @classmethod - def enum(cls, name, keys=None, values=None): - def returner(val): - return lambda _: val - enum_cls = type(name, (cls.Enum,), {}) - - if keys is None: - keys = [] - if values is None: - for key in keys: - prop = property(returner(cls.EnumItem(name, key))) - setattr(enum_cls, key, prop) - else: - for key, value in zip(keys, values): - prop = property(returner(cls.EnumItem(name, key, value))) - setattr(enum_cls, key, prop) - - setattr(enum_cls, "members", property(returner(set(keys)))) - return enum_cls() - - @classmethod - def enum_from_dict(cls, name, key_val_dict): - return cls.enum(name, key_val_dict.keys(), key_val_dict.values()) - - -class FixedFormatUnpacker(object): + if backup and not append: + backup_file(filename) + + mode = "a" if append else "w" + with open(filename, mode) as f: + if lines is not None: + for line in lines: + print(line, file=f) + + +def any_starts_with(iterable: typing.Iterable, char: str) -> bool: + """Return True if any string(s) in nested iterable starts with a given character. + + :param iterable iterable: Nested iterable of strings to check + :param str char: Char to check each string + :return bool: True if any string in nested iterable starts with char, else False """ - Unpack strings printed in fixed format. + if isinstance(iterable, str): + return iterable.startswith(char) + + recurse = functools.partial(any_starts_with, char=char) + return any(map(recurse, iterable)) + + +def load_optional_topology( + trajfile: typing.Union[str, pathlib.Path], + topfile: typing.Optional[typing.Union[str, pathlib.Path]] = None, +) -> mdtraj.Trajectory: + """Load an MDTraj trajectory with or without a separate topology file. + + :param trajfile: Trajectory file + :param topfile: Corresponding topology file + :return: MDTraj trajectory """ - FormatItem = namedtuple("FormatItem", ["type", "width"]) - FormatStyle = SimpleEnum.enum("FormatStyle", ["C", "Fortran"]) - - def __init__(self, format_string, format_style=FormatStyle.C): - """ - Does not support format strings containing spaces - """ - self._format_string = format_string - format_parsers = {self.FormatStyle.C: self._parse_c_format, - self.FormatStyle.Fortran: self._parse_fortran_format} - clean_format_string = self._clean_format_string(format_string) - self._format_items = format_parsers[format_style](clean_format_string) - - @staticmethod - def _clean_format_string(format_string): - cleaned = format_string.lower() - cleaned = cleaned.strip("-+#/") - return cleaned - - @classmethod - def _parse_c_format(cls, format_string): - """ - Parse a C format specifier string. - - :param format_string: C format string - :return: List of FormatItems - """ - types = {"d": int, "s": str, "f": float} - p = re.compile(r'%-?(?P[0-9]+)[.0-9]*(?P[dsfDSF])') - items = [cls.FormatItem(types[match.group("type")], int(match.group("width"))) for match in p.finditer(format_string)] - return items - - @classmethod - def _parse_fortran_format(cls, format_string): - """ - Parse a Fortran format specifier string. - - :param format_string: Fortran format string - :return: List of FormatItems - """ - items = [] - types = {"i": int, "a": str, "f": float, "x": None} - p = re.compile(r'\s*(?P[0-9]*)(?P[ixafIXAF])(?P[0-9]*)\s*') - for match in p.finditer(format_string): - repeat = int(match.group("repeat")) if match.group("repeat") else 1 - width = int(match.group("width")) if match.group("width") else 1 - for _ in range(repeat): - items.append(cls.FormatItem(types[match.group("type")], width)) - return items - - def unpack(self, string): - items = [] - start = 0 - for format_item in self._format_items: - string_part = string[start:start+format_item.width] - start += format_item.width - if format_item.type is not None: - items.append(format_item.type(string_part.strip())) - return items - - -def tqdm_dummy(iterable, **kwargs): - return iterable + if topfile is None: + return mdtraj.load(str(trajfile)) + + return mdtraj.load(str(trajfile), top=str(topfile)) + + +def compare_trajectories( + *trajectory_files: typing.Union[str, pathlib.Path], + topology_file: typing.Optional[typing.Union[str, pathlib.Path]] = None, + rtol: float = 0.001, +) -> bool: + """Compare multiple trajectory files for equality. + + :param trajectory_files: Paths of trajectory file to compare + :param topology_file: Topology file path + :param coords_only: Only compare coordinates from trajectory - e.g. not box size + """ + ref_traj = load_optional_topology(trajectory_files[0], topology_file) + + for traj_file in trajectory_files[1:]: + try: + traj = load_optional_topology(traj_file, topology_file) + + except ValueError as exc: + raise ValueError("Topology does not match") from exc + + # Conditions from Trajectory.__hash__ + if traj.topology != ref_traj.topology: + raise ValueError("Topology does not match") + + if len(traj) != len(ref_traj): + raise ValueError("Length does not match") + + if not np.allclose(traj.xyz, ref_traj.xyz, rtol=rtol): + raise ValueError("Coordinates do not match") + + if not np.allclose(traj.time, ref_traj.time, rtol=rtol): + raise ValueError("Time does not match") + + if not np.allclose(traj.unitcell_vectors, ref_traj.unitcell_vectors, rtol=rtol): + raise ValueError("Unitcell does not match") + + return True diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..bd96781 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,67 @@ +[tool.poetry] +name = "pycgtool" +version = "2.0.0-beta.5" +description = "Generate coarse-grained molecular dynamics models from atomistic trajectories." +authors = ["James Graham "] +license = "GPL-3.0-only" + +readme = "README.md" +homepage = "https://github.com/jag1g13/pycgtool" +repository = "https://github.com/jag1g13/pycgtool" +documentation = "https://pycgtool.readthedocs.io/en/master/" + +keywords = [ + "molecular-dynamics", +] + +classifiers = [ + "Development Status :: 4 - Beta", + "Environment :: Console", + "Intended Audience :: Science/Research", + "Topic :: Scientific/Engineering :: Chemistry", +] + +[tool.poetry.scripts] +# The actual entrypoint that users will call +pycgtool = "pycgtool.__main__:main" + +[tool.poetry.dependencies] +python = "^3.6.2" +wheel = "^0.35.1" +numpy = [ + { version = "^1.19.1", python = "<3.7" }, # Support for Python 3.6 was dropped in 1.20 + { version = "^1.20.0", python = ">=3.7" } # But 1.20 should resolve issue with MDTraj on macOS +] +astunparse = "1.6.2" # See https://github.com/mdtraj/mdtraj/issues/1613 +mdtraj = "^1.9.5, !=1.9.6" +rich = "^9.2.0" +cowsay = { version = "^4.0", optional = true } +mdplus = { version = "^0.0.5", optional = true } + +# Extra for building docs +Sphinx = { version = "^3.4.3", optional = true } +sphinx-autoapi = { version = "^1.5.1", optional = true } +sphinx-rtd-theme = { version = "^0.5.1", optional = true } +myst-parser = { version = "^0.13.5", optional = true } + +[tool.poetry.dev-dependencies] +prospector = "^1.3.0" +pytest = "^6.0.1" +pytest-cov = "^2.10.1" +vulture = "^2.1" +rstcheck = "^3.3.1" +flake8 = "^3.8.4" +Sphinx = "^3.4.3" +sphinx-autoapi = "^1.5.1" +sphinx-rtd-theme = "^0.5.1" +myst-parser = "^0.13.5" +tox = "^3.23.0" +black = "^22.1.0" + +[tool.poetry.extras] +backmapping = ["mdplus"] +docs = ["Sphinx", "sphinx-autoapi", "sphinx-rtd-theme", "myst-parser"] + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index e4494d3..0000000 --- a/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -numpy -cython -simpletraj diff --git a/sanitize.py b/sanitize.py index 05846d0..4c75ac2 100755 --- a/sanitize.py +++ b/sanitize.py @@ -1,15 +1,18 @@ #!/usr/bin/env python3 import argparse +EXPECTED_TOKS = { + "bonds": 5, + "angles": 6, + "dihedrals": 8, + "constraints": 4, + "pairs": -1 +} + def main(args): - with open(args.i) as infile, open(args.o, "w") as outfile: + with open(args.input) as infile, open(args.output, "w") as outfile: section = "" - expected_toks = {"bonds": 5, - "angles": 6, - "dihedrals": 8, - "constraints": 4, - "pairs": -1} has_constr = False constr_lines = [] @@ -17,7 +20,7 @@ def main(args): line = line.strip("\n") if line.startswith("["): section = line.strip("[ ]") - if args.fc is not None and section == "constraints": + if args.constraint_threshold is not None and section == "constraints": print(line, file=outfile) has_constr = True for c_line in constr_lines: @@ -34,18 +37,19 @@ def main(args): print(line, file=outfile) continue - elif line.startswith("#") or line.startswith(";") or line == "": + if line.startswith("#") or line.startswith(";") or line == "": print(line, file=outfile) continue - elif len(line.split()) < expected_toks.get(section, 0): + if len(line.split()) < EXPECTED_TOKS.get(section, 0): continue - elif expected_toks.get(section, 0) < 0: + if EXPECTED_TOKS.get(section, 0) < 0: continue # Convert high force constants to constraints - if args.fc is not None and section == "bonds" and float(line.split()[4]) >= args.fc: + if (args.constraint_threshold is not None and section == "bonds" + and float(line.split()[4]) >= args.constraint_threshold): constr_lines.append(line[:line.rindex(line.split()[4]) - 1]) continue @@ -53,11 +57,15 @@ def main(args): if __name__ == "__main__": - parser = argparse.ArgumentParser(description="Sanitize PDB2GMX output topology.") - parser.add_argument('-i', type=str, required=True, help="Input topology file") - parser.add_argument('-o', type=str, required=True, help="Output topology file") - parser.add_argument('-fc', type=float, default=None, help="Convert high force constants to constraints") + parser = argparse.ArgumentParser( + description="Sanitize PDB2GMX output topology.") - args = parser.parse_args() + parser.add_argument('input', type=str, help="Input topology file") + parser.add_argument('output', type=str, help="Output topology file") + parser.add_argument('-c', + '--constraint-threshold', + type=float, + default=None, + help="Convert high force constants to constraints") - main(args) + main(parser.parse_args()) diff --git a/test/data/sugar_out.xtc b/test/data/sugar_out.xtc deleted file mode 100644 index 88b6ed9..0000000 Binary files a/test/data/sugar_out.xtc and /dev/null differ diff --git a/test/data/water-cg.gro b/test/data/water-cg.gro deleted file mode 100644 index db53393..0000000 --- a/test/data/water-cg.gro +++ /dev/null @@ -1,224 +0,0 @@ -Water - 221 - 1SOL W 1 0.716 1.300 1.198 - 2SOL W 2 0.681 0.283 0.408 - 3SOL W 3 1.464 0.059 0.501 - 4SOL W 4 0.161 1.353 -0.019 - 5SOL W 5 0.959 0.155 0.241 - 6SOL W 6 0.501 1.870 0.471 - 7SOL W 7 1.806 0.612 1.024 - 8SOL W 8 0.892 1.694 0.882 - 9SOL W 9 0.419 1.496 0.596 - 10SOL W 10 0.913 -0.009 1.529 - 11SOL W 11 0.566 0.182 1.814 - 12SOL W 12 0.848 1.600 1.166 - 13SOL W 13 1.123 0.457 1.656 - 14SOL W 14 0.545 1.870 1.140 - 15SOL W 15 1.330 0.225 1.235 - 16SOL W 16 1.835 1.272 0.155 - 17SOL W 17 0.105 0.083 0.838 - 18SOL W 18 1.315 0.491 1.215 - 19SOL W 19 1.482 0.667 1.814 - 20SOL W 20 1.421 0.912 1.145 - 21SOL W 21 0.886 1.171 0.917 - 22SOL W 22 1.685 1.764 1.014 - 23SOL W 23 0.320 0.852 0.866 - 24SOL W 24 1.733 0.679 1.604 - 25SOL W 25 1.635 1.804 1.709 - 26SOL W 26 1.565 0.569 0.313 - 27SOL W 27 0.883 1.052 1.827 - 28SOL W 28 1.905 1.261 1.662 - 29SOL W 29 1.280 1.131 1.038 - 30SOL W 30 0.884 0.402 1.537 - 31SOL W 31 0.294 1.043 0.331 - 32SOL W 32 0.328 0.626 0.607 - 33SOL W 33 0.235 0.128 1.614 - 34SOL W 34 1.155 1.147 1.763 - 35SOL W 35 0.866 0.922 0.821 - 36SOL W 36 0.717 1.179 0.154 - 37SOL W 37 0.332 1.715 1.220 - 38SOL W 38 1.676 0.936 1.844 - 39SOL W 39 0.918 0.149 1.301 - 40SOL W 40 0.828 0.706 1.540 - 41SOL W 41 0.151 1.094 1.086 - 42SOL W 42 0.808 0.827 0.076 - 43SOL W 43 0.936 0.428 0.359 - 44SOL W 44 1.066 1.510 1.745 - 45SOL W 45 0.763 1.257 1.642 - 46SOL W 46 0.176 0.662 1.012 - 47SOL W 47 1.772 0.861 0.434 - 48SOL W 48 1.086 0.588 0.699 - 49SOL W 49 1.111 1.777 1.262 - 50SOL W 50 0.740 1.853 0.300 - 51SOL W 51 0.982 1.472 0.250 - 52SOL W 52 0.464 0.611 0.172 - 53SOL W 53 1.013 0.073 0.794 - 54SOL W 54 0.001 1.715 1.521 - 55SOL W 55 1.525 1.611 1.530 - 56SOL W 56 1.398 1.765 1.285 - 57SOL W 57 1.142 1.005 1.454 - 58SOL W 58 1.446 0.597 0.964 - 59SOL W 59 1.709 0.157 0.413 - 60SOL W 60 0.521 1.348 1.756 - 61SOL W 61 1.440 0.370 0.417 - 62SOL W 62 0.535 1.742 0.747 - 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186 1.451 1.555 0.034 - 187SOL W 187 0.178 1.404 1.460 - 188SOL W 188 0.025 0.759 0.123 - 189SOL W 189 0.743 0.310 0.103 - 190SOL W 190 0.414 1.629 1.826 - 191SOL W 191 0.818 0.524 0.600 - 192SOL W 192 0.520 0.833 0.344 - 193SOL W 193 0.509 0.434 1.167 - 194SOL W 194 0.885 0.339 0.814 - 195SOL W 195 0.599 1.631 0.989 - 196SOL W 196 1.500 0.397 0.755 - 197SOL W 197 0.771 1.879 0.000 - 198SOL W 198 0.800 0.607 1.055 - 199SOL W 199 1.577 0.042 1.409 - 200SOL W 200 1.581 1.067 0.686 - 201SOL W 201 0.498 0.502 0.411 - 202SOL W 202 1.694 0.567 0.712 - 203SOL W 203 0.285 0.863 0.097 - 204SOL W 204 1.692 1.029 1.420 - 205SOL W 205 0.946 0.176 1.726 - 206SOL W 206 1.841 0.121 1.583 - 207SOL W 207 1.162 0.478 0.972 - 208SOL W 208 1.258 0.750 1.327 - 209SOL W 209 1.116 0.121 1.099 - 210SOL W 210 1.426 1.085 1.818 - 211SOL W 211 0.828 1.810 0.594 - 212SOL W 212 0.162 1.546 0.519 - 213SOL W 213 0.129 0.139 1.366 - 214SOL W 214 1.307 1.634 0.241 - 215SOL W 215 1.254 0.260 1.536 - 216SOL W 216 0.203 1.841 0.417 - 217SOL W 217 1.807 1.906 1.243 - 218SOL W 218 1.017 0.969 0.269 - 219SOL W 219 0.536 0.096 0.893 - 220SOL W 220 0.806 0.975 1.222 - 221SOL W 221 0.924 1.192 0.366 - 1.89868 1.89868 1.89868 diff --git a/test/data/water.gro b/test/data/water.gro deleted file mode 100644 index 5ac8423..0000000 --- a/test/data/water.gro +++ /dev/null @@ -1,666 +0,0 @@ -Water - 663 - 1SOL OW 1 0.696 1.330 1.211 - 1SOL HW1 2 0.662 1.236 1.203 - 1SOL HW2 3 0.790 1.334 1.179 - 2SOL OW 4 0.700 0.289 0.376 - 2SOL HW1 5 0.714 0.211 0.436 - 2SOL HW2 6 0.629 0.348 0.413 - 3SOL OW 7 1.480 0.088 0.482 - 3SOL HW1 8 1.417 0.022 0.442 - 3SOL HW2 9 1.494 0.066 0.579 - 4SOL OW 10 0.131 1.339 0.001 - 4SOL HW1 11 0.222 1.299 0.000 - 4SOL HW2 12 0.129 1.420 -0.058 - 5SOL OW 13 0.962 0.163 0.279 - 5SOL HW1 14 1.026 0.106 0.228 - 5SOL HW2 15 0.890 0.197 0.217 - 6SOL OW 16 0.467 1.884 0.461 - 6SOL HW1 17 0.481 1.803 0.518 - 6SOL HW2 18 0.555 1.922 0.435 - 7SOL OW 19 1.823 0.625 0.991 - 7SOL HW1 20 1.782 0.683 1.062 - 7SOL HW2 21 1.814 0.529 1.018 - 8SOL OW 22 0.897 1.672 0.851 - 8SOL HW1 23 0.924 1.768 0.859 - 8SOL HW2 24 0.855 1.642 0.936 - 9SOL OW 25 0.394 1.470 0.608 - 9SOL HW1 26 0.405 1.562 0.646 - 9SOL HW2 27 0.459 1.457 0.533 - 10SOL OW 28 0.885 0.012 1.512 - 10SOL HW1 29 0.951 0.045 1.580 - 10SOL HW2 30 0.902 -0.085 1.494 - 11SOL OW 31 0.593 0.207 1.823 - 11SOL HW1 32 0.583 0.161 1.735 - 11SOL HW2 33 0.521 0.177 1.885 - 12SOL OW 34 0.873 1.618 1.189 - 12SOL HW1 35 0.790 1.658 1.150 - 12SOL HW2 36 0.882 1.523 1.159 - 13SOL OW 37 1.148 0.480 1.640 - 13SOL HW1 38 1.052 0.472 1.613 - 13SOL HW2 39 1.168 0.418 1.715 - 14SOL OW 40 0.564 1.866 1.107 - 14SOL HW1 41 0.576 1.942 1.171 - 14SOL HW2 42 0.495 1.803 1.142 - 15SOL OW 43 1.305 0.250 1.219 - 15SOL HW1 44 1.356 0.178 1.170 - 15SOL HW2 45 1.330 0.248 1.316 - 16SOL OW 46 1.817 1.238 0.153 - 16SOL HW1 47 1.799 1.309 0.221 - 16SOL HW2 48 1.889 1.269 0.091 - 17SOL OW 49 0.082 0.102 0.813 - 17SOL HW1 50 0.127 0.143 0.892 - 17SOL HW2 51 0.107 0.005 0.808 - 18SOL OW 52 1.292 0.522 1.217 - 18SOL HW1 53 1.390 0.524 1.196 - 18SOL HW2 54 1.263 0.428 1.232 - 19SOL OW 55 1.495 0.631 1.810 - 19SOL HW1 56 1.486 0.679 1.897 - 19SOL HW2 57 1.466 0.691 1.736 - 20SOL OW 58 1.416 0.951 1.145 - 20SOL HW1 59 1.479 0.900 1.086 - 20SOL HW2 60 1.367 0.886 1.203 - 21SOL OW 61 0.915 1.185 0.938 - 21SOL HW1 62 0.909 1.091 0.905 - 21SOL HW2 63 0.834 1.236 0.908 - 22SOL OW 64 1.654 1.787 1.011 - 22SOL HW1 65 1.720 1.789 1.085 - 22SOL HW2 66 1.680 1.716 0.945 - 23SOL OW 67 0.345 0.871 0.845 - 23SOL HW1 68 0.368 0.800 0.911 - 23SOL HW2 69 0.246 0.884 0.843 - 24SOL OW 70 1.769 0.692 1.599 - 24SOL HW1 71 1.745 0.601 1.632 - 24SOL HW2 72 1.686 0.744 1.580 - 25SOL OW 73 1.649 1.799 1.744 - 25SOL HW1 74 1.599 1.730 1.692 - 25SOL HW2 75 1.657 1.882 1.690 - 26SOL OW 76 1.592 0.543 0.324 - 26SOL HW1 77 1.562 0.621 0.379 - 26SOL HW2 78 1.542 0.543 0.237 - 27SOL OW 79 0.857 1.079 1.819 - 27SOL HW1 80 0.838 0.994 1.867 - 27SOL HW2 81 0.954 1.084 1.796 - 28SOL OW 82 1.889 1.288 1.639 - 28SOL HW1 83 1.900 1.192 1.614 - 28SOL HW2 84 1.925 1.302 1.732 - 29SOL OW 85 1.249 1.136 1.061 - 29SOL HW1 86 1.265 1.182 0.973 - 29SOL HW2 87 1.327 1.076 1.081 - 30SOL OW 88 0.911 0.389 1.562 - 30SOL HW1 89 0.896 0.356 1.468 - 30SOL HW2 90 0.844 0.461 1.582 - 31SOL OW 91 0.305 1.009 0.316 - 31SOL HW1 92 0.216 1.030 0.358 - 31SOL HW2 93 0.362 1.091 0.318 - 32SOL OW 94 0.357 0.611 0.586 - 32SOL HW1 95 0.260 0.605 0.563 - 32SOL HW2 96 0.368 0.661 0.672 - 33SOL OW 97 0.235 0.159 1.592 - 33SOL HW1 98 0.253 0.066 1.560 - 33SOL HW2 99 0.217 0.158 1.690 - 34SOL OW 100 1.120 1.156 1.750 - 34SOL HW1 101 1.141 1.078 1.808 - 34SOL HW2 102 1.203 1.208 1.730 - 35SOL OW 103 0.884 0.948 0.800 - 35SOL HW1 104 0.786 0.946 0.819 - 35SOL HW2 105 0.929 0.871 0.845 - 36SOL OW 106 0.697 1.207 0.172 - 36SOL HW1 107 0.683 1.177 0.077 - 36SOL HW2 108 0.771 1.154 0.213 - 37SOL OW 109 0.366 1.702 1.207 - 37SOL HW1 110 0.277 1.682 1.166 - 37SOL HW2 111 0.354 1.760 1.287 - 38SOL OW 112 1.675 0.923 1.880 - 38SOL HW1 113 1.749 0.906 1.816 - 38SOL HW2 114 1.605 0.980 1.836 - 39SOL OW 115 0.889 0.173 1.293 - 39SOL HW1 116 0.898 0.118 1.376 - 39SOL HW2 117 0.967 0.156 1.233 - 40SOL OW 118 0.826 0.670 1.527 - 40SOL HW1 119 0.755 0.718 1.580 - 40SOL HW2 120 0.904 0.731 1.514 - 41SOL OW 121 0.164 1.077 1.118 - 41SOL HW1 122 0.071 1.067 1.082 - 41SOL HW2 123 0.217 1.138 1.059 - 42SOL OW 124 0.794 0.860 0.062 - 42SOL HW1 125 0.863 0.853 0.134 - 42SOL HW2 126 0.768 0.768 0.032 - 43SOL OW 127 0.935 0.466 0.351 - 43SOL HW1 128 1.010 0.418 0.398 - 43SOL HW2 129 0.863 0.400 0.328 - 44SOL OW 130 1.042 1.515 1.774 - 44SOL HW1 131 1.051 1.431 1.721 - 44SOL HW2 132 1.106 1.584 1.739 - 45SOL OW 133 0.732 1.279 1.647 - 45SOL HW1 134 0.762 1.206 1.708 - 45SOL HW2 135 0.796 1.286 1.570 - 46SOL OW 136 0.202 0.654 0.985 - 46SOL HW1 137 0.218 0.645 1.083 - 46SOL HW2 138 0.109 0.688 0.969 - 47SOL OW 139 1.778 0.898 0.424 - 47SOL HW1 140 1.723 0.868 0.502 - 47SOL HW2 141 1.814 0.818 0.376 - 48SOL OW 142 1.077 0.576 0.664 - 48SOL HW1 143 1.114 0.666 0.685 - 48SOL HW2 144 1.068 0.523 0.748 - 49SOL OW 145 1.148 1.766 1.268 - 49SOL HW1 146 1.119 1.843 1.210 - 49SOL HW2 147 1.067 1.722 1.307 - 50SOL OW 148 0.703 1.844 0.294 - 50SOL HW1 149 0.751 1.830 0.380 - 50SOL HW2 150 0.766 1.884 0.227 - 51SOL OW 151 1.011 1.451 0.236 - 51SOL HW1 152 0.929 1.478 0.185 - 51SOL HW2 153 1.006 1.488 0.329 - 52SOL OW 154 0.494 0.588 0.166 - 52SOL HW1 155 0.486 0.655 0.240 - 52SOL HW2 156 0.411 0.591 0.110 - 53SOL OW 157 1.009 0.049 0.824 - 53SOL HW1 158 0.952 0.129 0.805 - 53SOL HW2 159 1.079 0.040 0.753 - 54SOL OW 160 0.024 1.703 1.550 - 54SOL HW1 161 -0.002 1.798 1.534 - 54SOL HW2 162 -0.019 1.645 1.480 - 55SOL OW 163 1.513 1.624 1.564 - 55SOL HW1 164 1.507 1.674 1.478 - 55SOL HW2 165 1.554 1.534 1.547 - 56SOL OW 166 1.414 1.776 1.318 - 56SOL HW1 167 1.316 1.781 1.295 - 56SOL HW2 168 1.465 1.739 1.241 - 57SOL OW 169 1.124 0.979 1.432 - 57SOL HW1 170 1.222 0.978 1.452 - 57SOL HW2 171 1.081 1.057 1.478 - 58SOL OW 172 1.430 0.630 0.950 - 58SOL HW1 173 1.428 0.541 0.904 - 58SOL HW2 174 1.479 0.621 1.037 - 59SOL OW 175 1.710 0.176 0.380 - 59SOL HW1 176 1.786 0.168 0.443 - 59SOL HW2 177 1.630 0.127 0.417 - 60SOL OW 178 0.508 1.384 1.751 - 60SOL HW1 179 0.459 1.312 1.800 - 60SOL HW2 180 0.595 1.349 1.718 - 61SOL OW 181 1.402 0.376 0.412 - 61SOL HW1 182 1.474 0.439 0.384 - 61SOL HW2 183 1.443 0.295 0.454 - 62SOL OW 184 0.530 1.733 0.710 - 62SOL HW1 185 0.502 1.819 0.754 - 62SOL HW2 186 0.572 1.674 0.778 - 63SOL OW 187 1.169 1.247 0.181 - 63SOL HW1 188 1.124 1.336 0.179 - 63SOL HW2 189 1.119 1.183 0.123 - 64SOL OW 190 0.987 0.755 0.963 - 64SOL HW1 191 1.033 0.667 0.952 - 64SOL HW2 192 1.048 0.818 1.011 - 65SOL OW 193 1.473 0.090 1.065 - 65SOL HW1 194 1.427 0.098 0.976 - 65SOL HW2 195 1.544 0.020 1.059 - 66SOL OW 196 1.340 1.311 1.703 - 66SOL HW1 197 1.394 1.384 1.746 - 66SOL HW2 198 1.355 1.311 1.605 - 67SOL OW 199 0.071 0.349 0.244 - 67SOL HW1 200 0.156 0.331 0.294 - 67SOL HW2 201 0.040 0.265 0.200 - 68SOL OW 202 1.491 0.458 1.481 - 68SOL HW1 203 1.530 0.429 1.393 - 68SOL HW2 204 1.410 0.404 1.501 - 69SOL OW 205 0.326 1.525 0.182 - 69SOL HW1 206 0.383 1.604 0.158 - 69SOL HW2 207 0.353 1.447 0.126 - 70SOL OW 208 1.511 0.008 0.720 - 70SOL HW1 209 1.531 0.083 0.784 - 70SOL HW2 210 1.583 -0.060 0.725 - 71SOL OW 211 1.207 0.721 1.830 - 71SOL HW1 212 1.147 0.665 1.887 - 71SOL HW2 213 1.218 0.677 1.740 - 72SOL OW 214 1.883 0.995 0.795 - 72SOL HW1 215 1.882 1.055 0.875 - 72SOL HW2 216 1.789 0.979 0.765 - 73SOL OW 217 1.261 0.202 0.278 - 73SOL HW1 218 1.234 0.226 0.185 - 73SOL HW2 219 1.309 0.279 0.320 - 74SOL OW 220 0.138 0.431 1.384 - 74SOL HW1 221 0.202 0.439 1.460 - 74SOL HW2 222 0.135 0.337 1.352 - 75SOL OW 223 1.231 0.791 0.752 - 75SOL HW1 224 1.275 0.878 0.732 - 75SOL HW2 225 1.293 0.734 0.806 - 76SOL OW 226 0.071 1.631 0.269 - 76SOL HW1 227 0.033 1.670 0.185 - 76SOL HW2 228 0.147 1.570 0.246 - 77SOL OW 229 0.160 0.236 1.047 - 77SOL HW1 230 0.255 0.252 1.021 - 77SOL HW2 231 0.157 0.185 1.133 - 78SOL OW 232 1.458 1.448 0.464 - 78SOL HW1 233 1.484 1.543 0.444 - 78SOL HW2 234 1.360 1.444 0.481 - 79SOL OW 235 0.449 1.250 0.283 - 79SOL HW1 236 0.546 1.228 0.272 - 79SOL HW2 237 0.439 1.336 0.332 - 80SOL OW 238 0.113 1.558 1.755 - 80SOL HW1 239 0.072 1.613 1.682 - 80SOL HW2 240 0.208 1.587 1.770 - 81SOL OW 241 0.365 0.421 0.927 - 81SOL HW1 242 0.451 0.449 0.882 - 81SOL HW2 243 0.301 0.498 0.925 - 82SOL OW 244 1.439 1.232 0.277 - 82SOL HW1 245 1.462 1.288 0.357 - 82SOL HW2 246 1.339 1.227 0.268 - 83SOL OW 247 1.019 0.524 0.076 - 83SOL HW1 248 0.951 0.563 0.013 - 83SOL HW2 249 0.975 0.501 0.163 - 84SOL OW 250 1.564 0.546 1.174 - 84SOL HW1 251 1.584 0.451 1.150 - 84SOL HW2 252 1.636 0.581 1.234 - 85SOL OW 253 0.617 0.087 1.548 - 85SOL HW1 254 0.706 0.051 1.577 - 85SOL HW2 255 0.630 0.143 1.465 - 86SOL OW 256 1.772 0.396 0.536 - 86SOL HW1 257 1.724 0.388 0.449 - 86SOL HW2 258 1.841 0.324 0.543 - 87SOL OW 259 0.398 0.674 1.746 - 87SOL HW1 260 0.408 0.725 1.661 - 87SOL HW2 261 0.466 0.706 1.812 - 88SOL OW 262 1.396 1.007 1.508 - 88SOL HW1 263 1.406 1.008 1.608 - 88SOL HW2 264 1.486 1.008 1.465 - 89SOL OW 265 0.366 0.124 0.077 - 89SOL HW1 266 0.331 0.183 0.150 - 89SOL HW2 267 0.292 0.101 0.014 - 90SOL OW 268 0.514 0.554 1.390 - 90SOL HW1 269 0.511 0.500 1.474 - 90SOL HW2 270 0.564 0.639 1.408 - 91SOL OW 271 1.575 0.885 0.927 - 91SOL HW1 272 1.578 0.942 0.844 - 91SOL HW2 273 1.543 0.793 0.902 - 92SOL OW 274 1.838 1.463 0.703 - 92SOL HW1 275 1.786 1.384 0.671 - 92SOL HW2 276 1.910 1.484 0.637 - 93SOL OW 277 1.517 1.000 0.374 - 93SOL HW1 278 1.616 0.994 0.387 - 93SOL HW2 279 1.492 1.096 0.357 - 94SOL OW 280 0.967 0.989 0.542 - 94SOL HW1 281 1.012 0.905 0.514 - 94SOL HW2 282 0.930 0.979 0.634 - 95SOL OW 283 1.422 1.287 1.433 - 95SOL HW1 284 1.498 1.336 1.477 - 95SOL HW2 285 1.452 1.196 1.405 - 96SOL OW 286 1.496 0.709 0.495 - 96SOL HW1 287 1.453 0.796 0.521 - 96SOL HW2 288 1.557 0.679 0.568 - 97SOL OW 289 1.538 0.161 1.635 - 97SOL HW1 290 1.551 0.256 1.665 - 97SOL HW2 291 1.442 0.137 1.641 - 98SOL OW 292 0.554 0.834 1.604 - 98SOL HW1 293 0.587 0.873 1.518 - 98SOL HW2 294 0.522 0.908 1.664 - 99SOL OW 295 1.661 1.673 0.286 - 99SOL HW1 296 1.635 1.738 0.215 - 99SOL HW2 297 1.714 1.720 0.356 - 100SOL OW 298 0.383 1.225 0.692 - 100SOL HW1 299 0.293 1.187 0.668 - 100SOL HW2 300 0.387 1.321 0.665 - 101SOL OW 301 0.328 0.250 0.345 - 101SOL HW1 302 0.384 0.331 0.364 - 101SOL HW2 303 0.367 0.171 0.393 - 102SOL OW 304 0.879 0.142 0.534 - 102SOL HW1 305 0.915 0.160 0.443 - 102SOL HW2 306 0.919 0.207 0.599 - 103SOL OW 307 0.625 0.174 1.286 - 103SOL HW1 308 0.725 0.178 1.292 - 103SOL HW2 309 0.591 0.257 1.242 - 104SOL OW 310 0.512 1.770 0.105 - 104SOL HW1 311 0.582 1.764 0.176 - 104SOL HW2 312 0.456 1.851 0.119 - 105SOL OW 313 0.128 1.738 0.835 - 105SOL HW1 314 0.157 1.667 0.771 - 105SOL HW2 315 0.141 1.706 0.929 - 106SOL OW 316 1.504 0.771 0.146 - 106SOL HW1 317 1.539 0.855 0.105 - 106SOL HW2 318 1.469 0.791 0.237 - 107SOL OW 319 1.879 0.052 0.174 - 107SOL HW1 320 1.836 -0.032 0.141 - 107SOL HW2 321 1.815 0.102 0.233 - 108SOL OW 322 1.355 1.642 1.073 - 108SOL HW1 323 1.285 1.642 1.144 - 108SOL HW2 324 1.312 1.626 0.984 - 109SOL OW 325 0.088 1.666 1.105 - 109SOL HW1 326 0.020 1.708 1.164 - 109SOL HW2 327 0.047 1.588 1.057 - 110SOL OW 328 1.787 1.410 0.349 - 110SOL HW1 329 1.729 1.483 0.314 - 110SOL HW2 330 1.866 1.450 0.396 - 111SOL OW 331 0.103 1.034 1.547 - 111SOL HW1 332 0.120 1.003 1.453 - 111SOL HW2 333 0.060 0.961 1.600 - 112SOL OW 334 1.681 1.498 1.111 - 112SOL HW1 335 1.587 1.522 1.086 - 112SOL HW2 336 1.728 1.463 1.031 - 113SOL OW 337 1.809 0.303 1.792 - 113SOL HW1 338 1.796 0.402 1.803 - 113SOL HW2 339 1.759 0.255 1.863 - 114SOL OW 340 1.174 0.126 0.619 - 114SOL HW1 341 1.168 0.213 0.570 - 114SOL HW2 342 1.173 0.051 0.553 - 115SOL OW 343 1.219 1.853 0.415 - 115SOL HW1 344 1.221 1.940 0.365 - 115SOL HW2 345 1.222 1.777 0.351 - 116SOL OW 346 0.060 1.438 0.935 - 116SOL HW1 347 0.139 1.377 0.937 - 116SOL HW2 348 0.024 1.443 0.842 - 117SOL OW 349 0.654 1.243 0.793 - 117SOL HW1 350 0.568 1.242 0.741 - 117SOL HW2 351 0.668 1.154 0.836 - 118SOL OW 352 0.302 0.428 1.591 - 118SOL HW1 353 0.305 0.329 1.607 - 118SOL HW2 354 0.258 0.473 1.668 - 119SOL OW 355 1.833 0.578 0.237 - 119SOL HW1 356 1.744 0.552 0.273 - 119SOL HW2 357 1.892 0.497 0.231 - 120SOL OW 358 1.053 0.933 1.175 - 120SOL HW1 359 1.099 1.011 1.133 - 120SOL HW2 360 1.077 0.928 1.271 - 121SOL OW 361 1.842 1.185 1.010 - 121SOL HW1 362 1.747 1.199 1.039 - 121SOL HW2 363 1.884 1.273 0.990 - 122SOL OW 364 0.009 1.125 0.375 - 122SOL HW1 365 -0.039 1.039 0.393 - 122SOL HW2 366 -0.031 1.170 0.295 - 123SOL OW 367 0.033 0.152 0.544 - 123SOL HW1 368 0.077 0.070 0.508 - 123SOL HW2 369 0.051 0.158 0.643 - 124SOL OW 370 1.208 1.437 0.472 - 124SOL HW1 371 1.166 1.347 0.475 - 124SOL HW2 372 1.141 1.506 0.501 - 125SOL OW 373 0.045 0.850 1.728 - 125SOL HW1 374 -0.022 0.785 1.692 - 125SOL HW2 375 0.094 0.808 1.804 - 126SOL OW 376 1.809 0.580 1.342 - 126SOL HW1 377 1.801 0.635 1.425 - 126SOL HW2 378 1.899 0.535 1.341 - 127SOL OW 379 0.723 0.600 0.019 - 127SOL HW1 380 0.640 0.588 0.073 - 127SOL HW2 381 0.718 0.545 -0.064 - 128SOL OW 382 1.886 1.213 1.303 - 128SOL HW1 383 1.937 1.171 1.228 - 128SOL HW2 384 1.950 1.258 1.366 - 129SOL OW 385 1.794 0.354 1.067 - 129SOL HW1 386 1.744 0.306 1.139 - 129SOL HW2 387 1.891 0.328 1.071 - 130SOL OW 388 0.373 1.214 0.026 - 130SOL HW1 389 0.389 1.125 -0.016 - 130SOL HW2 390 0.391 1.208 0.124 - 131SOL OW 391 1.739 0.253 0.818 - 131SOL HW1 392 1.760 0.289 0.909 - 131SOL HW2 393 1.821 0.211 0.779 - 132SOL OW 394 0.295 1.267 0.973 - 132SOL HW1 395 0.347 1.332 1.027 - 132SOL HW2 396 0.350 1.235 0.896 - 133SOL OW 397 1.197 1.151 0.433 - 133SOL HW1 398 1.163 1.173 0.342 - 133SOL HW2 399 1.128 1.098 0.482 - 134SOL OW 400 1.280 1.694 1.706 - 134SOL HW1 401 1.313 1.674 1.798 - 134SOL HW2 402 1.349 1.668 1.639 - 135SOL OW 403 0.940 1.566 0.474 - 135SOL HW1 404 0.899 1.507 0.544 - 135SOL HW2 405 0.920 1.661 0.495 - 136SOL OW 406 1.494 0.719 1.534 - 136SOL HW1 407 1.483 0.623 1.507 - 136SOL HW2 408 1.457 0.778 1.462 - 137SOL OW 409 1.665 1.292 0.576 - 137SOL HW1 410 1.585 1.351 0.562 - 137SOL HW2 411 1.723 1.295 0.495 - 138SOL OW 412 0.282 0.618 1.248 - 138SOL HW1 413 0.211 0.571 1.299 - 138SOL HW2 414 0.364 0.627 1.306 - 139SOL OW 415 0.123 0.138 1.846 - 139SOL HW1 416 0.081 0.100 1.928 - 139SOL HW2 417 0.060 0.203 1.803 - 140SOL OW 418 0.625 0.462 1.693 - 140SOL HW1 419 0.628 0.368 1.726 - 140SOL HW2 420 0.534 0.500 1.710 - 141SOL OW 421 1.160 1.540 0.826 - 141SOL HW1 422 1.072 1.584 0.840 - 141SOL HW2 423 1.216 1.597 0.766 - 142SOL OW 424 1.302 0.181 0.869 - 142SOL HW1 425 1.247 0.144 0.793 - 142SOL HW2 426 1.355 0.259 0.837 - 143SOL OW 427 0.573 1.463 0.429 - 143SOL HW1 428 0.596 1.475 0.333 - 143SOL HW2 429 0.653 1.481 0.485 - 144SOL OW 430 1.766 0.551 1.871 - 144SOL HW1 431 1.672 0.582 1.855 - 144SOL HW2 432 1.786 0.556 1.969 - 145SOL OW 433 0.593 0.573 0.850 - 145SOL HW1 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0.791 - 203SOL OW 607 0.300 0.868 0.062 - 203SOL HW1 608 0.340 0.903 0.147 - 203SOL HW2 609 0.216 0.818 0.083 - 204SOL OW 610 1.661 1.029 1.443 - 204SOL HW1 611 1.734 1.097 1.446 - 204SOL HW2 612 1.680 0.962 1.370 - 205SOL OW 613 0.980 0.158 1.719 - 205SOL HW1 614 0.947 0.239 1.670 - 205SOL HW2 615 0.912 0.131 1.788 - 206SOL OW 616 1.838 0.093 1.557 - 206SOL HW1 617 1.789 0.180 1.555 - 206SOL HW2 618 1.897 0.090 1.638 - 207SOL OW 619 1.139 0.505 0.956 - 207SOL HW1 620 1.126 0.406 0.949 - 207SOL HW2 621 1.221 0.523 1.011 - 208SOL OW 622 1.291 0.771 1.329 - 208SOL HW1 623 1.280 0.682 1.283 - 208SOL HW2 624 1.204 0.798 1.370 - 209SOL OW 625 1.091 0.103 1.122 - 209SOL HW1 626 1.168 0.160 1.152 - 209SOL HW2 627 1.088 0.101 1.022 - 210SOL OW 628 1.442 1.065 1.789 - 210SOL HW1 629 1.382 1.026 1.859 - 210SOL HW2 630 1.453 1.163 1.806 - 211SOL OW 631 0.829 1.788 0.562 - 211SOL HW1 632 0.861 1.883 0.569 - 211SOL HW2 633 0.794 1.758 0.650 - 212SOL OW 634 0.134 1.538 0.544 - 212SOL HW1 635 0.231 1.519 0.559 - 212SOL HW2 636 0.122 1.582 0.455 - 213SOL OW 637 0.124 0.148 1.329 - 213SOL HW1 638 0.212 0.137 1.376 - 213SOL HW2 639 0.050 0.132 1.394 - 214SOL OW 640 1.289 1.665 0.254 - 214SOL HW1 641 1.328 1.655 0.162 - 214SOL HW2 642 1.303 1.581 0.306 - 215SOL OW 643 1.284 0.269 1.513 - 215SOL HW1 644 1.227 0.335 1.562 - 215SOL HW2 645 1.252 0.176 1.532 - 216SOL OW 646 0.178 1.847 0.446 - 216SOL HW1 647 0.156 1.809 0.356 - 216SOL HW2 648 0.276 1.868 0.450 - 217SOL OW 649 1.806 1.872 1.224 - 217SOL HW1 650 1.755 1.892 1.308 - 217SOL HW2 651 1.859 1.953 1.198 - 218SOL OW 652 1.039 0.970 0.237 - 218SOL HW1 653 1.040 0.898 0.307 - 218SOL HW2 654 0.972 1.040 0.263 - 219SOL OW 655 0.560 0.086 0.864 - 219SOL HW1 656 0.559 0.043 0.954 - 219SOL HW2 657 0.490 0.158 0.860 - 220SOL OW 658 0.791 1.006 1.206 - 220SOL HW1 659 0.884 0.973 1.190 - 220SOL HW2 660 0.744 0.945 1.269 - 221SOL OW 661 0.904 1.172 0.340 - 221SOL HW1 662 0.921 1.144 0.435 - 221SOL HW2 663 0.948 1.260 0.324 - 1.89868 1.89868 1.89868 diff --git a/test/test_bondset.py b/test/test_bondset.py deleted file mode 100644 index 66eb451..0000000 --- a/test/test_bondset.py +++ /dev/null @@ -1,201 +0,0 @@ -import unittest - -import logging -import math - -from pycgtool.bondset import BondSet -from pycgtool.frame import Frame -from pycgtool.mapping import Mapping -from pycgtool.util import cmp_whitespace_float - -try: - import mdtraj - mdtraj_present = True -except ImportError: - mdtraj_present = False - - -class DummyOptions: - constr_threshold = 100000 - map_center = "geom" - angle_default_fc = False - generate_angles = True - generate_dihedrals = False - - -class BondSetTest(unittest.TestCase): - # Columns are: eqm value, standard fc, MARTINI defaults fc - invert_test_ref_data = [ - ( 0.220474419132, 72658.18163, 1250), - ( 0.221844516963, 64300.01188, 1250), - ( 0.216313356504, 67934.93368, 1250), - ( 0.253166204438, 19545.27388, 1250), - ( 0.205958461836, 55359.06367, 1250), - ( 0.180550961226, 139643.66601, 1250), - ( 1.359314249473, 503.24211, 25), - ( 2.026002746003, 837.76904, 25), - ( 1.937848056214, 732.87969, 25), - ( 1.453592079716, 945.32633, 25), - ( 2.504189933347, 771.63691, 25), - ( 1.733002945619, 799.82825, 25), - (-1.446051810383, 253.75691, 50), - ( 1.067436470329, 125.04591, 50), - (-0.373528903861, 135.50927, 50), - ( 0.927837103158, 51.13975, 50), - (-1.685096988856, 59.38162, 50), - ( 1.315458354592, 279.80889, 50) - ] - - def test_bondset_create(self): - measure = BondSet("test/data/sugar.bnd", DummyOptions) - self.assertEqual(1, len(measure)) - self.assertTrue("ALLA" in measure) - self.assertEqual(18, len(measure["ALLA"])) - - def test_bondset_apply(self): - measure = BondSet("test/data/sugar.bnd", DummyOptions) - frame = Frame("test/data/sugar-cg.gro") - measure.apply(frame) - # First six are bond lengths - self.assertEqual(1, len(measure["ALLA"][0].values)) - self.assertAlmostEqual(0.2225376, measure["ALLA"][0].values[0], - delta=0.2225376 / 500) - # Second six are angles - self.assertEqual(1, len(measure["ALLA"][6].values)) - expected = math.radians(77.22779289) - self.assertAlmostEqual(expected, measure["ALLA"][6].values[0], - delta=expected / 500) - # Final six are dihedrals - self.assertEqual(1, len(measure["ALLA"][12].values)) - expected = math.radians(-89.5552903) - self.assertAlmostEqual(expected, measure["ALLA"][12].values[0], - delta=abs(expected) / 500) - - def test_bondset_remove_triangles(self): - bondset = BondSet("test/data/triangle.bnd", DummyOptions) - angles = bondset.get_bond_angles("TRI", exclude_triangle=False) - self.assertEqual(3, len(angles)) - angles = bondset.get_bond_angles("TRI", exclude_triangle=True) - self.assertEqual(0, len(angles)) - - def support_check_mean_fc(self, mol_bonds, fc_column_number): - # Require accuracy to 0.5% - # Allows for slight modifications to code - accuracy = 0.005 - - for i, bond in enumerate(mol_bonds): - ref = self.invert_test_ref_data - self.assertAlmostEqual(ref[i][0], bond.eqm, - delta=abs(ref[i][0] * accuracy)) - self.assertAlmostEqual(ref[i][fc_column_number], bond.fconst, - delta=abs(ref[i][fc_column_number] * accuracy)) - - def test_bondset_boltzmann_invert(self): - measure = BondSet("test/data/sugar.bnd", DummyOptions) - frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") - mapping = Mapping("test/data/sugar.map", DummyOptions) - - cgframe = mapping.apply(frame) - while frame.next_frame(): - cgframe = mapping.apply(frame, cgframe=cgframe) - measure.apply(cgframe) - - measure.boltzmann_invert() - self.support_check_mean_fc(measure["ALLA"], 1) - - def test_bondset_boltzmann_invert_default_fc(self): - class DefaultOptions(DummyOptions): - default_fc = True - - measure = BondSet("test/data/sugar.bnd", DefaultOptions) - frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") - mapping = Mapping("test/data/sugar.map", DefaultOptions) - - cgframe = mapping.apply(frame) - while frame.next_frame(): - cgframe = mapping.apply(frame, cgframe=cgframe) - measure.apply(cgframe) - - measure.boltzmann_invert() - self.support_check_mean_fc(measure["ALLA"], 2) - - def test_bondset_boltzmann_invert_manual_default_fc(self): - class FuncFormOptions(DummyOptions): - length_form = "MartiniDefaultLength" - angle_form = "MartiniDefaultAngle" - dihedral_form = "MartiniDefaultDihedral" - - measure = BondSet("test/data/sugar.bnd", FuncFormOptions) - frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") - mapping = Mapping("test/data/sugar.map", DummyOptions) - - cgframe = mapping.apply(frame) - while frame.next_frame(): - cgframe = mapping.apply(frame, cgframe=cgframe) - measure.apply(cgframe) - - measure.boltzmann_invert() - self.support_check_mean_fc(measure["ALLA"], 2) - - @unittest.skipIf(not mdtraj_present, "MDTRAJ or Scipy not present") - def test_bondset_boltzmann_invert_mdtraj(self): - logging.disable(logging.WARNING) - frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc", - xtc_reader="mdtraj") - logging.disable(logging.NOTSET) - - measure = BondSet("test/data/sugar.bnd", DummyOptions) - mapping = Mapping("test/data/sugar.map", DummyOptions) - - cgframe = mapping.apply(frame) - while frame.next_frame(): - cgframe = mapping.apply(frame, cgframe=cgframe) - measure.apply(cgframe) - - measure.boltzmann_invert() - self.support_check_mean_fc(measure["ALLA"], 1) - - def test_bondset_polymer(self): - bondset = BondSet("test/data/polyethene.bnd", DummyOptions) - frame = Frame("test/data/polyethene.gro") - bondset.apply(frame) - self.assertEqual(5, len(bondset["ETH"][0].values)) - self.assertEqual(4, len(bondset["ETH"][1].values)) - self.assertEqual(4, len(bondset["ETH"][2].values)) - self.assertEqual(4, len(bondset["ETH"][3].values)) - bondset.boltzmann_invert() - self.assertAlmostEqual(0.107, bondset["ETH"][0].eqm, - delta=0.107 / 500) - self.assertAlmostEqual(0.107, bondset["ETH"][1].eqm, - delta=0.107 / 500) - - def test_bondset_pbc(self): - bondset = BondSet("test/data/polyethene.bnd", DummyOptions) - frame = Frame("test/data/pbcpolyethene.gro") - bondset.apply(frame) - bondset.boltzmann_invert() - for bond in bondset.get_bond_lengths("ETH", True): - self.assertAlmostEqual(1., bond.eqm) - self.assertEqual(float("inf"), bond.fconst) - - def test_full_itp_sugar(self): - measure = BondSet("test/data/sugar.bnd", DummyOptions) - frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc") - mapping = Mapping("test/data/sugar.map", DummyOptions) - cgframe = mapping.apply(frame) - - while frame.next_frame(): - cgframe = mapping.apply(frame, cgframe=cgframe) - measure.apply(cgframe) - - measure.boltzmann_invert() - - logging.disable(logging.WARNING) - measure.write_itp("sugar_out.itp", mapping) - logging.disable(logging.NOTSET) - - self.assertTrue(cmp_whitespace_float("sugar_out.itp", "test/data/sugar_out.itp", float_rel_error=0.001)) - - def test_duplicate_atoms_in_bond(self): - with self.assertRaises(ValueError): - bondset = BondSet("test/data/duplicate_atoms.bnd", DummyOptions) diff --git a/test/test_forcefield.py b/test/test_forcefield.py deleted file mode 100644 index bb4933c..0000000 --- a/test/test_forcefield.py +++ /dev/null @@ -1,17 +0,0 @@ -import unittest -import os - -from pycgtool.forcefield import ForceField - - -class ForceFieldTest(unittest.TestCase): - def test_create(self): - name = "test" - dirname = "fftest.ff" - ForceField(name) - self.assertTrue(os.path.exists(dirname)) - self.assertTrue(os.path.isdir(dirname)) - ForceField(name) - -if __name__ == '__main__': - unittest.main() diff --git a/test/test_frame.py b/test/test_frame.py deleted file mode 100644 index 725d6bd..0000000 --- a/test/test_frame.py +++ /dev/null @@ -1,222 +0,0 @@ -import unittest -import filecmp -import os -import logging - -import numpy as np - -from pycgtool.frame import Atom, Residue, Frame -from pycgtool.framereader import FrameReaderSimpleTraj, FrameReaderMDAnalysis, FrameReaderMDTraj -from pycgtool.framereader import FrameReader, get_frame_reader, UnsupportedFormatException - -try: - import mdtraj - mdtraj_present = True -except ImportError: - mdtraj_present = False - -try: - import MDAnalysis - mdanalysis_present = True -except ImportError: - mdanalysis_present = False - - -class AtomTest(unittest.TestCase): - def test_atom_create(self): - atom = Atom(name="Name", num=0, type="Type") - self.assertEqual("Name", atom.name) - self.assertEqual(0, atom.num) - self.assertEqual("Type", atom.type) - - def test_atom_add_missing_data(self): - atom1 = Atom("Name1", 0, type="Type") - atom2 = Atom("Name2", 0, mass=1) - - with self.assertRaises(AssertionError): - atom1.add_missing_data(atom2) - - atom2 = Atom("Name1", 0, mass=1) - atom1.add_missing_data(atom2) - self.assertEqual(1, atom1.mass) - - -class ResidueTest(unittest.TestCase): - def test_residue_create(self): - residue = Residue(name="Resname") - self.assertEqual("Resname", residue.name) - - def test_residue_add_atoms(self): - atom = Atom(name="Name", num=0, type="Type") - residue = Residue() - residue.add_atom(atom) - self.assertEqual(atom, residue.atoms[0]) - self.assertTrue(atom is residue.atoms[0]) - - -class FrameTest(unittest.TestCase): - def helper_read_xtc(self, frame, first_only=False, skip_names=False): - self.assertEqual(663, frame.natoms) - self.assertEqual(221, len(frame.residues)) - self.assertEqual(3, len(frame.residues[0].atoms)) - if not skip_names: # MDTraj renames water - self.assertEqual("SOL", frame.residues[0].name) - self.assertEqual("OW", frame.residues[0].atoms[0].name) - - atom0_coords = np.array([ - [0.696, 1.330, 1.211], - [1.176, 1.152, 1.586], - [1.122, 1.130, 1.534] - ]) - - box_vectors = np.array([ - [1.89868, 1.89868, 1.89868], - [1.9052, 1.9052, 1.9052], - [1.90325272, 1.90325272, 1.90325272] - ]) - - for i in range(1 if first_only else len(atom0_coords)): - np.testing.assert_allclose(atom0_coords[i], frame.residues[0].atoms[0].coords) - np.testing.assert_allclose(box_vectors[i], frame.box, rtol=1e-4) # PDB files are f9.3 - frame.next_frame() - - def test_frame_create(self): - Frame() - - def test_frame_add_residue(self): - residue = Residue() - frame = Frame() - frame.add_residue(residue) - self.assertEqual(residue, frame.residues[0]) - self.assertTrue(residue is frame.residues[0]) - - def test_frame_simpletraj_read_gro(self): - frame = Frame("test/data/water.gro", xtc_reader="simpletraj") - - self.helper_read_xtc(frame, first_only=True) - - @unittest.skipIf(not mdtraj_present, "MDTraj or Scipy not present") - def test_frame_mdtraj_read_gro(self): - logging.disable(logging.WARNING) - frame = Frame("test/data/water.gro", xtc_reader="mdtraj") - logging.disable(logging.NOTSET) - - self.helper_read_xtc(frame, first_only=True, skip_names=True) - - @unittest.skipIf(not mdanalysis_present, "MDAnalysis not present") - def test_frame_mdanalysis_read_gro(self): - reader = FrameReaderMDAnalysis("test/data/water.gro") - frame = Frame.instance_from_reader(reader) - - self.helper_read_xtc(frame, first_only=True) - - @unittest.skipIf(not mdtraj_present, "MDTraj or Scipy not present") - def test_frame_mdtraj_read_pdb(self): - reader = FrameReaderMDTraj("test/data/water.pdb") - frame = Frame.instance_from_reader(reader) - - self.helper_read_xtc(frame, first_only=True, skip_names=True) - - @unittest.skipIf(not mdtraj_present and not mdanalysis_present, "Neither MDTraj or MDAnalysis is present") - def test_frame_any_read_pdb(self): - reader = get_frame_reader("test/data/water.pdb") - frame = Frame.instance_from_reader(reader) - - self.helper_read_xtc(frame, first_only=True, skip_names=True) - - def test_frame_any_read_unsupported(self): - with self.assertRaises(UnsupportedFormatException): - reader = get_frame_reader("test/data/dppc.map") - - @unittest.skipIf(not mdanalysis_present, "MDAnalysis not present") - def test_frame_mdanalysis_read_pdb(self): - reader = FrameReaderMDAnalysis("test/data/water.pdb") - frame = Frame.instance_from_reader(reader) - - self.helper_read_xtc(frame, first_only=True) - - def test_frame_output_gro(self): - frame = Frame("test/data/water.gro") - frame.output("water-out.gro", format="gro") - self.assertTrue(filecmp.cmp("test/data/water.gro", "water-out.gro")) - os.remove("water-out.gro") - - def test_frame_read_xtc_simpletraj_numframes(self): - frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc", - xtc_reader="simpletraj") - self.assertEqual(11, frame.numframes) - - @unittest.skipIf(not mdtraj_present, "MDTraj or Scipy not present") - def test_frame_read_xtc_mdtraj_numframes(self): - logging.disable(logging.WARNING) - frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc", - xtc_reader="mdtraj") - logging.disable(logging.NOTSET) - self.assertEqual(11, frame.numframes) - - def test_frame_simpletraj_read_xtc(self): - frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc", - xtc_reader="simpletraj") - self.helper_read_xtc(frame) - - @unittest.skipIf(not mdtraj_present, "MDTraj or Scipy not present") - def test_frame_mdtraj_read_xtc(self): - logging.disable(logging.WARNING) - frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc", - xtc_reader="mdtraj") - logging.disable(logging.NOTSET) - - self.helper_read_xtc(frame, skip_names=True) - - @unittest.skipIf(not mdanalysis_present, "MDAnalysis not present") - def test_frame_mdanalysis_read_xtc(self): - reader = FrameReaderMDAnalysis("test/data/water.gro", "test/data/water.xtc") - frame = Frame.instance_from_reader(reader) - - self.helper_read_xtc(frame) - - @unittest.skipIf(not mdtraj_present, "MDTraj or Scipy not present") - def test_frame_write_xtc_mdtraj(self): - try: - os.remove("water_test2.xtc") - except IOError: - pass - - logging.disable(logging.WARNING) - frame = Frame(gro="test/data/water.gro", xtc="test/data/water.xtc", - xtc_reader="mdtraj") - logging.disable(logging.NOTSET) - - while frame.next_frame(): - frame.write_xtc("water_test2.xtc") - - def test_frame_instance_from_reader(self): - reader = FrameReaderSimpleTraj("test/data/water.gro") - frame = Frame.instance_from_reader(reader) - - self.helper_read_xtc(frame, first_only=True) - - def test_frame_instance_from_reader_dummy(self): - class DummyReader(FrameReader): - def _initialise_frame(self, frame): - frame.dummy_reader = True - - def _read_frame_number(self, number): - return number * 10, [], None - - reader = DummyReader(None) - frame = Frame.instance_from_reader(reader) - self.assertTrue(frame.dummy_reader) - - frame.next_frame() - self.assertEqual(frame.number, 0) - self.assertEqual(frame.time, 0) - np.testing.assert_array_equal(np.zeros(3), frame.box) # Reader replaces None with (0, 0, 0) - - frame.next_frame() - self.assertEqual(frame.number, 1) - self.assertEqual(frame.time, 10) - - -if __name__ == '__main__': - unittest.main() diff --git a/test/test_functionalforms.py b/test/test_functionalforms.py deleted file mode 100644 index b68da28..0000000 --- a/test/test_functionalforms.py +++ /dev/null @@ -1,32 +0,0 @@ -import unittest - -from pycgtool.functionalforms import FunctionalForms, FunctionalForm - - -class FunctionalFormTest(unittest.TestCase): - def test_functional_form(self): - funcs = FunctionalForms() - harmonic_form = funcs.Harmonic - self.assertIsNotNone(harmonic_form) - cos_harmonic_form = funcs.CosHarmonic - self.assertIsNotNone(cos_harmonic_form) - - def test_functional_form_new(self): - class TestFunc(FunctionalForm): - gromacs_type_ids = (None, None, None) - - @staticmethod - def eqm(values, temp): - return "TestResultEqm" - - @staticmethod - def fconst(values, temp): - return "TestResultFconst" - - funcs = FunctionalForms() - self.assertIn("TestFunc", funcs) - self.assertEqual("TestResultEqm", funcs.TestFunc.eqm(None, None)) - self.assertEqual("TestResultFconst", funcs.TestFunc.fconst(None, None)) - -if __name__ == '__main__': - unittest.main() diff --git a/test/test_interface.py b/test/test_interface.py deleted file mode 100644 index 4483de9..0000000 --- a/test/test_interface.py +++ /dev/null @@ -1,46 +0,0 @@ -import unittest - -from pycgtool.interface import Options, Progress - - -class UtilTest(unittest.TestCase): - def test_progress_iterations(self): - sum = 0 - for i in Progress(10, quiet=True): - sum += i - self.assertEqual(45, sum) - - def test_progress_postwhile(self): - sum = 0 - for i in Progress(20, dowhile=lambda: sum < 20, quiet=True): - sum += i - self.assertEqual(21, sum) - - def test_options_init(self): - opt = Options([("a", True), ("b", 10), ("c", "hello")]) - self.assertEqual(True, opt.a) - self.assertEqual(10, opt.b) - self.assertEqual("hello", opt.c) - - def test_options_set(self): - opt = Options([("a", True), ("b", 10), ("c", "hello")]) - opt.set("a", False) - opt.set("b", 11) - self.assertEqual(False, opt.a) - self.assertEqual(11, opt.b) - self.assertEqual("hello", opt.c) - opt.set("a", "yEs") - opt.set("b", "12") - self.assertEqual(True, opt.a) - self.assertEqual(12, opt.b) - opt.set("a", "f") - self.assertEqual(False, opt.a) - with self.assertRaises(ValueError): - opt.set("a", "hello") - with self.assertRaises(ValueError): - opt.set("b", "hello") - - def test_options_toggle(self): - opt = Options([("a", True), ("b", 10), ("c", "hello")]) - opt.toggle_boolean("a") - self.assertEqual(False, opt.a) diff --git a/test/test_mapping.py b/test/test_mapping.py deleted file mode 100644 index c0b7e56..0000000 --- a/test/test_mapping.py +++ /dev/null @@ -1,83 +0,0 @@ -import unittest -import filecmp -import os - -import numpy as np - -from pycgtool.mapping import Mapping -from pycgtool.frame import Frame - - -class DummyOptions: - map_center = "geom" - - -class MappingTest(unittest.TestCase): - def test_mapping_create(self): - mapping = Mapping("test/data/water.map", DummyOptions) - self.assertEqual(1, len(mapping)) - self.assertTrue("SOL" in mapping) - self.assertEqual(1, len(mapping["SOL"])) - self.assertEqual(3, len(mapping["SOL"][0].atoms)) - self.assertEqual("OW", mapping["SOL"][0].atoms[0]) - - def test_mapping_apply(self): - mapping = Mapping("test/data/water.map", DummyOptions) - frame = Frame("test/data/water.gro") - cgframe = mapping.apply(frame) - self.assertEqual(len(frame), len(cgframe)) - cgframe.output("water-cg.gro", format="gro") - self.assertTrue(filecmp.cmp("test/data/water-cg.gro", "water-cg.gro")) - os.remove("water-cg.gro") - - def test_mapping_charges(self): - mapping = Mapping("test/data/dppc.map", DummyOptions) - self.assertEqual( 1, mapping["DPPC"][0].charge) - self.assertEqual(-1, mapping["DPPC"][1].charge) - frame = Frame("test/data/dppc.gro") - cgframe = mapping.apply(frame) - self.assertEqual( 1, cgframe[0][0].charge) - self.assertEqual(-1, cgframe[0][1].charge) - - def test_mapping_pbc(self): - mapping = Mapping("test/data/water.map", DummyOptions) - frame = Frame("test/data/pbcwater.gro") - cgframe = mapping.apply(frame) - np.testing.assert_allclose(frame[0][0].coords, cgframe[0][0].coords) - - def test_mapping_weights_geom(self): - frame = Frame("test/data/two.gro") - mapping = Mapping("test/data/two.map", DummyOptions) - cg = mapping.apply(frame) - np.testing.assert_allclose(np.array([1.5, 1.5, 1.5]), cg[0][0].coords) - - def test_mapping_weights_mass(self): - frame = Frame("test/data/two.gro") - options = DummyOptions() - options.map_center = "mass" - - mapping = Mapping("test/data/two.map", options, itp="test/data/two.itp") - cg = mapping.apply(frame) - np.testing.assert_allclose(np.array([2., 2., 2.]), cg[0][0].coords) - - def test_mapping_weights_guess_mass(self): - frame = Frame("test/data/two.gro") - options = DummyOptions() - options.map_center = "mass" - - mapping = Mapping("test/data/two.map", options) - cg = mapping.apply(frame) - np.testing.assert_allclose(np.array([1.922575, 1.922575, 1.922575], dtype=np.float32), - cg[0][0].coords, rtol=0.01) - - def test_mapping_weights_first(self): - frame = Frame("test/data/two.gro") - options = DummyOptions() - options.map_center = "first" - - mapping = Mapping("test/data/two.map", options, itp="test/data/two.itp") - cg = mapping.apply(frame) - np.testing.assert_allclose(np.array([1., 1., 1.]), cg[0][0].coords) - - - diff --git a/test/test_pycgtool.py b/test/test_pycgtool.py deleted file mode 100644 index ab03b97..0000000 --- a/test/test_pycgtool.py +++ /dev/null @@ -1,81 +0,0 @@ -import unittest -import subprocess -import os -import logging - -import numpy as np - -from simpletraj.trajectory import XtcTrajectory - -try: - import mdtraj - mdtraj_present = True -except ImportError: - mdtraj_present = False - -from pycgtool.interface import Options -from pycgtool.util import cmp_whitespace_float -from pycgtool.pycgtool import main, map_only - - -class Args: - def __init__(self, name, map=True, bnd=True): - self.gro = os.path.join("test/data", name+".gro") - self.xtc = os.path.join("test/data", name+".xtc") - self.map = os.path.join("test/data", name+".map") if map else None - self.bnd = os.path.join("test/data", name+".bnd") if bnd else None - self.begin = 0 - self.end = -1 - self.quiet = True - - -class PycgtoolTest(unittest.TestCase): - config = Options([("output_name", "out"), - ("output", "gro"), - ("output_xtc", True), - ("map_only", False), - ("map_center", "geom"), - ("constr_threshold", 100000), - ("dump_measurements", False), - ("dump_n_values", 10000), - ("output_forcefield", False), - ("temperature", 310), - ("default_fc", False), - ("generate_angles", True), - ("generate_dihedrals", False)]) - - def test_run_help(self): - path = os.path.dirname(os.path.dirname(__file__)) - self.assertEqual(0, subprocess.check_call([os.path.join(path, "pycgtool.py"), "-h"], stdout=subprocess.PIPE)) - - @unittest.skipIf(not mdtraj_present, "MDTRAJ or Scipy not present") - def test_map_only(self): - logging.disable(logging.WARNING) - map_only(Args("sugar"), self.config) - logging.disable(logging.NOTSET) - - xtc = XtcTrajectory("out.xtc") - xtc_ref = XtcTrajectory("test/data/sugar_out.xtc") - self.assertEqual(xtc_ref.numframes, xtc.numframes) - - for i in range(xtc_ref.numframes): - xtc.get_frame(i) - xtc_ref.get_frame(i) - np.testing.assert_array_almost_equal(xtc_ref.box, xtc.box, decimal=3) - np.testing.assert_array_almost_equal(xtc_ref.x, xtc.x, decimal=3) - - def test_full(self): - path = os.path.dirname(os.path.dirname(__file__)) - self.assertEqual(0, subprocess.check_call([os.path.join(path, "pycgtool.py"), - "-g", "test/data/sugar.gro", - "-x", "test/data/sugar.xtc", - "-m", "test/data/sugar_only.map", - "-b", "test/data/sugar.bnd", - ], stdout=subprocess.PIPE, stderr=subprocess.PIPE)) - self.assertTrue(cmp_whitespace_float("out.itp", "test/data/sugar_out.itp", float_rel_error=0.001)) - self.assertTrue(cmp_whitespace_float("out.gro", "test/data/sugar_out.gro", float_rel_error=0.001)) - # TODO more tests - - -if __name__ == '__main__': - unittest.main() diff --git a/test/test_util.py b/test/test_util.py deleted file mode 100644 index 604fa49..0000000 --- a/test/test_util.py +++ /dev/null @@ -1,203 +0,0 @@ -import unittest -import os -import logging - -import numpy as np -import numpy.testing - -from pycgtool.util import tuple_equivalent, extend_graph_chain, stat_moments, transpose_and_sample -from pycgtool.util import dir_up, backup_file, sliding, r_squared, dist_with_pbc -from pycgtool.util import SimpleEnum, FixedFormatUnpacker - - -class UtilTest(unittest.TestCase): - def test_tuple_equivalent(self): - t1 = (0, 1, 2) - t2 = (0, 1, 2) - self.assertTrue(tuple_equivalent(t1, t2)) - t2 = (2, 1, 0) - self.assertTrue(tuple_equivalent(t1, t2)) - t2 = (2, 1, 3) - self.assertFalse(tuple_equivalent(t1, t2)) - - def test_dist_with_pbc(self): - pos_a = np.array([1., 1., 1.]) - pos_b = np.array([9., 9., 9.]) - numpy.testing.assert_equal(np.array([8., 8., 8.]), - dist_with_pbc(pos_a, pos_b, np.array([0., 0., 0.]))) - numpy.testing.assert_equal(np.array([8., 8., 8.]), - dist_with_pbc(pos_a, pos_b, np.array([20., 20., 20.]))) - numpy.testing.assert_equal(np.array([-2., -2., -2.]), - dist_with_pbc(pos_a, pos_b, np.array([10., 10., 10.]))) - - def test_triplets_from_pairs(self): - pairs = [(0, 1), (1, 2), (2, 3)] - result = [(0, 1, 2), (1, 2, 3)] - self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs))) - pairs = [(0, 1), (1, 2), (2, 3), (3, 0)] - result = [(0, 1, 2), (1, 0, 3), (1, 2, 3), (2, 3, 0)] - self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs))) - - def test_triplets_from_pairs_multires(self): - pairs = [("a", "b"), ("b", "c"), ("c", "d"), ("d", "+a")] - result = [("a", "b", "c"), ("b", "c", "d"), ("c", "d", "+a"), ("d", "+a", "+b")] - self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs))) - - def test_quadruplets_from_pairs(self): - pairs = [(0, 1), (1, 2), (2, 3)] - result = [(0, 1, 2, 3)] - triplets = extend_graph_chain(pairs, pairs) - self.assertEqual(result, sorted(extend_graph_chain(triplets, pairs))) - pairs = [(0, 1), (1, 2), (2, 3), (3, 0)] - triplets = extend_graph_chain(pairs, pairs) - result = [(0, 1, 2, 3), (1, 0, 3, 2), (1, 2, 3, 0), (2, 1, 0, 3)] - self.assertEqual(result, sorted(extend_graph_chain(triplets, pairs))) - - def test_stat_moments(self): - t1 = [3, 3, 3, 3, 3] - t2 = [1, 2, 3, 4, 5] - np.testing.assert_allclose(np.array([3, 0]), stat_moments(t1)) - np.testing.assert_allclose(np.array([3, 2]), stat_moments(t2)) - - def test_dir_up(self): - path = os.path.realpath(__file__) - self.assertEqual(path, dir_up(path, 0)) - self.assertEqual(os.path.dirname(path), dir_up(path)) - self.assertEqual(os.path.dirname(os.path.dirname(path)), dir_up(path, 2)) - - def test_backup_file(self): - try: - os.remove("testfile") - os.remove("#testfile.1#") - os.remove("#testfile.2#") - except OSError: - pass - - logging.disable(logging.WARNING) - open("testfile", "a").close() - self.assertEqual("#testfile.1#", backup_file("testfile")) - open("testfile", "a").close() - self.assertTrue(os.path.exists("#testfile.1#")) - self.assertEqual("#testfile.2#", backup_file("testfile")) - open("testfile", "a").close() - self.assertTrue(os.path.exists("#testfile.2#")) - logging.disable(logging.NOTSET) - - os.remove("testfile") - os.remove("#testfile.1#") - os.remove("#testfile.2#") - - def test_sliding(self): - l = [0, 1, 2, 3, 4] - res = [(None, 0, 1), (0, 1, 2), (1, 2, 3), (2, 3, 4), (3, 4, None)] - for res, pair in zip(res, sliding(l)): - self.assertEqual(res, pair) - - def test_r_squared(self): - ref = [i for i in range(5)] - fit = ref - self.assertEqual(1, r_squared(ref, fit)) - fit = [2 for _ in range(5)] - self.assertEqual(0, r_squared(ref, fit)) - fit = [i for i in range(1, 6)] - self.assertEqual(0.5, r_squared(ref, fit)) - - def test_transpose_and_sample_no_sample(self): - l = [(1, 2), (3, 4), (5, 6)] - l_t = [(1, 3, 5), (2, 4, 6)] - self.assertEqual(l_t, transpose_and_sample(l, None)) - - def test_transpose_and_sample(self): - l = [(1, 2), (3, 4), (5, 6)] - l_t = [(1, 3, 5), (2, 4, 6)] - - l_t_test = transpose_and_sample(l, n=1) - self.assertEqual(1, len(l_t_test)) - self.assertIn(l_t_test[0], l_t) - - def test_simple_enum(self): - enum = SimpleEnum.enum("enum", ["one", "two", "three"]) - self.assertTrue(enum.one == enum.one) - self.assertTrue(enum.one.compare_value(enum.one)) - - self.assertFalse(enum.two == enum.three) - self.assertFalse(enum.two.compare_value(enum.three)) - - with self.assertRaises(AttributeError): - _ = enum.four - with self.assertRaises(AttributeError): - enum.one = 2 - - enum2 = SimpleEnum.enum("enum2", ["one", "two", "three"]) - with self.assertRaises(TypeError): - assert enum2.one == enum.one - - self.assertTrue("one" in enum) - self.assertFalse("four" in enum) - - def test_simple_enum_values(self): - enum = SimpleEnum.enum_from_dict("enum", {"one": 111, - "two": 111, - "three": 333}) - self.assertTrue(enum.one == enum.one) - self.assertTrue(enum.one.compare_value(enum.one)) - - self.assertFalse(enum.one == enum.two) - self.assertTrue(enum.one.compare_value(enum.two)) - - self.assertFalse(enum.two == enum.three) - self.assertFalse(enum.two.compare_value(enum.three)) - - with self.assertRaises(AttributeError): - _ = enum.four - with self.assertRaises(AttributeError): - enum.one = 2 - - enum2 = SimpleEnum.enum("enum2", ["one", "two", "three"]) - with self.assertRaises(TypeError): - assert enum2.one == enum.one - - self.assertTrue("one" in enum) - self.assertEqual(111, enum.one.value) - - self.assertFalse("four" in enum) - - def test_fixed_format_unpacker_c(self): - unpacker = FixedFormatUnpacker("%-4d%5s%4.1f") - toks = unpacker.unpack("1234hello12.3") - self.assertEqual(3, len(toks)) - self.assertEqual(1234, toks[0]) - self.assertEqual("hello", toks[1]) - self.assertAlmostEqual(12.3, toks[2]) - - def test_fixed_format_unpacker_fortran(self): - unpacker = FixedFormatUnpacker("I4,A5,F4.1", - FixedFormatUnpacker.FormatStyle.Fortran) - toks = unpacker.unpack("1234hello12.3") - self.assertEqual(3, len(toks)) - self.assertEqual(1234, toks[0]) - self.assertEqual("hello", toks[1]) - self.assertAlmostEqual(12.3, toks[2]) - - def test_fixed_format_unpacker_fortran_space(self): - unpacker = FixedFormatUnpacker("I4,X3,A5,X2,F4.1", - FixedFormatUnpacker.FormatStyle.Fortran) - toks = unpacker.unpack("1234 x hello x12.3") - self.assertEqual(3, len(toks)) - self.assertEqual(1234, toks[0]) - self.assertEqual("hello", toks[1]) - self.assertAlmostEqual(12.3, toks[2]) - - def test_fixed_format_unpacker_fortran_repeat(self): - unpacker = FixedFormatUnpacker("2I2,X3,A5,2X,F4.1", - FixedFormatUnpacker.FormatStyle.Fortran) - toks = unpacker.unpack("1234 x hello x12.3") - self.assertEqual(4, len(toks)) - self.assertEqual(12, toks[0]) - self.assertEqual(34, toks[1]) - self.assertEqual("hello", toks[2]) - self.assertAlmostEqual(12.3, toks[3]) - - -if __name__ == '__main__': - unittest.main() diff --git a/test/__init__.py b/tests/__init__.py similarity index 100% rename from test/__init__.py rename to tests/__init__.py diff --git a/tests/data/ALLA_angle.dat b/tests/data/ALLA_angle.dat new file mode 100644 index 0000000..2377679 --- /dev/null +++ b/tests/data/ALLA_angle.dat @@ -0,0 +1,1001 @@ + 76.98026 115.93467 109.40350 84.42555 149.74403 99.25974 + 75.62878 105.42109 112.14338 86.37606 151.96346 98.40435 + 70.50335 118.14827 105.66918 81.15248 141.43194 98.30403 + 72.32151 108.59754 102.13610 81.32983 136.97937 100.53963 + 77.97404 119.12349 109.65250 84.20645 147.81346 99.98239 + 83.71318 125.71758 110.85334 81.89284 157.61803 101.85913 + 86.78917 118.38125 114.72019 77.98291 151.09059 104.87222 + 75.84638 115.28435 108.49897 77.09841 133.56749 97.06234 + 75.40909 116.76422 105.68688 79.14868 143.12676 96.45060 + 77.45517 113.63139 108.26685 80.95397 142.19821 101.74004 + 82.03027 114.55203 106.58329 79.05378 155.95543 99.77045 + 77.83048 117.22580 111.35641 88.19590 142.95940 105.32454 + 78.52059 117.36505 111.12029 82.98674 141.91972 101.21238 + 81.00128 114.67688 103.45162 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0.22200 0.24968 0.20176 0.17777 + 0.22191 0.22114 0.21448 0.27147 0.20521 0.18032 + 0.21772 0.22236 0.21855 0.23384 0.21663 0.17639 + 0.22729 0.23170 0.21475 0.25840 0.20129 0.17866 + 0.22484 0.22711 0.21841 0.24261 0.21119 0.18296 diff --git a/tests/data/ALLA_length_one.dat b/tests/data/ALLA_length_one.dat new file mode 100644 index 0000000..e4d87cd --- /dev/null +++ b/tests/data/ALLA_length_one.dat @@ -0,0 +1 @@ + 0.15361 0.15057 0.15191 0.15219 0.14398 0.14278 diff --git a/test/data/dppc.gro b/tests/data/dppc.gro similarity index 100% rename from test/data/dppc.gro rename to tests/data/dppc.gro diff --git a/test/data/dppc.map b/tests/data/dppc.map similarity index 100% rename from test/data/dppc.map rename to tests/data/dppc.map diff --git a/test/data/duplicate_atoms.bnd b/tests/data/duplicate_atoms.bnd similarity index 100% rename from test/data/duplicate_atoms.bnd rename to tests/data/duplicate_atoms.bnd diff --git a/tests/data/ffout.ff/atomtypes.atp b/tests/data/ffout.ff/atomtypes.atp new file mode 100644 index 0000000..4829441 --- /dev/null +++ b/tests/data/ffout.ff/atomtypes.atp @@ -0,0 +1,39 @@ +P5 72.0 0.000 A 0.0 0.0 +P4 72.0 0.000 A 0.0 0.0 +P3 72.0 0.000 A 0.0 0.0 +P2 72.0 0.000 A 0.0 0.0 +P1 72.0 0.000 A 0.0 0.0 +Nda 72.0 0.000 A 0.0 0.0 +Nd 72.0 0.000 A 0.0 0.0 +Na 72.0 0.000 A 0.0 0.0 +N0 72.0 0.000 A 0.0 0.0 +C5 72.0 0.000 A 0.0 0.0 +C4 72.0 0.000 A 0.0 0.0 +C3 72.0 0.000 A 0.0 0.0 +C2 72.0 0.000 A 0.0 0.0 +C1 72.0 0.000 A 0.0 0.0 +Qda 72.0 0.000 A 0.0 0.0 +Qd 72.0 0.000 A 0.0 0.0 +Qa 72.0 0.000 A 0.0 0.0 +Q0 72.0 0.000 A 0.0 0.0 +SP5 45.0 0.000 A 0.0 0.0 +SP4 45.0 0.000 A 0.0 0.0 +SP3 45.0 0.000 A 0.0 0.0 +SP2 45.0 0.000 A 0.0 0.0 +SP1 45.0 0.000 A 0.0 0.0 +SNda 45.0 0.000 A 0.0 0.0 +SNd 45.0 0.000 A 0.0 0.0 +SNa 45.0 0.000 A 0.0 0.0 +SN0 45.0 0.000 A 0.0 0.0 +SC5 45.0 0.000 A 0.0 0.0 +SC4 45.0 0.000 A 0.0 0.0 +SC3 45.0 0.000 A 0.0 0.0 +SC2 45.0 0.000 A 0.0 0.0 +SC1 45.0 0.000 A 0.0 0.0 +SQda 45.0 0.000 A 0.0 0.0 +SQd 45.0 0.000 A 0.0 0.0 +SQa 45.0 0.000 A 0.0 0.0 +SQ0 45.0 0.000 A 0.0 0.0 +AC2 72.0 0.000 A 0.0 0.0 +AC1 72.0 0.000 A 0.0 0.0 +BP4 72.0 0.000 A 0.0 0.0 diff --git a/tests/data/ffout.ff/forcefield.doc b/tests/data/ffout.ff/forcefield.doc new file mode 100644 index 0000000..52ce43a --- /dev/null +++ b/tests/data/ffout.ff/forcefield.doc @@ -0,0 +1 @@ +PyCGTOOL produced MARTINI force field - out diff --git a/tests/data/ffout.ff/forcefield.itp b/tests/data/ffout.ff/forcefield.itp new file mode 100644 index 0000000..86fcb77 --- /dev/null +++ b/tests/data/ffout.ff/forcefield.itp @@ -0,0 +1,2 @@ +#define _FF_PYCGTOOL_out +#include "martini_v2.2.itp" diff --git a/tests/data/ffout.ff/martini_v2.2.itp b/tests/data/ffout.ff/martini_v2.2.itp new file mode 100644 index 0000000..fa16da9 --- /dev/null +++ b/tests/data/ffout.ff/martini_v2.2.itp @@ -0,0 +1,910 @@ +; MARTINI FORCEFIELD V2.2 +; +; SJ MARRINK (last modified: 04-12-2012 by DdJ) +; +; NOTE 1: Bead definitinions in this file have not been changed with respect to +; martini_v2.1.itp. This file is purely here for clarity sake. Differences +; between V2.1 and V2.2 are created by the martinize script and can be found +; in martini_v2.2_aminoacids.itp. +; +; please cite: +; +; D.H. de Jong, G. Singh, W.F.D. Bennet, C. Arnarez, T.A. Wassenaar, L.V. Schafer, +; X. Periole, D.P. Tieleman, S.J. Marrink. +; Improved Parameters for the Martini Coarse-Grained Protein Force Field +; J. Chem. Theory Comput., DOI: 10.1021/ct300646g + +; L. Monticelli, S. Kandasamy, X. Periole, R. Larson, D.P. Tieleman, S.J. Marrink. +; The MARTINI coarse grained force field: extension to proteins. +; J. Chem. Th. Comp., 4:819-834, 2008. +; +; S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. +; The MARTINI forcefield: coarse grained model for biomolecular simulations. +; JPC-B, 111:7812-7824, 2007. +; +; and (if using lipid topologies): +; +; S.J. Marrink, A.H. de Vries, A.E. Mark. +; Coarse grained model for semi-quantitative lipid simulations. +; JPC-B, 108:750-760, 2004. + + +[ defaults ] +1 1 + +[ atomtypes ] + +; Currently eighteen particle types are defined, divided into four main categories +; (P, polar; N, intermediate; C, apolar; Q, charged) +; each of which has a number of sublevels (0,a,d, or ad) +; subtype 0 has no hydrogen bond forming capacities, +; subtype d has some hydrogen donor capacities, +; subtype a some hydrogen acceptor capacities, +; and subtype da has both donor and acceptor capacities +; or (1,2,3,4,5) where subtype 5 is more polar than 1. + +; Two main classes of particles are furthermore distinguished, namely +; STANDARD particles which are mapped using a 4:1 mapping scheme, and +; RING particles which are used for ring compounds mapped 2-3:1. +; A special BIG particle type is defined in addition to prevent freezing of CG water. +; Two AMINO acid particle types are used to avoid Q-C clashes inside proteins. + +; For reasons of computational efficiency, all particle masses are set to 72 amu, +; except for ring types which are set to 45 amu. +; For realistic dynamics, the particle masses should be adapted. +; This might require a reduction of the integration timestep, however. + +; name mass charge ptype c6 c12 + +; STANDARD types, 4:1 mapping +; polar type +P5 72.0 0.000 A 0.0 0.0 +P4 72.0 0.000 A 0.0 0.0 +P3 72.0 0.000 A 0.0 0.0 +P2 72.0 0.000 A 0.0 0.0 +P1 72.0 0.000 A 0.0 0.0 +; intermediate polar +Nda 72.0 0.000 A 0.0 0.0 +Nd 72.0 0.000 A 0.0 0.0 +Na 72.0 0.000 A 0.0 0.0 +N0 72.0 0.000 A 0.0 0.0 +; apolar +C5 72.0 0.000 A 0.0 0.0 +C4 72.0 0.000 A 0.0 0.0 +C3 72.0 0.000 A 0.0 0.0 +C2 72.0 0.000 A 0.0 0.0 +C1 72.0 0.000 A 0.0 0.0 +; charged +Qda 72.0 0.000 A 0.0 0.0 +Qd 72.0 0.000 A 0.0 0.0 +Qa 72.0 0.000 A 0.0 0.0 +Q0 72.0 0.000 A 0.0 0.0 + +; RING types, 2-3:1 mapping +SP5 45.0 0.000 A 0.0 0.0 +SP4 45.0 0.000 A 0.0 0.0 +SP3 45.0 0.000 A 0.0 0.0 +SP2 45.0 0.000 A 0.0 0.0 +SP1 45.0 0.000 A 0.0 0.0 +SNda 45.0 0.000 A 0.0 0.0 +SNd 45.0 0.000 A 0.0 0.0 +SNa 45.0 0.000 A 0.0 0.0 +SN0 45.0 0.000 A 0.0 0.0 +SC5 45.0 0.000 A 0.0 0.0 +SC4 45.0 0.000 A 0.0 0.0 +SC3 45.0 0.000 A 0.0 0.0 +SC2 45.0 0.000 A 0.0 0.0 +SC1 45.0 0.000 A 0.0 0.0 +SQda 45.0 0.000 A 0.0 0.0 +SQd 45.0 0.000 A 0.0 0.0 +SQa 45.0 0.000 A 0.0 0.0 +SQ0 45.0 0.000 A 0.0 0.0 + +; AMINO ACIDS (required for Q-C interactions inside proteins) +AC2 72.0 0.000 A 0.0 0.0 +AC1 72.0 0.000 A 0.0 0.0 + +; BIG particle type (to prevent freezing of water) +BP4 72.0 0.000 A 0.0 0.0 + + +[ nonbond_params ] + +; levels of LJ interaction: + +; O - supra attractive: (eps=5.6, s=0.47) +; I - attractive: (eps=5.0, s=0.47) +; II - almost attractive: (eps=4.5, s=0.47) +; III - semi attractive: (eps=4.0, s=0.47) +; IV - intermediate: (eps=3.5, s=0.47) +; V - almost intermediate: (eps=3.1, s=0.47) +; VI - semi repulsive: (eps=2.7, s=0.47) +; VII - almost repulsive: (eps=2.3, s=0.47) +; VIII - repulsive: (eps=2.0, s=0.47) +; IX - super repulsive: (eps=2.0, s=0.62) +; +; RINGS: for ring-ring interactions eps is reduced to 75%, sigma=0.43. + +; i j funda c6 c12 +; self terms + P5 P5 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 SP5 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + P4 P4 1 0.21558E-00 0.23238E-02 ; attractive + BP4 BP4 1 0.21558E-00 0.23238E-02 ; attractive + SP4 SP4 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + P3 P3 1 0.21558E-00 0.23238E-02 ; attractive + SP3 SP3 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + P2 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + SP2 SP2 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + P1 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + SP1 SP1 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + Nda Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + SNda SNda 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + Nd Nd 1 0.17246E-00 0.18590E-02 ; semi attractive + SNd SNd 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + Na Na 1 0.17246E-00 0.18590E-02 ; semi attractive + SNa SNa 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + N0 N0 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 SN0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C5 C5 1 0.15091E-00 0.16267E-02 ; intermediate + SC5 SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C4 C4 1 0.15091E-00 0.16267E-02 ; intermediate + SC4 SC4 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C3 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C2 C2 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 AC2 1 0.15091E-00 0.16267E-02 ; intermediate + SC2 SC2 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C1 C1 1 0.15091E-00 0.16267E-02 ; intermediate + AC1 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + SC1 SC1 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + Qda Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + SQda SQda 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + Qd Qd 1 0.21558E-00 0.23238E-02 ; attractive + SQd SQd 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + Qa Qa 1 0.21558E-00 0.23238E-02 ; attractive + SQa SQa 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + Q0 Q0 1 0.15091E-00 0.16267E-02 ; intermediate + SQ0 SQ0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 +; cross terms + P5 SP5 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 P4 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 BP4 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SP4 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 P3 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SP3 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 P2 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SP2 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 P1 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SP1 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 Nda 1 0.21558E-00 0.23238E-02 ; attractive + P5 SNda 1 0.21558E-00 0.23238E-02 ; attractive + P5 Nd 1 0.21558E-00 0.23238E-02 ; attractive + P5 SNd 1 0.21558E-00 0.23238E-02 ; attractive + P5 Na 1 0.21558E-00 0.23238E-02 ; attractive + P5 SNa 1 0.21558E-00 0.23238E-02 ; attractive + P5 N0 1 0.15091E-00 0.16267E-02 ; intermediate + P5 SN0 1 0.15091E-00 0.16267E-02 ; intermediate + P5 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + P5 SC5 1 0.13366E-00 0.14408E-02 ; almost intermediate + P5 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + P5 SC4 1 0.11642E-00 0.12549E-02 ; semi repulsive + P5 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + P5 SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + P5 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P5 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P5 SC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P5 C1 1 0.86233E-01 0.92953E-03 ; repulsive + P5 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + P5 SC1 1 0.86233E-01 0.92953E-03 ; repulsive + P5 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SQda 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SQd 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SQa 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 Q0 1 0.21558E-00 0.23238E-02 ; attractive + P5 SQ0 1 0.21558E-00 0.23238E-02 ; attractive + SP5 P4 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 BP4 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 SP4 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP5 P3 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 SP3 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP5 P2 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 SP2 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP5 P1 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 SP1 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP5 Nda 1 0.21558E-00 0.23238E-02 ; attractive + SP5 SNda 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP5 Nd 1 0.21558E-00 0.23238E-02 ; attractive + SP5 SNd 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP5 Na 1 0.21558E-00 0.23238E-02 ; attractive + SP5 SNa 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP5 N0 1 0.15091E-00 0.16267E-02 ; intermediate + SP5 SN0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP5 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP5 SC5 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SP5 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP5 SC4 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP5 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP5 SC3 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP5 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP5 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP5 SC2 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + SP5 C1 1 0.86233E-01 0.92953E-03 ; repulsive + SP5 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + SP5 SC1 1 0.37928E-01 0.23976E-03 ; 75repulsive, s=0.43 + SP5 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 SQda 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP5 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 SQd 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP5 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + SP5 SQa 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP5 Q0 1 0.21558E-00 0.23238E-02 ; attractive + SP5 SQ0 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + P4 BP4 1 0.76824E-00 0.26348E-01 ; supra attractive, s=0.57 + P4 SP4 1 0.21558E-00 0.23238E-02 ; attractive + P4 P3 1 0.21558E-00 0.23238E-02 ; attractive + P4 SP3 1 0.21558E-00 0.23238E-02 ; attractive + P4 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + P4 SP2 1 0.19402E-00 0.20914E-02 ; almost attractive + P4 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + P4 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + P4 Nda 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 SNda 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 Nd 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 SNd 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 Na 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 SNa 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 N0 1 0.15091E-00 0.16267E-02 ; intermediate + P4 SN0 1 0.15091E-00 0.16267E-02 ; intermediate + P4 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + P4 SC5 1 0.13366E-00 0.14408E-02 ; almost intermediate + P4 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + P4 SC4 1 0.11642E-00 0.12549E-02 ; semi repulsive + P4 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + P4 SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + P4 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P4 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P4 SC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P4 C1 1 0.86233E-01 0.92953E-03 ; repulsive + P4 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + P4 SC1 1 0.86233E-01 0.92953E-03 ; repulsive + P4 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 SQda 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 SQd 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 SQa 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 Q0 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 SQ0 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 SP4 1 0.21558E-00 0.23238E-02 ; attractive + BP4 P3 1 0.21558E-00 0.23238E-02 ; attractive + BP4 SP3 1 0.21558E-00 0.23238E-02 ; attractive + BP4 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + BP4 SP2 1 0.19402E-00 0.20914E-02 ; almost attractive + BP4 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + BP4 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + BP4 Nda 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 SNda 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 Nd 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 SNd 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 Na 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 SNa 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 N0 1 0.15091E-00 0.16267E-02 ; intermediate + BP4 SN0 1 0.15091E-00 0.16267E-02 ; intermediate + BP4 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + BP4 SC5 1 0.13366E-00 0.14408E-02 ; almost intermediate + BP4 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + BP4 SC4 1 0.11642E-00 0.12549E-02 ; semi repulsive + BP4 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + BP4 SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + BP4 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + BP4 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + BP4 SC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + BP4 C1 1 0.86233E-01 0.92953E-03 ; repulsive + BP4 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + BP4 SC1 1 0.86233E-01 0.92953E-03 ; repulsive + BP4 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 SQda 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 SQd 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 SQa 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 Q0 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 SQ0 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 P3 1 0.21558E-00 0.23238E-02 ; attractive + SP4 SP3 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP4 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + SP4 SP2 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP4 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + SP4 SP1 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP4 Nda 1 0.17246E-00 0.18590E-02 ; semi attractive + SP4 SNda 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SP4 Nd 1 0.17246E-00 0.18590E-02 ; semi attractive + SP4 SNd 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SP4 Na 1 0.17246E-00 0.18590E-02 ; semi attractive + SP4 SNa 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SP4 N0 1 0.15091E-00 0.16267E-02 ; intermediate + SP4 SN0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP4 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP4 SC5 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SP4 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP4 SC4 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP4 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP4 SC3 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP4 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP4 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP4 SC2 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + SP4 C1 1 0.86233E-01 0.92953E-03 ; repulsive + SP4 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + SP4 SC1 1 0.37928E-01 0.23976E-03 ; 75repulsive, s=0.43 + SP4 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 SQda 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP4 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 SQd 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP4 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 SQa 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP4 Q0 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 SQ0 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + P3 SP3 1 0.21558E-00 0.23238E-02 ; attractive + P3 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 SP2 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 SNda 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 SNd 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 N0 1 0.15091E-00 0.16267E-02 ; intermediate + P3 SN0 1 0.15091E-00 0.16267E-02 ; intermediate + P3 C5 1 0.15091E-00 0.16267E-02 ; intermediate + P3 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + P3 C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + P3 SC4 1 0.13366E-00 0.14408E-02 ; almost intermediate + P3 C3 1 0.13366E-00 0.14408E-02 ; almost intermediate + P3 SC3 1 0.13366E-00 0.14408E-02 ; almost intermediate + P3 C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P3 AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P3 SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P3 C1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P3 AC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P3 SC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P3 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 SQda 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 SQd 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 SQa 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 Q0 1 0.21558E-00 0.23238E-02 ; attractive + P3 SQ0 1 0.21558E-00 0.23238E-02 ; attractive + SP3 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + SP3 SP2 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP3 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + SP3 SP1 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP3 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + SP3 SNda 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP3 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + SP3 SNd 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP3 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + SP3 SNa 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP3 N0 1 0.15091E-00 0.16267E-02 ; intermediate + SP3 SN0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP3 C5 1 0.15091E-00 0.16267E-02 ; intermediate + SP3 SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP3 C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP3 SC4 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SP3 C3 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP3 SC3 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SP3 C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP3 AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP3 SC2 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP3 C1 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP3 AC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP3 SC1 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + SP3 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + SP3 SQda 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP3 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + SP3 SQd 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP3 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + SP3 SQa 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SP3 Q0 1 0.21558E-00 0.23238E-02 ; attractive + SP3 SQ0 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + P2 SP2 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 SNda 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 SNd 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 N0 1 0.17246E-00 0.18590E-02 ; semi attractive + P2 SN0 1 0.17246E-00 0.18590E-02 ; semi attractive + P2 C5 1 0.15091E-00 0.16267E-02 ; intermediate + P2 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + P2 C4 1 0.15091E-00 0.16267E-02 ; intermediate + P2 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + P2 C3 1 0.13366E-00 0.14408E-02 ; almost intermediate + P2 SC3 1 0.13366E-00 0.14408E-02 ; almost intermediate + P2 C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P2 AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P2 SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P2 C1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P2 AC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P2 SC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P2 Qda 1 0.21558E-00 0.23238E-02 ; attractive + P2 SQda 1 0.21558E-00 0.23238E-02 ; attractive + P2 Qd 1 0.21558E-00 0.23238E-02 ; attractive + P2 SQd 1 0.21558E-00 0.23238E-02 ; attractive + P2 Qa 1 0.21558E-00 0.23238E-02 ; attractive + P2 SQa 1 0.21558E-00 0.23238E-02 ; attractive + P2 Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 SQ0 1 0.19402E-00 0.20914E-02 ; almost attractive + SP2 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + SP2 SP1 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP2 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + SP2 SNda 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP2 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + SP2 SNd 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP2 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + SP2 SNa 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP2 N0 1 0.17246E-00 0.18590E-02 ; semi attractive + SP2 SN0 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SP2 C5 1 0.15091E-00 0.16267E-02 ; intermediate + SP2 SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP2 C4 1 0.15091E-00 0.16267E-02 ; intermediate + SP2 SC4 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP2 C3 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP2 SC3 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SP2 C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP2 AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP2 SC2 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP2 C1 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP2 AC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP2 SC1 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + SP2 Qda 1 0.21558E-00 0.23238E-02 ; attractive + SP2 SQda 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP2 Qd 1 0.21558E-00 0.23238E-02 ; attractive + SP2 SQd 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP2 Qa 1 0.21558E-00 0.23238E-02 ; attractive + SP2 SQa 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP2 Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + SP2 SQ0 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + P1 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 SNda 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 SNd 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 N0 1 0.17246E-00 0.18590E-02 ; semi attractive + P1 SN0 1 0.17246E-00 0.18590E-02 ; semi attractive + P1 C5 1 0.15091E-00 0.16267E-02 ; intermediate + P1 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + P1 C4 1 0.15091E-00 0.16267E-02 ; intermediate + P1 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + P1 C3 1 0.15091E-00 0.16267E-02 ; intermediate + P1 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + P1 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + P1 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + P1 SC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + P1 C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + P1 AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + P1 SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + P1 Qda 1 0.21558E-00 0.23238E-02 ; attractive + P1 SQda 1 0.21558E-00 0.23238E-02 ; attractive + P1 Qd 1 0.21558E-00 0.23238E-02 ; attractive + P1 SQd 1 0.21558E-00 0.23238E-02 ; attractive + P1 Qa 1 0.21558E-00 0.23238E-02 ; attractive + P1 SQa 1 0.21558E-00 0.23238E-02 ; attractive + P1 Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + P1 SQ0 1 0.17246E-00 0.18590E-02 ; semi attractive + SP1 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + SP1 SNda 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP1 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + SP1 SNd 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP1 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + SP1 SNa 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP1 N0 1 0.17246E-00 0.18590E-02 ; semi attractive + SP1 SN0 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SP1 C5 1 0.15091E-00 0.16267E-02 ; intermediate + SP1 SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP1 C4 1 0.15091E-00 0.16267E-02 ; intermediate + SP1 SC4 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP1 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SP1 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP1 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP1 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP1 SC2 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SP1 C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP1 AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP1 SC1 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP1 Qda 1 0.21558E-00 0.23238E-02 ; attractive + SP1 SQda 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP1 Qd 1 0.21558E-00 0.23238E-02 ; attractive + SP1 SQd 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP1 Qa 1 0.21558E-00 0.23238E-02 ; attractive + SP1 SQa 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SP1 Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + SP1 SQ0 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + Nda SNda 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda SNd 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda Na 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda N0 1 0.15091E-00 0.16267E-02 ; intermediate + Nda SN0 1 0.15091E-00 0.16267E-02 ; intermediate + Nda C5 1 0.15091E-00 0.16267E-02 ; intermediate + Nda SC5 1 0.15091E-00 0.16267E-02 ; intermediate + Nda C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Nda SC4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Nda C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda Qda 1 0.21558E-00 0.23238E-02 ; attractive + Nda SQda 1 0.21558E-00 0.23238E-02 ; attractive + Nda Qd 1 0.21558E-00 0.23238E-02 ; attractive + Nda SQd 1 0.21558E-00 0.23238E-02 ; attractive + Nda Qa 1 0.21558E-00 0.23238E-02 ; attractive + Nda SQa 1 0.21558E-00 0.23238E-02 ; attractive + Nda Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + Nda SQ0 1 0.17246E-00 0.18590E-02 ; semi attractive + SNda Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + SNda SNd 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SNda Na 1 0.19402E-00 0.20914E-02 ; almost attractive + SNda SNa 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SNda N0 1 0.15091E-00 0.16267E-02 ; intermediate + SNda SN0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SNda C5 1 0.15091E-00 0.16267E-02 ; intermediate + SNda SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SNda C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + SNda SC4 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SNda C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNda SC3 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNda C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNda AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNda SC2 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNda C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNda AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNda SC1 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNda Qda 1 0.21558E-00 0.23238E-02 ; attractive + SNda SQda 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SNda Qd 1 0.21558E-00 0.23238E-02 ; attractive + SNda SQd 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SNda Qa 1 0.21558E-00 0.23238E-02 ; attractive + SNda SQa 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SNda Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + SNda SQ0 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + Nd SNd 1 0.17246E-00 0.18590E-02 ; semi attractive + Nd Na 1 0.19402E-00 0.20914E-02 ; almost attractive + Nd SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + Nd N0 1 0.15091E-00 0.16267E-02 ; intermediate + Nd SN0 1 0.15091E-00 0.16267E-02 ; intermediate + Nd C5 1 0.15091E-00 0.16267E-02 ; intermediate + Nd SC5 1 0.15091E-00 0.16267E-02 ; intermediate + Nd C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Nd SC4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Nd C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd Qda 1 0.21558E-00 0.23238E-02 ; attractive + Nd SQda 1 0.21558E-00 0.23238E-02 ; attractive + Nd Qd 1 0.17246E-00 0.18590E-02 ; semi attractive + Nd SQd 1 0.17246E-00 0.18590E-02 ; semi attractive + Nd Qa 1 0.21558E-00 0.23238E-02 ; attractive + Nd SQa 1 0.21558E-00 0.23238E-02 ; attractive + Nd Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + Nd SQ0 1 0.17246E-00 0.18590E-02 ; semi attractive + SNd Na 1 0.19402E-00 0.20914E-02 ; almost attractive + SNd SNa 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SNd N0 1 0.15091E-00 0.16267E-02 ; intermediate + SNd SN0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SNd C5 1 0.15091E-00 0.16267E-02 ; intermediate + SNd SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SNd C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + SNd SC4 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SNd C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd SC3 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNd C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd SC2 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNd C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd SC1 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNd Qda 1 0.21558E-00 0.23238E-02 ; attractive + SNd SQda 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SNd Qd 1 0.17246E-00 0.18590E-02 ; semi attractive + SNd SQd 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SNd Qa 1 0.21558E-00 0.23238E-02 ; attractive + SNd SQa 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SNd Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + SNd SQ0 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + Na SNa 1 0.17246E-00 0.18590E-02 ; semi attractive + Na N0 1 0.15091E-00 0.16267E-02 ; intermediate + Na SN0 1 0.15091E-00 0.16267E-02 ; intermediate + Na C5 1 0.15091E-00 0.16267E-02 ; intermediate + Na SC5 1 0.15091E-00 0.16267E-02 ; intermediate + Na C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Na SC4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Na C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na Qda 1 0.21558E-00 0.23238E-02 ; attractive + Na SQda 1 0.21558E-00 0.23238E-02 ; attractive + Na Qd 1 0.21558E-00 0.23238E-02 ; attractive + Na SQd 1 0.21558E-00 0.23238E-02 ; attractive + Na Qa 1 0.17246E-00 0.18590E-02 ; semi attractive + Na SQa 1 0.17246E-00 0.18590E-02 ; semi attractive + Na Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + Na SQ0 1 0.17246E-00 0.18590E-02 ; semi attractive + SNa N0 1 0.15091E-00 0.16267E-02 ; intermediate + SNa SN0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SNa C5 1 0.15091E-00 0.16267E-02 ; intermediate + SNa SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SNa C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + SNa SC4 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SNa C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa SC3 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNa C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa SC2 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNa C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa SC1 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNa Qda 1 0.21558E-00 0.23238E-02 ; attractive + SNa SQda 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SNa Qd 1 0.21558E-00 0.23238E-02 ; attractive + SNa SQd 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + SNa Qa 1 0.17246E-00 0.18590E-02 ; semi attractive + SNa SQa 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SNa Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + SNa SQ0 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + N0 SN0 1 0.15091E-00 0.16267E-02 ; intermediate + N0 C5 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + N0 C4 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + N0 C3 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + N0 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + N0 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + N0 SC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + N0 C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + N0 AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + N0 SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + N0 Qda 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SQda 1 0.15091E-00 0.16267E-02 ; intermediate + N0 Qd 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SQd 1 0.15091E-00 0.16267E-02 ; intermediate + N0 Qa 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SQa 1 0.15091E-00 0.16267E-02 ; intermediate + N0 Q0 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SQ0 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 C5 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SN0 C4 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 SC4 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SN0 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SN0 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SN0 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SN0 SC2 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SN0 C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SN0 AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SN0 SC1 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SN0 Qda 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 SQda 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SN0 Qd 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 SQd 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SN0 Qa 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 SQa 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SN0 Q0 1 0.15091E-00 0.16267E-02 ; intermediate + SN0 SQ0 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C5 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + C5 C4 1 0.15091E-00 0.16267E-02 ; intermediate + C5 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + C5 C3 1 0.15091E-00 0.16267E-02 ; intermediate + C5 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + C5 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 SC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 C1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 AC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 SC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 Qda 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 SQda 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 Qd 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 SQd 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 Qa 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 SQa 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 Q0 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 SQ0 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 C4 1 0.15091E-00 0.16267E-02 ; intermediate + SC5 SC4 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC5 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SC5 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC5 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 SC2 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC5 C1 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 AC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 SC1 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC5 Qda 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 SQda 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC5 Qd 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 SQd 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC5 Qa 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 SQa 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC5 Q0 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 SQ0 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + C4 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + C4 C3 1 0.15091E-00 0.16267E-02 ; intermediate + C4 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + C4 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 SC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 C1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 AC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 SC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 Qda 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 SQda 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 Qd 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 SQd 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 Qa 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 SQa 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 Q0 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 SQ0 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SC4 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC4 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC4 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC4 SC2 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC4 C1 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC4 AC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC4 SC1 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC4 Qda 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 SQda 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SC4 Qd 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 SQd 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SC4 Qa 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 SQa 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SC4 Q0 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 SQ0 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + C3 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + C3 C2 1 0.15091E-00 0.16267E-02 ; intermediate + C3 AC2 1 0.15091E-00 0.16267E-02 ; intermediate + C3 SC2 1 0.15091E-00 0.16267E-02 ; intermediate + C3 C1 1 0.15091E-00 0.16267E-02 ; intermediate + C3 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + C3 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + C3 Qda 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 SQda 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 Qd 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 SQd 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 Qa 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 SQa 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 Q0 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 SQ0 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 C2 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 AC2 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 SC2 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC3 C1 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 SC1 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC3 Qda 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 SQda 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + SC3 Qd 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 SQd 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + SC3 Qa 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 SQa 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + SC3 Q0 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 SQ0 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + C2 AC2 1 0.15091E-00 0.16267E-02 ; intermediate + C2 SC2 1 0.15091E-00 0.16267E-02 ; intermediate + C2 C1 1 0.15091E-00 0.16267E-02 ; intermediate + C2 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + C2 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + C2 Qda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 SQda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 Qd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 SQd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 Qa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 SQa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 Q0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 SQ0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + AC2 SC2 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 C1 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 Qda 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 SQda 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 Qd 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 SQd 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 Qa 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 SQa 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 Q0 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 SQ0 1 0.86233E-01 0.92953E-03 ; repulsive + SC2 C1 1 0.15091E-00 0.16267E-02 ; intermediate + SC2 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + SC2 SC1 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC2 Qda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 SQda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 Qd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 SQd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 Qa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 SQa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 Q0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 SQ0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + C1 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + C1 Qda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 SQda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 Qd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 SQd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 Qa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 SQa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 Q0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 SQ0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + AC1 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + AC1 Qda 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 SQda 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 Qd 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 SQd 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 Qa 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 SQa 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 Q0 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 SQ0 1 0.86233E-01 0.92953E-03 ; repulsive + SC1 Qda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 SQda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 Qd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 SQd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 Qa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 SQa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 Q0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 SQ0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + Qda SQda 1 0.24145E-00 0.26027E-02 ; supra attractive + Qda Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + Qda SQd 1 0.24145E-00 0.26027E-02 ; supra attractive + Qda Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + Qda SQa 1 0.24145E-00 0.26027E-02 ; supra attractive + Qda Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + Qda SQ0 1 0.19402E-00 0.20914E-02 ; almost attractive + SQda Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + SQda SQd 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SQda Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + SQda SQa 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SQda Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + SQda SQ0 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + Qd SQd 1 0.21558E-00 0.23238E-02 ; attractive + Qd Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + Qd SQa 1 0.24145E-00 0.26027E-02 ; supra attractive + Qd Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + Qd SQ0 1 0.19402E-00 0.20914E-02 ; almost attractive + SQd Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + SQd SQa 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 + SQd Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + SQd SQ0 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + Qa SQa 1 0.21558E-00 0.23238E-02 ; attractive + Qa Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + Qa SQ0 1 0.19402E-00 0.20914E-02 ; almost attractive + SQa Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + SQa SQ0 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + Q0 SQ0 1 0.15091E-00 0.16267E-02 ; intermediate diff --git a/tests/data/ffout.ff/out.r2b b/tests/data/ffout.ff/out.r2b new file mode 100644 index 0000000..a4ac647 --- /dev/null +++ b/tests/data/ffout.ff/out.r2b @@ -0,0 +1,2 @@ +; rtp residue to rtp building block table +; main N-ter C-ter 2-ter diff --git a/tests/data/ffout.ff/out.rtp b/tests/data/ffout.ff/out.rtp new file mode 100644 index 0000000..f5c6357 --- /dev/null +++ b/tests/data/ffout.ff/out.rtp @@ -0,0 +1,31 @@ +[ bondedtypes ] + 1 1 1 1 1 1 0 0 +[ ALLA ] + [ atoms ] + C1 P3 0.000000 0 + C2 P3 0.000000 0 + C3 P3 0.000000 0 + C4 P3 0.000000 0 + C5 P2 0.000000 0 + O5 P4 0.000000 0 + [ bonds ] + C1 C2 0.22048 72722.85384 + C2 C3 0.22184 64326.39740 + C3 C4 0.21632 67918.78902 + C4 C5 0.25315 19536.67041 + C5 O5 0.20597 55319.40505 + O5 C1 0.18055 139769.28667 + [ angles ] + C1 C2 C3 1.35928 503.72847 + C2 C3 C4 2.02600 838.60152 + C3 C4 C5 1.93782 733.44785 + C4 C5 O5 1.45361 946.13124 + C5 O5 C1 2.50429 771.63346 + O5 C1 C2 1.73300 800.62808 + [ dihedrals ] + C1 C2 C3 C4 1.69535 253.69294 1 + C2 C3 C4 C5 -2.07382 125.03029 1 + C3 C4 C5 O5 2.76795 135.64448 1 + C4 C5 O5 C1 -2.21270 51.18142 1 + C5 O5 C1 C2 1.45570 59.39031 1 + O5 C1 C2 C3 -1.82618 279.84587 1 diff --git a/tests/data/ffout.ff/w.itp b/tests/data/ffout.ff/w.itp new file mode 100644 index 0000000..f11253e --- /dev/null +++ b/tests/data/ffout.ff/w.itp @@ -0,0 +1,49 @@ +; MARTINI FORCEFIELD V2.2 +; +; SJ MARRINK (last modified: 04-12-2012 by DdJ) +; +; NOTE 1: Bead definitinions in this file have not been changed with respect to +; martini_v2.1.itp. This file is purely here for clarity sake. Differences +; between V2.1 and V2.2 are created by the martinize script and can be found +; in martini_v2.2_aminoacids.itp. +; +; please cite: +; +; D.H. de Jong, G. Singh, W.F.D. Bennet, C. Arnarez, T.A. Wassenaar, L.V. Schafer, +; X. Periole, D.P. Tieleman, S.J. Marrink. +; Improved Parameters for the Martini Coarse-Grained Protein Force Field +; J. Chem. Theory Comput., DOI: 10.1021/ct300646g + +; L. Monticelli, S. Kandasamy, X. Periole, R. Larson, D.P. Tieleman, S.J. Marrink. +; The MARTINI coarse grained force field: extension to proteins. +; J. Chem. Th. Comp., 4:819-834, 2008. +; +; S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. +; The MARTINI forcefield: coarse grained model for biomolecular simulations. +; JPC-B, 111:7812-7824, 2007. +; +; and (if using lipid topologies): +; +; S.J. Marrink, A.H. de Vries, A.E. Mark. +; Coarse grained model for semi-quantitative lipid simulations. +; JPC-B, 108:750-760, 2004. + +;;;;;; WATER (representing 4 H2O molecules) + +[ moleculetype ] +; molname nrexcl + W 1 + +[ atoms ] +;id type resnr residu atom cgnr charge + 1 P4 1 W W 1 0 + +;;;;;; ANTIFREEZE (prevents freezing of water) + +[ moleculetype ] +; molname nrexcl + WF 1 + +[ atoms ] +;id type resnr residu atom cgnr charge + 1 BP4 1 WF WF 1 0 diff --git a/tests/data/ffout.ff/watermodels.dat b/tests/data/ffout.ff/watermodels.dat new file mode 100644 index 0000000..1c7b262 --- /dev/null +++ b/tests/data/ffout.ff/watermodels.dat @@ -0,0 +1,2 @@ +w W Standard MARTINI water +pw PW Polarisable MARTINI water diff --git a/test/data/martini.map b/tests/data/martini.map similarity index 100% rename from test/data/martini.map rename to tests/data/martini.map diff --git a/tests/data/martini3/four.gro b/tests/data/martini3/four.gro new file mode 100644 index 0000000..5c67ba9 --- /dev/null +++ b/tests/data/martini3/four.gro @@ -0,0 +1,7 @@ +Test + 4 + 1FOUR C1 1 2.000 2.000 2.000 + 1FOUR H1 2 1.000 1.000 1.000 + 1FOUR C2 3 3.000 3.000 3.000 + 1FOUR N2 4 4.000 4.000 4.000 + 5.00000 5.00000 5.00000 diff --git a/tests/data/martini3/four.itp b/tests/data/martini3/four.itp new file mode 100644 index 0000000..482d585 --- /dev/null +++ b/tests/data/martini3/four.itp @@ -0,0 +1,8 @@ +[ moleculetype ] +FOUR 1 + +[ atoms ] + 1 C 1 FOUR C1 1 0.000 1.00 + 2 H 1 FOUR H1 1 0.000 0.00 + 3 C 1 FOUR C2 1 0.000 0.00 + 4 N 1 FOUR N2 1 0.000 3.00 diff --git a/tests/data/martini3/four.map b/tests/data/martini3/four.map new file mode 100644 index 0000000..21c9521 --- /dev/null +++ b/tests/data/martini3/four.map @@ -0,0 +1,4 @@ +[FOUR] +CD1 C C1 H1 +CD2 C C2 N2 +@v CV1 C CD1 CD2 diff --git a/tests/data/martini3/naphthalene.bnd b/tests/data/martini3/naphthalene.bnd new file mode 100644 index 0000000..49d7308 --- /dev/null +++ b/tests/data/martini3/naphthalene.bnd @@ -0,0 +1,9 @@ +[ NAPH ] +R1 R2 ; around outside +R2 R5 +R5 R4 +R4 R1 +R1 R5 ; across diagonal + +; disabled because we use a single frame for testing +; R2 R1 R5 R4 ; dihedral along diagonal diff --git a/tests/data/martini3/naphthalene.gro b/tests/data/martini3/naphthalene.gro new file mode 100644 index 0000000..c4d3655 --- /dev/null +++ b/tests/data/martini3/naphthalene.gro @@ -0,0 +1,21 @@ +GROup of MAchos and Cynical Suckers + 18 + 1NAPH C1 1 0.001 0.243 -0.000 + 1NAPH H1 2 -0.052 0.337 -0.000 + 1NAPH C2 3 0.141 0.242 0.000 + 1NAPH H2 4 0.195 0.336 0.000 + 1NAPH C3 5 0.211 0.121 0.000 + 1NAPH H3 6 0.319 0.121 0.000 + 1NAPH C4 7 0.141 -0.001 0.000 + 1NAPH H4 8 0.197 -0.093 0.000 + 1NAPH C5 9 0.001 -0.001 0.000 + 1NAPH C6 10 -0.070 -0.122 0.000 + 1NAPH H6 11 -0.018 -0.217 0.000 + 1NAPH C7 12 -0.210 -0.122 0.000 + 1NAPH H7 13 -0.264 -0.215 0.000 + 1NAPH C8 14 -0.280 -0.001 0.000 + 1NAPH H8 15 -0.388 -0.001 0.000 + 1NAPH C9 16 -0.211 0.121 0.000 + 1NAPH H9 17 -0.266 0.214 0.000 + 1NAPH C10 18 -0.070 0.122 0.000 + 0.00000 0.00000 0.00000 diff --git a/tests/data/martini3/naphthalene.map b/tests/data/martini3/naphthalene.map new file mode 100644 index 0000000..04ef992 --- /dev/null +++ b/tests/data/martini3/naphthalene.map @@ -0,0 +1,6 @@ +[ NAPH ] +R1 TC4 C8 H8 C9 H9 +R2 TC4 C6 H6 C7 H7 +@v R3 TC4 R1 R2 R4 R5 +R4 TC4 C1 H1 C2 H2 +R5 TC4 C3 H3 C4 H4 diff --git a/tests/data/martini3/naphthalene_out.itp b/tests/data/martini3/naphthalene_out.itp new file mode 100644 index 0000000..445f5dd --- /dev/null +++ b/tests/data/martini3/naphthalene_out.itp @@ -0,0 +1,29 @@ +; +; Topology prepared automatically using PyCGTOOL +; James Graham 2016 +; University of Southampton +; https://github.com/jag1g13/pycgtool +; + +[ moleculetype ] +NAPH 1 + +[ atoms ] + 1 TC4 1 NAPH R1 1 0.000 + 2 TC4 1 NAPH R2 2 0.000 + 3 TC4 1 NAPH R3 3 0.000 0.000 + 4 TC4 1 NAPH R4 4 0.000 + 5 TC4 1 NAPH R5 5 0.000 + +[ virtual_sitesn ] + 3 1 1 2 4 5 + +[ exclusions ] +3 1 2 4 5 + +[ constraints ] + 1 2 1 0.29133 + 2 5 1 0.41260 + 5 4 1 0.29155 + 4 1 1 0.41273 + 1 5 1 0.50537 diff --git a/test/data/martini_aminoacids.map b/tests/data/martini_aminoacids.map similarity index 100% rename from test/data/martini_aminoacids.map rename to tests/data/martini_aminoacids.map diff --git a/test/data/martini_lipids.map b/tests/data/martini_lipids.map similarity index 100% rename from test/data/martini_lipids.map rename to tests/data/martini_lipids.map diff --git a/tests/data/membrane/AT_AA_POPE.itp b/tests/data/membrane/AT_AA_POPE.itp new file mode 100755 index 0000000..99859f7 --- /dev/null +++ b/tests/data/membrane/AT_AA_POPE.itp @@ -0,0 +1,1184 @@ +;; +;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 +;; +;; psf2itp.py +;; +;; Correspondance: +;; jul316@lehigh.edu or wonpil@lehigh.edu +;; +;; GROMACS topology file for POPE +;; + + +[ moleculetype ] +; name nrexcl +POPE 3 + +[ atoms ] +; nr type resnr residu atom cgnr charge mass + 1 NH3L 1 POPE N 1 -0.300 14.0070 ; qtot -0.300 + 2 HCL 1 POPE HN1 2 0.330 1.0080 ; qtot 0.030 + 3 HCL 1 POPE HN2 3 0.330 1.0080 ; qtot 0.360 + 4 HCL 1 POPE HN3 4 0.330 1.0080 ; qtot 0.690 + 5 CTL2 1 POPE C12 5 0.130 12.0110 ; qtot 0.820 + 6 HAL2 1 POPE H12A 6 0.090 1.0080 ; qtot 0.910 + 7 HAL2 1 POPE H12B 7 0.090 1.0080 ; qtot 1.000 + 8 CTL2 1 POPE C11 8 -0.080 12.0110 ; qtot 0.920 + 9 HAL2 1 POPE H11A 9 0.090 1.0080 ; qtot 1.010 + 10 HAL2 1 POPE H11B 10 0.090 1.0080 ; qtot 1.100 + 11 PL 1 POPE P 11 1.500 30.9740 ; qtot 2.600 + 12 O2L 1 POPE O13 12 -0.780 15.9994 ; qtot 1.820 + 13 O2L 1 POPE O14 13 -0.780 15.9994 ; qtot 1.040 + 14 OSLP 1 POPE O11 14 -0.570 15.9994 ; qtot 0.470 + 15 OSLP 1 POPE O12 15 -0.570 15.9994 ; qtot -0.100 + 16 CTL2 1 POPE C1 16 -0.080 12.0110 ; qtot -0.180 + 17 HAL2 1 POPE HA 17 0.090 1.0080 ; qtot -0.090 + 18 HAL2 1 POPE HB 18 0.090 1.0080 ; qtot 0.000 + 19 CTL1 1 POPE C2 19 0.170 12.0110 ; qtot 0.170 + 20 HAL1 1 POPE HS 20 0.090 1.0080 ; qtot 0.260 + 21 OSL 1 POPE O21 21 -0.490 15.9994 ; qtot -0.230 + 22 CL 1 POPE C21 22 0.900 12.0110 ; qtot 0.670 + 23 OBL 1 POPE O22 23 -0.630 15.9994 ; qtot 0.040 + 24 CTL2 1 POPE C22 24 -0.220 12.0110 ; qtot -0.180 + 25 HAL2 1 POPE H2R 25 0.090 1.0080 ; qtot -0.090 + 26 HAL2 1 POPE H2S 26 0.090 1.0080 ; qtot 0.000 + 27 CTL2 1 POPE C3 27 0.080 12.0110 ; qtot 0.080 + 28 HAL2 1 POPE HX 28 0.090 1.0080 ; qtot 0.170 + 29 HAL2 1 POPE HY 29 0.090 1.0080 ; qtot 0.260 + 30 OSL 1 POPE O31 30 -0.490 15.9994 ; qtot -0.230 + 31 CL 1 POPE C31 31 0.900 12.0110 ; qtot 0.670 + 32 OBL 1 POPE O32 32 -0.630 15.9994 ; qtot 0.040 + 33 CTL2 1 POPE C32 33 -0.220 12.0110 ; qtot -0.180 + 34 HAL2 1 POPE H2X 34 0.090 1.0080 ; qtot -0.090 + 35 HAL2 1 POPE H2Y 35 0.090 1.0080 ; qtot 0.000 + 36 CTL2 1 POPE C23 36 -0.180 12.0110 ; qtot -0.180 + 37 HAL2 1 POPE H3R 37 0.090 1.0080 ; qtot -0.090 + 38 HAL2 1 POPE H3S 38 0.090 1.0080 ; qtot 0.000 + 39 CTL2 1 POPE C24 39 -0.180 12.0110 ; qtot -0.180 + 40 HAL2 1 POPE H4R 40 0.090 1.0080 ; qtot -0.090 + 41 HAL2 1 POPE H4S 41 0.090 1.0080 ; qtot 0.000 + 42 CTL2 1 POPE C25 42 -0.180 12.0110 ; qtot -0.180 + 43 HAL2 1 POPE H5R 43 0.090 1.0080 ; qtot -0.090 + 44 HAL2 1 POPE H5S 44 0.090 1.0080 ; qtot 0.000 + 45 CTL2 1 POPE C26 45 -0.180 12.0110 ; qtot -0.180 + 46 HAL2 1 POPE H6R 46 0.090 1.0080 ; qtot -0.090 + 47 HAL2 1 POPE H6S 47 0.090 1.0080 ; qtot 0.000 + 48 CTL2 1 POPE C27 48 -0.180 12.0110 ; qtot -0.180 + 49 HAL2 1 POPE H7R 49 0.090 1.0080 ; qtot -0.090 + 50 HAL2 1 POPE H7S 50 0.090 1.0080 ; qtot 0.000 + 51 CTL2 1 POPE C28 51 -0.180 12.0110 ; qtot -0.180 + 52 HAL2 1 POPE H8R 52 0.090 1.0080 ; qtot -0.090 + 53 HAL2 1 POPE H8S 53 0.090 1.0080 ; qtot 0.000 + 54 CEL1 1 POPE C29 54 -0.150 12.0110 ; qtot -0.150 + 55 HEL1 1 POPE H91 55 0.150 1.0080 ; qtot 0.000 + 56 CEL1 1 POPE C210 56 -0.150 12.0110 ; qtot -0.150 + 57 HEL1 1 POPE H101 57 0.150 1.0080 ; qtot 0.000 + 58 CTL2 1 POPE C211 58 -0.180 12.0110 ; qtot -0.180 + 59 HAL2 1 POPE H11R 59 0.090 1.0080 ; qtot -0.090 + 60 HAL2 1 POPE H11S 60 0.090 1.0080 ; qtot 0.000 + 61 CTL2 1 POPE C212 61 -0.180 12.0110 ; qtot -0.180 + 62 HAL2 1 POPE H12R 62 0.090 1.0080 ; qtot -0.090 + 63 HAL2 1 POPE H12S 63 0.090 1.0080 ; qtot 0.000 + 64 CTL2 1 POPE C213 64 -0.180 12.0110 ; qtot -0.180 + 65 HAL2 1 POPE H13R 65 0.090 1.0080 ; qtot -0.090 + 66 HAL2 1 POPE H13S 66 0.090 1.0080 ; qtot 0.000 + 67 CTL2 1 POPE C214 67 -0.180 12.0110 ; qtot -0.180 + 68 HAL2 1 POPE H14R 68 0.090 1.0080 ; qtot -0.090 + 69 HAL2 1 POPE H14S 69 0.090 1.0080 ; qtot 0.000 + 70 CTL2 1 POPE C215 70 -0.180 12.0110 ; qtot -0.180 + 71 HAL2 1 POPE H15R 71 0.090 1.0080 ; qtot -0.090 + 72 HAL2 1 POPE H15S 72 0.090 1.0080 ; qtot 0.000 + 73 CTL2 1 POPE C216 73 -0.180 12.0110 ; qtot -0.180 + 74 HAL2 1 POPE H16R 74 0.090 1.0080 ; qtot -0.090 + 75 HAL2 1 POPE H16S 75 0.090 1.0080 ; qtot 0.000 + 76 CTL2 1 POPE C217 76 -0.180 12.0110 ; qtot -0.180 + 77 HAL2 1 POPE H17R 77 0.090 1.0080 ; qtot -0.090 + 78 HAL2 1 POPE H17S 78 0.090 1.0080 ; qtot 0.000 + 79 CTL3 1 POPE C218 79 -0.270 12.0110 ; qtot -0.270 + 80 HAL3 1 POPE H18R 80 0.090 1.0080 ; qtot -0.180 + 81 HAL3 1 POPE H18S 81 0.090 1.0080 ; qtot -0.090 + 82 HAL3 1 POPE H18T 82 0.090 1.0080 ; qtot 0.000 + 83 CTL2 1 POPE C33 83 -0.180 12.0110 ; qtot -0.180 + 84 HAL2 1 POPE H3X 84 0.090 1.0080 ; qtot -0.090 + 85 HAL2 1 POPE H3Y 85 0.090 1.0080 ; qtot 0.000 + 86 CTL2 1 POPE C34 86 -0.180 12.0110 ; qtot -0.180 + 87 HAL2 1 POPE H4X 87 0.090 1.0080 ; qtot -0.090 + 88 HAL2 1 POPE H4Y 88 0.090 1.0080 ; qtot 0.000 + 89 CTL2 1 POPE C35 89 -0.180 12.0110 ; qtot -0.180 + 90 HAL2 1 POPE H5X 90 0.090 1.0080 ; qtot -0.090 + 91 HAL2 1 POPE H5Y 91 0.090 1.0080 ; qtot 0.000 + 92 CTL2 1 POPE C36 92 -0.180 12.0110 ; qtot -0.180 + 93 HAL2 1 POPE H6X 93 0.090 1.0080 ; qtot -0.090 + 94 HAL2 1 POPE H6Y 94 0.090 1.0080 ; qtot 0.000 + 95 CTL2 1 POPE C37 95 -0.180 12.0110 ; qtot -0.180 + 96 HAL2 1 POPE H7X 96 0.090 1.0080 ; qtot -0.090 + 97 HAL2 1 POPE H7Y 97 0.090 1.0080 ; qtot 0.000 + 98 CTL2 1 POPE C38 98 -0.180 12.0110 ; qtot -0.180 + 99 HAL2 1 POPE H8X 99 0.090 1.0080 ; qtot -0.090 + 100 HAL2 1 POPE H8Y 100 0.090 1.0080 ; qtot 0.000 + 101 CTL2 1 POPE C39 101 -0.180 12.0110 ; qtot -0.180 + 102 HAL2 1 POPE H9X 102 0.090 1.0080 ; qtot -0.090 + 103 HAL2 1 POPE H9Y 103 0.090 1.0080 ; qtot 0.000 + 104 CTL2 1 POPE C310 104 -0.180 12.0110 ; qtot -0.180 + 105 HAL2 1 POPE H10X 105 0.090 1.0080 ; qtot -0.090 + 106 HAL2 1 POPE H10Y 106 0.090 1.0080 ; qtot 0.000 + 107 CTL2 1 POPE C311 107 -0.180 12.0110 ; qtot -0.180 + 108 HAL2 1 POPE H11X 108 0.090 1.0080 ; qtot -0.090 + 109 HAL2 1 POPE H11Y 109 0.090 1.0080 ; qtot 0.000 + 110 CTL2 1 POPE C312 110 -0.180 12.0110 ; qtot -0.180 + 111 HAL2 1 POPE H12X 111 0.090 1.0080 ; qtot -0.090 + 112 HAL2 1 POPE H12Y 112 0.090 1.0080 ; qtot 0.000 + 113 CTL2 1 POPE C313 113 -0.180 12.0110 ; qtot -0.180 + 114 HAL2 1 POPE H13X 114 0.090 1.0080 ; qtot -0.090 + 115 HAL2 1 POPE H13Y 115 0.090 1.0080 ; qtot 0.000 + 116 CTL2 1 POPE C314 116 -0.180 12.0110 ; qtot -0.180 + 117 HAL2 1 POPE H14X 117 0.090 1.0080 ; qtot -0.090 + 118 HAL2 1 POPE H14Y 118 0.090 1.0080 ; qtot 0.000 + 119 CTL2 1 POPE C315 119 -0.180 12.0110 ; qtot -0.180 + 120 HAL2 1 POPE H15X 120 0.090 1.0080 ; qtot -0.090 + 121 HAL2 1 POPE H15Y 121 0.090 1.0080 ; qtot 0.000 + 122 CTL3 1 POPE C316 122 -0.270 12.0110 ; qtot -0.270 + 123 HAL3 1 POPE H16X 123 0.090 1.0080 ; qtot -0.180 + 124 HAL3 1 POPE H16Y 124 0.090 1.0080 ; qtot -0.090 + 125 HAL3 1 POPE H16Z 125 0.090 1.0080 ; qtot 0.000 + +[ bonds ] +; ai aj funct b0 Kb + 1 2 1 + 1 3 1 + 1 4 1 + 1 5 1 + 5 6 1 + 5 7 1 + 5 8 1 + 8 9 1 + 8 10 1 + 8 15 1 + 11 12 1 + 11 13 1 + 11 14 1 + 11 15 1 + 14 16 1 + 16 17 1 + 16 18 1 + 16 19 1 + 19 20 1 + 19 21 1 + 19 27 1 + 21 22 1 + 22 23 1 + 22 24 1 + 24 25 1 + 24 26 1 + 24 36 1 + 27 28 1 + 27 29 1 + 27 30 1 + 30 31 1 + 31 32 1 + 31 33 1 + 33 34 1 + 33 35 1 + 33 83 1 + 36 37 1 + 36 38 1 + 36 39 1 + 39 40 1 + 39 41 1 + 39 42 1 + 42 43 1 + 42 44 1 + 42 45 1 + 45 46 1 + 45 47 1 + 45 48 1 + 48 49 1 + 48 50 1 + 48 51 1 + 51 52 1 + 51 53 1 + 51 54 1 + 54 55 1 + 54 56 1 + 56 57 1 + 56 58 1 + 58 59 1 + 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88 90 1 + 88 91 1 + 88 92 1 + 89 96 1 + 89 97 1 + 89 98 1 + 90 93 1 + 90 94 1 + 90 95 1 + 91 93 1 + 91 94 1 + 91 95 1 + 92 99 1 + 92 100 1 + 92 101 1 + 93 96 1 + 93 97 1 + 93 98 1 + 94 96 1 + 94 97 1 + 94 98 1 + 95 102 1 + 95 103 1 + 95 104 1 + 96 99 1 + 96 100 1 + 96 101 1 + 97 99 1 + 97 100 1 + 97 101 1 + 98 105 1 + 98 106 1 + 98 107 1 + 99 102 1 + 99 103 1 + 99 104 1 + 100 102 1 + 100 103 1 + 100 104 1 + 101 108 1 + 101 109 1 + 101 110 1 + 102 105 1 + 102 106 1 + 102 107 1 + 103 105 1 + 103 106 1 + 103 107 1 + 104 111 1 + 104 112 1 + 104 113 1 + 105 108 1 + 105 109 1 + 105 110 1 + 106 108 1 + 106 109 1 + 106 110 1 + 107 114 1 + 107 115 1 + 107 116 1 + 108 111 1 + 108 112 1 + 108 113 1 + 109 111 1 + 109 112 1 + 109 113 1 + 110 117 1 + 110 118 1 + 110 119 1 + 111 114 1 + 111 115 1 + 111 116 1 + 112 114 1 + 112 115 1 + 112 116 1 + 113 120 1 + 113 121 1 + 113 122 1 + 114 117 1 + 114 118 1 + 114 119 1 + 115 117 1 + 115 118 1 + 115 119 1 + 116 123 1 + 116 124 1 + 116 125 1 + 117 120 1 + 117 121 1 + 117 122 1 + 118 120 1 + 118 121 1 + 118 122 1 + 120 123 1 + 120 124 1 + 120 125 1 + 121 123 1 + 121 124 1 + 121 125 1 + +[ angles ] +; ai aj ak funct th0 cth S0 Kub + 2 1 3 5 + 2 1 4 5 + 2 1 5 5 + 3 1 4 5 + 3 1 5 5 + 4 1 5 5 + 1 5 6 5 + 1 5 7 5 + 1 5 8 5 + 6 5 7 5 + 6 5 8 5 + 7 5 8 5 + 5 8 9 5 + 5 8 10 5 + 5 8 15 5 + 9 8 10 5 + 9 8 15 5 + 10 8 15 5 + 12 11 13 5 + 12 11 14 5 + 12 11 15 5 + 13 11 14 5 + 13 11 15 5 + 14 11 15 5 + 11 14 16 5 + 8 15 11 5 + 14 16 17 5 + 14 16 18 5 + 14 16 19 5 + 17 16 18 5 + 17 16 19 5 + 18 16 19 5 + 16 19 20 5 + 16 19 21 5 + 16 19 27 5 + 20 19 21 5 + 20 19 27 5 + 21 19 27 5 + 19 21 22 5 + 21 22 23 5 + 21 22 24 5 + 23 22 24 5 + 22 24 25 5 + 22 24 26 5 + 22 24 36 5 + 25 24 26 5 + 25 24 36 5 + 26 24 36 5 + 19 27 28 5 + 19 27 29 5 + 19 27 30 5 + 28 27 29 5 + 28 27 30 5 + 29 27 30 5 + 27 30 31 5 + 30 31 32 5 + 30 31 33 5 + 32 31 33 5 + 31 33 34 5 + 31 33 35 5 + 31 33 83 5 + 34 33 35 5 + 34 33 83 5 + 35 33 83 5 + 24 36 37 5 + 24 36 38 5 + 24 36 39 5 + 37 36 38 5 + 37 36 39 5 + 38 36 39 5 + 36 39 40 5 + 36 39 41 5 + 36 39 42 5 + 40 39 41 5 + 40 39 42 5 + 41 39 42 5 + 39 42 43 5 + 39 42 44 5 + 39 42 45 5 + 43 42 44 5 + 43 42 45 5 + 44 42 45 5 + 42 45 46 5 + 42 45 47 5 + 42 45 48 5 + 46 45 47 5 + 46 45 48 5 + 47 45 48 5 + 45 48 49 5 + 45 48 50 5 + 45 48 51 5 + 49 48 50 5 + 49 48 51 5 + 50 48 51 5 + 48 51 52 5 + 48 51 53 5 + 48 51 54 5 + 52 51 53 5 + 52 51 54 5 + 53 51 54 5 + 51 54 55 5 + 51 54 56 5 + 55 54 56 5 + 54 56 57 5 + 54 56 58 5 + 57 56 58 5 + 56 58 59 5 + 56 58 60 5 + 56 58 61 5 + 59 58 60 5 + 59 58 61 5 + 60 58 61 5 + 58 61 62 5 + 58 61 63 5 + 58 61 64 5 + 62 61 63 5 + 62 61 64 5 + 63 61 64 5 + 61 64 65 5 + 61 64 66 5 + 61 64 67 5 + 65 64 66 5 + 65 64 67 5 + 66 64 67 5 + 64 67 68 5 + 64 67 69 5 + 64 67 70 5 + 68 67 69 5 + 68 67 70 5 + 69 67 70 5 + 67 70 71 5 + 67 70 72 5 + 67 70 73 5 + 71 70 72 5 + 71 70 73 5 + 72 70 73 5 + 70 73 74 5 + 70 73 75 5 + 70 73 76 5 + 74 73 75 5 + 74 73 76 5 + 75 73 76 5 + 73 76 77 5 + 73 76 78 5 + 73 76 79 5 + 77 76 78 5 + 77 76 79 5 + 78 76 79 5 + 76 79 80 5 + 76 79 81 5 + 76 79 82 5 + 80 79 81 5 + 80 79 82 5 + 81 79 82 5 + 33 83 84 5 + 33 83 85 5 + 33 83 86 5 + 84 83 85 5 + 84 83 86 5 + 85 83 86 5 + 83 86 87 5 + 83 86 88 5 + 83 86 89 5 + 87 86 88 5 + 87 86 89 5 + 88 86 89 5 + 86 89 90 5 + 86 89 91 5 + 86 89 92 5 + 90 89 91 5 + 90 89 92 5 + 91 89 92 5 + 89 92 93 5 + 89 92 94 5 + 89 92 95 5 + 93 92 94 5 + 93 92 95 5 + 94 92 95 5 + 92 95 96 5 + 92 95 97 5 + 92 95 98 5 + 96 95 97 5 + 96 95 98 5 + 97 95 98 5 + 95 98 99 5 + 95 98 100 5 + 95 98 101 5 + 99 98 100 5 + 99 98 101 5 + 100 98 101 5 + 98 101 102 5 + 98 101 103 5 + 98 101 104 5 + 102 101 103 5 + 102 101 104 5 + 103 101 104 5 + 101 104 105 5 + 101 104 106 5 + 101 104 107 5 + 105 104 106 5 + 105 104 107 5 + 106 104 107 5 + 104 107 108 5 + 104 107 109 5 + 104 107 110 5 + 108 107 109 5 + 108 107 110 5 + 109 107 110 5 + 107 110 111 5 + 107 110 112 5 + 107 110 113 5 + 111 110 112 5 + 111 110 113 5 + 112 110 113 5 + 110 113 114 5 + 110 113 115 5 + 110 113 116 5 + 114 113 115 5 + 114 113 116 5 + 115 113 116 5 + 113 116 117 5 + 113 116 118 5 + 113 116 119 5 + 117 116 118 5 + 117 116 119 5 + 118 116 119 5 + 116 119 120 5 + 116 119 121 5 + 116 119 122 5 + 120 119 121 5 + 120 119 122 5 + 121 119 122 5 + 119 122 123 5 + 119 122 124 5 + 119 122 125 5 + 123 122 124 5 + 123 122 125 5 + 124 122 125 5 + +[ dihedrals ] +; ai aj ak al funct phi0 cp mult + 2 1 5 6 9 + 2 1 5 7 9 + 2 1 5 8 9 + 3 1 5 6 9 + 3 1 5 7 9 + 3 1 5 8 9 + 4 1 5 6 9 + 4 1 5 7 9 + 4 1 5 8 9 + 1 5 8 9 9 + 1 5 8 10 9 + 1 5 8 15 9 + 6 5 8 9 9 + 6 5 8 10 9 + 6 5 8 15 9 + 7 5 8 9 9 + 7 5 8 10 9 + 7 5 8 15 9 + 5 8 15 11 9 + 9 8 15 11 9 + 10 8 15 11 9 + 12 11 14 16 9 + 13 11 14 16 9 + 15 11 14 16 9 + 11 14 16 17 9 + 11 14 16 18 9 + 11 14 16 19 9 + 8 15 11 12 9 + 8 15 11 13 9 + 8 15 11 14 9 + 14 16 19 20 9 + 14 16 19 21 9 + 14 16 19 27 9 + 17 16 19 20 9 + 17 16 19 21 9 + 17 16 19 27 9 + 18 16 19 20 9 + 18 16 19 21 9 + 18 16 19 27 9 + 16 19 21 22 9 + 20 19 21 22 9 + 16 19 27 28 9 + 16 19 27 29 9 + 16 19 27 30 9 + 20 19 27 28 9 + 20 19 27 29 9 + 20 19 27 30 9 + 21 19 27 28 9 + 21 19 27 29 9 + 21 19 27 30 9 + 22 21 19 27 9 + 19 21 22 23 9 + 19 21 22 24 9 + 21 22 24 25 9 + 21 22 24 26 9 + 21 22 24 36 9 + 23 22 24 25 9 + 23 22 24 26 9 + 23 22 24 36 9 + 22 24 36 37 9 + 22 24 36 38 9 + 22 24 36 39 9 + 25 24 36 37 9 + 25 24 36 38 9 + 25 24 36 39 9 + 26 24 36 37 9 + 26 24 36 38 9 + 26 24 36 39 9 + 19 27 30 31 9 + 28 27 30 31 9 + 29 27 30 31 9 + 27 30 31 32 9 + 27 30 31 33 9 + 30 31 33 34 9 + 30 31 33 35 9 + 30 31 33 83 9 + 32 31 33 34 9 + 32 31 33 35 9 + 32 31 33 83 9 + 31 33 83 84 9 + 31 33 83 85 9 + 31 33 83 86 9 + 34 33 83 84 9 + 34 33 83 85 9 + 34 33 83 86 9 + 35 33 83 84 9 + 35 33 83 85 9 + 35 33 83 86 9 + 24 36 39 40 9 + 24 36 39 41 9 + 24 36 39 42 9 + 37 36 39 40 9 + 37 36 39 41 9 + 37 36 39 42 9 + 38 36 39 40 9 + 38 36 39 41 9 + 38 36 39 42 9 + 36 39 42 43 9 + 36 39 42 44 9 + 36 39 42 45 9 + 40 39 42 43 9 + 40 39 42 44 9 + 40 39 42 45 9 + 41 39 42 43 9 + 41 39 42 44 9 + 41 39 42 45 9 + 39 42 45 46 9 + 39 42 45 47 9 + 39 42 45 48 9 + 43 42 45 46 9 + 43 42 45 47 9 + 43 42 45 48 9 + 44 42 45 46 9 + 44 42 45 47 9 + 44 42 45 48 9 + 42 45 48 49 9 + 42 45 48 50 9 + 42 45 48 51 9 + 46 45 48 49 9 + 46 45 48 50 9 + 46 45 48 51 9 + 47 45 48 49 9 + 47 45 48 50 9 + 47 45 48 51 9 + 45 48 51 52 9 + 45 48 51 53 9 + 45 48 51 54 9 + 49 48 51 52 9 + 49 48 51 53 9 + 49 48 51 54 9 + 50 48 51 52 9 + 50 48 51 53 9 + 50 48 51 54 9 + 48 51 54 55 9 + 48 51 54 56 9 + 52 51 54 55 9 + 52 51 54 56 9 + 53 51 54 55 9 + 53 51 54 56 9 + 51 54 56 57 9 + 51 54 56 58 9 + 55 54 56 57 9 + 55 54 56 58 9 + 54 56 58 59 9 + 54 56 58 60 9 + 54 56 58 61 9 + 57 56 58 59 9 + 57 56 58 60 9 + 57 56 58 61 9 + 56 58 61 62 9 + 56 58 61 63 9 + 56 58 61 64 9 + 59 58 61 62 9 + 59 58 61 63 9 + 59 58 61 64 9 + 60 58 61 62 9 + 60 58 61 63 9 + 60 58 61 64 9 + 58 61 64 65 9 + 58 61 64 66 9 + 58 61 64 67 9 + 62 61 64 65 9 + 62 61 64 66 9 + 62 61 64 67 9 + 63 61 64 65 9 + 63 61 64 66 9 + 63 61 64 67 9 + 61 64 67 68 9 + 61 64 67 69 9 + 61 64 67 70 9 + 65 64 67 68 9 + 65 64 67 69 9 + 65 64 67 70 9 + 66 64 67 68 9 + 66 64 67 69 9 + 66 64 67 70 9 + 64 67 70 71 9 + 64 67 70 72 9 + 64 67 70 73 9 + 68 67 70 71 9 + 68 67 70 72 9 + 68 67 70 73 9 + 69 67 70 71 9 + 69 67 70 72 9 + 69 67 70 73 9 + 67 70 73 74 9 + 67 70 73 75 9 + 67 70 73 76 9 + 71 70 73 74 9 + 71 70 73 75 9 + 71 70 73 76 9 + 72 70 73 74 9 + 72 70 73 75 9 + 72 70 73 76 9 + 70 73 76 77 9 + 70 73 76 78 9 + 70 73 76 79 9 + 74 73 76 77 9 + 74 73 76 78 9 + 74 73 76 79 9 + 75 73 76 77 9 + 75 73 76 78 9 + 75 73 76 79 9 + 73 76 79 80 9 + 73 76 79 81 9 + 73 76 79 82 9 + 77 76 79 80 9 + 77 76 79 81 9 + 77 76 79 82 9 + 78 76 79 80 9 + 78 76 79 81 9 + 78 76 79 82 9 + 33 83 86 87 9 + 33 83 86 88 9 + 33 83 86 89 9 + 84 83 86 87 9 + 84 83 86 88 9 + 84 83 86 89 9 + 85 83 86 87 9 + 85 83 86 88 9 + 85 83 86 89 9 + 83 86 89 90 9 + 83 86 89 91 9 + 83 86 89 92 9 + 87 86 89 90 9 + 87 86 89 91 9 + 87 86 89 92 9 + 88 86 89 90 9 + 88 86 89 91 9 + 88 86 89 92 9 + 86 89 92 93 9 + 86 89 92 94 9 + 86 89 92 95 9 + 90 89 92 93 9 + 90 89 92 94 9 + 90 89 92 95 9 + 91 89 92 93 9 + 91 89 92 94 9 + 91 89 92 95 9 + 89 92 95 96 9 + 89 92 95 97 9 + 89 92 95 98 9 + 93 92 95 96 9 + 93 92 95 97 9 + 93 92 95 98 9 + 94 92 95 96 9 + 94 92 95 97 9 + 94 92 95 98 9 + 92 95 98 99 9 + 92 95 98 100 9 + 92 95 98 101 9 + 96 95 98 99 9 + 96 95 98 100 9 + 96 95 98 101 9 + 97 95 98 99 9 + 97 95 98 100 9 + 97 95 98 101 9 + 95 98 101 102 9 + 95 98 101 103 9 + 95 98 101 104 9 + 99 98 101 102 9 + 99 98 101 103 9 + 99 98 101 104 9 + 100 98 101 102 9 + 100 98 101 103 9 + 100 98 101 104 9 + 98 101 104 105 9 + 98 101 104 106 9 + 98 101 104 107 9 + 102 101 104 105 9 + 102 101 104 106 9 + 102 101 104 107 9 + 103 101 104 105 9 + 103 101 104 106 9 + 103 101 104 107 9 + 101 104 107 108 9 + 101 104 107 109 9 + 101 104 107 110 9 + 105 104 107 108 9 + 105 104 107 109 9 + 105 104 107 110 9 + 106 104 107 108 9 + 106 104 107 109 9 + 106 104 107 110 9 + 104 107 110 111 9 + 104 107 110 112 9 + 104 107 110 113 9 + 108 107 110 111 9 + 108 107 110 112 9 + 108 107 110 113 9 + 109 107 110 111 9 + 109 107 110 112 9 + 109 107 110 113 9 + 107 110 113 114 9 + 107 110 113 115 9 + 107 110 113 116 9 + 111 110 113 114 9 + 111 110 113 115 9 + 111 110 113 116 9 + 112 110 113 114 9 + 112 110 113 115 9 + 112 110 113 116 9 + 110 113 116 117 9 + 110 113 116 118 9 + 110 113 116 119 9 + 114 113 116 117 9 + 114 113 116 118 9 + 114 113 116 119 9 + 115 113 116 117 9 + 115 113 116 118 9 + 115 113 116 119 9 + 113 116 119 120 9 + 113 116 119 121 9 + 113 116 119 122 9 + 117 116 119 120 9 + 117 116 119 121 9 + 117 116 119 122 9 + 118 116 119 120 9 + 118 116 119 121 9 + 118 116 119 122 9 + 116 119 122 123 9 + 116 119 122 124 9 + 116 119 122 125 9 + 120 119 122 123 9 + 120 119 122 124 9 + 120 119 122 125 9 + 121 119 122 123 9 + 121 119 122 124 9 + 121 119 122 125 9 + +[ dihedrals ] +; ai aj ak al funct q0 cq + 22 21 24 23 2 + 31 30 33 32 2 + +;#ifdef REST_ON +;#include "../restraints/POPE_rest.itp" +;#endif diff --git a/tests/data/membrane/AT_AA_POPG.itp b/tests/data/membrane/AT_AA_POPG.itp new file mode 100755 index 0000000..a6d0b0a --- /dev/null +++ b/tests/data/membrane/AT_AA_POPG.itp @@ -0,0 +1,1202 @@ +;; +;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 +;; +;; psf2itp.py +;; +;; Correspondance: +;; jul316@lehigh.edu or wonpil@lehigh.edu +;; +;; GROMACS topology file for POPG +;; + + +[ moleculetype ] +; name nrexcl +POPG 3 + +[ atoms ] +; nr type resnr residu atom cgnr charge mass + 1 CTL2 1 POPG C13 1 0.050 12.0110 ; qtot 0.050 + 2 HAL2 1 POPG H13A 2 0.090 1.0080 ; qtot 0.140 + 3 HAL2 1 POPG H13B 3 0.090 1.0080 ; qtot 0.230 + 4 OHL 1 POPG OC3 4 -0.650 15.9994 ; qtot -0.420 + 5 HOL 1 POPG HO3 5 0.420 1.0080 ; qtot -0.000 + 6 CTL1 1 POPG C12 6 0.140 12.0110 ; qtot 0.140 + 7 HAL1 1 POPG H12A 7 0.090 1.0080 ; qtot 0.230 + 8 OHL 1 POPG OC2 8 -0.650 15.9994 ; qtot -0.420 + 9 HOL 1 POPG HO2 9 0.420 1.0080 ; qtot -0.000 + 10 CTL2 1 POPG C11 10 -0.080 12.0110 ; qtot -0.080 + 11 HAL2 1 POPG H11A 11 0.090 1.0080 ; qtot 0.010 + 12 HAL2 1 POPG H11B 12 0.090 1.0080 ; qtot 0.100 + 13 PL 1 POPG P 13 1.500 30.9740 ; qtot 1.600 + 14 O2L 1 POPG O13 14 -0.780 15.9994 ; qtot 0.820 + 15 O2L 1 POPG O14 15 -0.780 15.9994 ; qtot 0.040 + 16 OSLP 1 POPG O12 16 -0.570 15.9994 ; qtot -0.530 + 17 OSLP 1 POPG O11 17 -0.570 15.9994 ; qtot -1.100 + 18 CTL2 1 POPG C1 18 -0.080 12.0110 ; qtot -1.180 + 19 HAL2 1 POPG HA 19 0.090 1.0080 ; qtot -1.090 + 20 HAL2 1 POPG HB 20 0.090 1.0080 ; qtot -1.000 + 21 CTL1 1 POPG C2 21 0.170 12.0110 ; qtot -0.830 + 22 HAL1 1 POPG HS 22 0.090 1.0080 ; qtot -0.740 + 23 OSL 1 POPG O21 23 -0.490 15.9994 ; qtot -1.230 + 24 CL 1 POPG C21 24 0.900 12.0110 ; qtot -0.330 + 25 OBL 1 POPG O22 25 -0.630 15.9994 ; qtot -0.960 + 26 CTL2 1 POPG C22 26 -0.220 12.0110 ; qtot -1.180 + 27 HAL2 1 POPG H2R 27 0.090 1.0080 ; qtot -1.090 + 28 HAL2 1 POPG H2S 28 0.090 1.0080 ; qtot -1.000 + 29 CTL2 1 POPG C3 29 0.080 12.0110 ; qtot -0.920 + 30 HAL2 1 POPG HX 30 0.090 1.0080 ; qtot -0.830 + 31 HAL2 1 POPG HY 31 0.090 1.0080 ; qtot -0.740 + 32 OSL 1 POPG O31 32 -0.490 15.9994 ; qtot -1.230 + 33 CL 1 POPG C31 33 0.900 12.0110 ; qtot -0.330 + 34 OBL 1 POPG O32 34 -0.630 15.9994 ; qtot -0.960 + 35 CTL2 1 POPG C32 35 -0.220 12.0110 ; qtot -1.180 + 36 HAL2 1 POPG H2X 36 0.090 1.0080 ; qtot -1.090 + 37 HAL2 1 POPG H2Y 37 0.090 1.0080 ; qtot -1.000 + 38 CTL2 1 POPG C23 38 -0.180 12.0110 ; qtot -1.180 + 39 HAL2 1 POPG H3R 39 0.090 1.0080 ; qtot -1.090 + 40 HAL2 1 POPG H3S 40 0.090 1.0080 ; qtot -1.000 + 41 CTL2 1 POPG C24 41 -0.180 12.0110 ; qtot -1.180 + 42 HAL2 1 POPG H4R 42 0.090 1.0080 ; qtot -1.090 + 43 HAL2 1 POPG H4S 43 0.090 1.0080 ; qtot -1.000 + 44 CTL2 1 POPG C25 44 -0.180 12.0110 ; qtot -1.180 + 45 HAL2 1 POPG H5R 45 0.090 1.0080 ; qtot -1.090 + 46 HAL2 1 POPG H5S 46 0.090 1.0080 ; qtot -1.000 + 47 CTL2 1 POPG C26 47 -0.180 12.0110 ; qtot -1.180 + 48 HAL2 1 POPG H6R 48 0.090 1.0080 ; qtot -1.090 + 49 HAL2 1 POPG H6S 49 0.090 1.0080 ; qtot -1.000 + 50 CTL2 1 POPG C27 50 -0.180 12.0110 ; qtot -1.180 + 51 HAL2 1 POPG H7R 51 0.090 1.0080 ; qtot -1.090 + 52 HAL2 1 POPG H7S 52 0.090 1.0080 ; qtot -1.000 + 53 CTL2 1 POPG C28 53 -0.180 12.0110 ; qtot -1.180 + 54 HAL2 1 POPG H8R 54 0.090 1.0080 ; qtot -1.090 + 55 HAL2 1 POPG H8S 55 0.090 1.0080 ; qtot -1.000 + 56 CEL1 1 POPG C29 56 -0.150 12.0110 ; qtot -1.150 + 57 HEL1 1 POPG H91 57 0.150 1.0080 ; qtot -1.000 + 58 CEL1 1 POPG C210 58 -0.150 12.0110 ; qtot -1.150 + 59 HEL1 1 POPG H101 59 0.150 1.0080 ; qtot -1.000 + 60 CTL2 1 POPG C211 60 -0.180 12.0110 ; qtot -1.180 + 61 HAL2 1 POPG H11R 61 0.090 1.0080 ; qtot -1.090 + 62 HAL2 1 POPG H11S 62 0.090 1.0080 ; qtot -1.000 + 63 CTL2 1 POPG C212 63 -0.180 12.0110 ; qtot -1.180 + 64 HAL2 1 POPG H12R 64 0.090 1.0080 ; qtot -1.090 + 65 HAL2 1 POPG H12S 65 0.090 1.0080 ; qtot -1.000 + 66 CTL2 1 POPG C213 66 -0.180 12.0110 ; qtot -1.180 + 67 HAL2 1 POPG H13R 67 0.090 1.0080 ; qtot -1.090 + 68 HAL2 1 POPG H13S 68 0.090 1.0080 ; qtot -1.000 + 69 CTL2 1 POPG C214 69 -0.180 12.0110 ; qtot -1.180 + 70 HAL2 1 POPG H14R 70 0.090 1.0080 ; qtot -1.090 + 71 HAL2 1 POPG H14S 71 0.090 1.0080 ; qtot -1.000 + 72 CTL2 1 POPG C215 72 -0.180 12.0110 ; qtot -1.180 + 73 HAL2 1 POPG H15R 73 0.090 1.0080 ; qtot -1.090 + 74 HAL2 1 POPG H15S 74 0.090 1.0080 ; qtot -1.000 + 75 CTL2 1 POPG C216 75 -0.180 12.0110 ; qtot -1.180 + 76 HAL2 1 POPG H16R 76 0.090 1.0080 ; qtot -1.090 + 77 HAL2 1 POPG H16S 77 0.090 1.0080 ; qtot -1.000 + 78 CTL2 1 POPG C217 78 -0.180 12.0110 ; qtot -1.180 + 79 HAL2 1 POPG H17R 79 0.090 1.0080 ; qtot -1.090 + 80 HAL2 1 POPG H17S 80 0.090 1.0080 ; qtot -1.000 + 81 CTL3 1 POPG C218 81 -0.270 12.0110 ; qtot -1.270 + 82 HAL3 1 POPG H18R 82 0.090 1.0080 ; qtot -1.180 + 83 HAL3 1 POPG H18S 83 0.090 1.0080 ; qtot -1.090 + 84 HAL3 1 POPG H18T 84 0.090 1.0080 ; qtot -1.000 + 85 CTL2 1 POPG C33 85 -0.180 12.0110 ; qtot -1.180 + 86 HAL2 1 POPG H3X 86 0.090 1.0080 ; qtot -1.090 + 87 HAL2 1 POPG H3Y 87 0.090 1.0080 ; qtot -1.000 + 88 CTL2 1 POPG C34 88 -0.180 12.0110 ; qtot -1.180 + 89 HAL2 1 POPG H4X 89 0.090 1.0080 ; qtot -1.090 + 90 HAL2 1 POPG H4Y 90 0.090 1.0080 ; qtot -1.000 + 91 CTL2 1 POPG C35 91 -0.180 12.0110 ; qtot -1.180 + 92 HAL2 1 POPG H5X 92 0.090 1.0080 ; qtot -1.090 + 93 HAL2 1 POPG H5Y 93 0.090 1.0080 ; qtot -1.000 + 94 CTL2 1 POPG C36 94 -0.180 12.0110 ; qtot -1.180 + 95 HAL2 1 POPG H6X 95 0.090 1.0080 ; qtot -1.090 + 96 HAL2 1 POPG H6Y 96 0.090 1.0080 ; qtot -1.000 + 97 CTL2 1 POPG C37 97 -0.180 12.0110 ; qtot -1.180 + 98 HAL2 1 POPG H7X 98 0.090 1.0080 ; qtot -1.090 + 99 HAL2 1 POPG H7Y 99 0.090 1.0080 ; qtot -1.000 + 100 CTL2 1 POPG C38 100 -0.180 12.0110 ; qtot -1.180 + 101 HAL2 1 POPG H8X 101 0.090 1.0080 ; qtot -1.090 + 102 HAL2 1 POPG H8Y 102 0.090 1.0080 ; qtot -1.000 + 103 CTL2 1 POPG C39 103 -0.180 12.0110 ; qtot -1.180 + 104 HAL2 1 POPG H9X 104 0.090 1.0080 ; qtot -1.090 + 105 HAL2 1 POPG H9Y 105 0.090 1.0080 ; qtot -1.000 + 106 CTL2 1 POPG C310 106 -0.180 12.0110 ; qtot -1.180 + 107 HAL2 1 POPG H10X 107 0.090 1.0080 ; qtot -1.090 + 108 HAL2 1 POPG H10Y 108 0.090 1.0080 ; qtot -1.000 + 109 CTL2 1 POPG C311 109 -0.180 12.0110 ; qtot -1.180 + 110 HAL2 1 POPG H11X 110 0.090 1.0080 ; qtot -1.090 + 111 HAL2 1 POPG H11Y 111 0.090 1.0080 ; qtot -1.000 + 112 CTL2 1 POPG C312 112 -0.180 12.0110 ; qtot -1.180 + 113 HAL2 1 POPG H12X 113 0.090 1.0080 ; qtot -1.090 + 114 HAL2 1 POPG H12Y 114 0.090 1.0080 ; qtot -1.000 + 115 CTL2 1 POPG C313 115 -0.180 12.0110 ; qtot -1.180 + 116 HAL2 1 POPG H13X 116 0.090 1.0080 ; qtot -1.090 + 117 HAL2 1 POPG H13Y 117 0.090 1.0080 ; qtot -1.000 + 118 CTL2 1 POPG C314 118 -0.180 12.0110 ; qtot -1.180 + 119 HAL2 1 POPG H14X 119 0.090 1.0080 ; qtot -1.090 + 120 HAL2 1 POPG H14Y 120 0.090 1.0080 ; qtot -1.000 + 121 CTL2 1 POPG C315 121 -0.180 12.0110 ; qtot -1.180 + 122 HAL2 1 POPG H15X 122 0.090 1.0080 ; qtot -1.090 + 123 HAL2 1 POPG H15Y 123 0.090 1.0080 ; qtot -1.000 + 124 CTL3 1 POPG C316 124 -0.270 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25 2 + 33 32 35 34 2 + +;#ifdef REST_ON +;#include "../restraints/POPG_rest.itp" +;#endif diff --git a/tests/data/membrane/PII_charmm36.itp b/tests/data/membrane/PII_charmm36.itp new file mode 100755 index 0000000..271414e --- /dev/null +++ b/tests/data/membrane/PII_charmm36.itp @@ -0,0 +1,2542 @@ +[ moleculetype ] +; Name nrexcl + PII 3 + +[ atoms ] +; 283 atoms + 1 CC3161 1 PII C13 1 0.1400 12.0110 + 2 HCA1 1 PII H13 2 0.0900 1.0080 + 3 OC311 1 PII O13 3 -0.6500 15.9994 + 4 HCP1 1 PII HO13 4 0.4200 1.0080 + 5 CC3161 1 PII C14 5 0.1400 12.0110 + 6 HCA1 1 PII H14 6 0.0900 1.0080 + 7 OC311 1 PII O14 7 -0.6500 15.9994 + 8 HCP1 1 PII HO14 8 0.4200 1.0080 + 9 CC321 1 PII C16 9 0.0500 12.0110 + 10 HCA2 1 PII H161 10 0.0900 1.0080 + 11 HCA2 1 PII H162 11 0.0900 1.0080 + 12 OC311 1 PII O16 12 -0.6500 15.9994 + 13 HCP1 1 PII HO16 13 0.4200 1.0080 + 14 CC3161 1 PII C12 14 0.0700 12.0110 + 15 HCA1 1 PII H12 15 0.0900 1.0080 + 16 NC2D1 1 PII N17 16 -0.4700 14.0070 + 17 HCP1 1 PII H17 17 0.3100 1.0080 + 18 CC2O1 1 PII C18 18 0.5100 12.0110 + 19 OC2D1 1 PII O18 19 -0.5100 15.9994 + 20 CC331 1 PII C19 20 -0.2700 12.0110 + 21 HCA3 1 PII H191 21 0.0900 1.0080 + 22 HCA3 1 PII H192 22 0.0900 1.0080 + 23 HCA3 1 PII H193 23 0.0900 1.0080 + 24 CC3162 1 PII C11 24 0.2900 12.0110 + 25 HCA1 1 PII H11 25 0.0900 1.0080 + 26 OC3C61 1 PII O15 26 -0.4000 15.9994 + 27 CC3163 1 PII C15 27 0.1100 12.0110 + 28 HCA1 1 PII H15 28 0.0900 1.0080 + 29 OC301 1 PII O24 29 -0.3600 15.9994 + 30 CC3161 1 PII C24 30 0.0900 12.0110 + 31 HCA1 1 PII H24 31 0.0900 1.0080 + 32 CC321 1 PII C26 32 0.0500 12.0110 + 33 HCA2 1 PII H261 33 0.0900 1.0080 + 34 HCA2 1 PII H262 34 0.0900 1.0080 + 35 OC311 1 PII O26 35 -0.6500 15.9994 + 36 HCP1 1 PII HO26 36 0.4200 1.0080 + 37 CC3161 1 PII C22 37 0.0700 12.0110 + 38 HCA1 1 PII H22 38 0.0900 1.0080 + 39 NC2D1 1 PII N27 39 -0.4700 14.0070 + 40 HCP1 1 PII H27 40 0.3100 1.0080 + 41 CC2O1 1 PII C28 41 0.5100 12.0110 + 42 OC2D1 1 PII O28 42 -0.5100 15.9994 + 43 CC331 1 PII C29 43 -0.2700 12.0110 + 44 HCA3 1 PII H291 44 0.0900 1.0080 + 45 HCA3 1 PII H292 45 0.0900 1.0080 + 46 HCA3 1 PII H293 46 0.0900 1.0080 + 47 CC3161 1 PII C23 47 0.0900 12.0110 + 48 HCA1 1 PII H23 48 0.0900 1.0080 + 49 OC301 1 PII O23 49 -0.3600 15.9994 + 50 CT1 1 PII C31 50 0.0900 12.0110 + 51 HA1 1 PII H31 51 0.0900 1.0080 + 52 CT3 1 PII C32 52 -0.2700 12.0110 + 53 HA3 1 PII H321 53 0.0900 1.0080 + 54 HA3 1 PII H322 54 0.0900 1.0080 + 55 HA3 1 PII H323 55 0.0900 1.0080 + 56 C 1 PII C 56 0.5100 12.0110 + 57 O 1 PII O33 57 -0.5100 15.9990 + 58 CC3163 1 PII C25 58 0.1100 12.0110 + 59 HCA1 1 PII H25 59 0.0900 1.0080 + 60 OC3C61 1 PII O25 60 -0.4000 15.9994 + 61 CC3162 1 PII C21 61 0.2200 12.0110 + 62 HCA1 1 PII H21 62 0.0900 1.0080 + 63 OC30P 1 PII O41 63 -0.6200 15.9994 + 64 OG2P1 1 PII O42 64 -0.8200 15.9994 + 65 OG2P1 1 PII O43 65 -0.8200 15.9994 + 66 PG1 1 PII P44 66 1.5000 30.9738 + 67 OG304 1 PII O45 67 -0.6800 15.9994 + 68 OG2P1 1 PII O46 68 -0.8200 15.9994 + 69 OG2P1 1 PII O47 69 -0.8200 15.9994 + 70 PG1 1 PII P48 70 1.5000 30.9738 + 71 OG303 1 PII O49 71 -0.6200 15.9994 + 72 CTL2 1 PII C51 72 -0.0900 12.0110 + 73 HAL2 1 PII H511 73 0.0900 1.0080 + 74 HAL2 1 PII H512 74 0.0900 1.0080 + 75 CEL1 1 PII C52 75 -0.1500 12.0110 + 76 HEL1 1 PII H521 76 0.1500 1.0080 + 77 CEL1 1 PII C53 77 0.0000 12.0110 + 78 CTL3 1 PII C530 78 -0.2700 12.0110 + 79 HAL3 1 PII H530 79 0.0900 1.0080 + 80 HAL3 1 PII H531 80 0.0900 1.0080 + 81 HAL3 1 PII H532 81 0.0900 1.0080 + 82 CTL2 1 PII C54 82 -0.1800 12.0110 + 83 HAL2 1 PII H541 83 0.0900 1.0080 + 84 HAL2 1 PII H542 84 0.0900 1.0080 + 85 CTL2 1 PII C55 85 -0.1800 12.0110 + 86 HAL2 1 PII H551 86 0.0900 1.0080 + 87 HAL2 1 PII H552 87 0.0900 1.0080 + 88 CEL1 1 PII C56 88 -0.1500 12.0110 + 89 HEL1 1 PII H561 89 0.1500 1.0080 + 90 CEL1 1 PII C57 90 0.0000 12.0110 + 91 CTL3 1 PII C570 91 -0.2700 12.0110 + 92 HAL3 1 PII H570 92 0.0900 1.0080 + 93 HAL3 1 PII H571 93 0.0900 1.0080 + 94 HAL3 1 PII H572 94 0.0900 1.0080 + 95 CTL2 1 PII C58 95 -0.1800 12.0110 + 96 HAL2 1 PII H581 96 0.0900 1.0080 + 97 HAL2 1 PII H582 97 0.0900 1.0080 + 98 CTL2 1 PII C59 98 -0.1800 12.0110 + 99 HAL2 1 PII H591 99 0.0900 1.0080 + 100 HAL2 1 PII H592 100 0.0900 1.0080 + 101 CEL1 1 PII C60 101 -0.1500 12.0110 + 102 HEL1 1 PII H601 102 0.1500 1.0080 + 103 CEL1 1 PII C61 103 0.0000 12.0110 + 104 CTL3 1 PII C610 104 -0.2700 12.0110 + 105 HAL3 1 PII H610 105 0.0900 1.0080 + 106 HAL3 1 PII H611 106 0.0900 1.0080 + 107 HAL3 1 PII H612 107 0.0900 1.0080 + 108 CTL2 1 PII C62 108 -0.1800 12.0110 + 109 HAL2 1 PII H621 109 0.0900 1.0080 + 110 HAL2 1 PII H622 110 0.0900 1.0080 + 111 CTL2 1 PII C63 111 -0.1800 12.0110 + 112 HAL2 1 PII H631 112 0.0900 1.0080 + 113 HAL2 1 PII H632 113 0.0900 1.0080 + 114 CEL1 1 PII C64 114 -0.1500 12.0110 + 115 HEL1 1 PII H641 115 0.1500 1.0080 + 116 CEL1 1 PII C65 116 0.0000 12.0110 + 117 CTL3 1 PII C650 117 -0.2700 12.0110 + 118 HAL3 1 PII H650 118 0.0900 1.0080 + 119 HAL3 1 PII H651 119 0.0900 1.0080 + 120 HAL3 1 PII H652 120 0.0900 1.0080 + 121 CTL2 1 PII C66 121 -0.1800 12.0110 + 122 HAL2 1 PII H661 122 0.0900 1.0080 + 123 HAL2 1 PII H662 123 0.0900 1.0080 + 124 CTL2 1 PII C67 124 -0.1800 12.0110 + 125 HAL2 1 PII H671 125 0.0900 1.0080 + 126 HAL2 1 PII H672 126 0.0900 1.0080 + 127 CEL1 1 PII C68 127 -0.1500 12.0110 + 128 HEL1 1 PII H681 128 0.1500 1.0080 + 129 CEL1 1 PII C69 129 0.0000 12.0110 + 130 CTL3 1 PII C690 130 -0.2700 12.0110 + 131 HAL3 1 PII H690 131 0.0900 1.0080 + 132 HAL3 1 PII H691 132 0.0900 1.0080 + 133 HAL3 1 PII H692 133 0.0900 1.0080 + 134 CTL2 1 PII C70 134 -0.1800 12.0110 + 135 HAL2 1 PII H701 135 0.0900 1.0080 + 136 HAL2 1 PII H702 136 0.0900 1.0080 + 137 CTL2 1 PII C71 137 -0.1800 12.0110 + 138 HAL2 1 PII H711 138 0.0900 1.0080 + 139 HAL2 1 PII H712 139 0.0900 1.0080 + 140 CEL1 1 PII C72 140 -0.1500 12.0110 + 141 HEL1 1 PII H721 141 0.1500 1.0080 + 142 CEL1 1 PII C73 142 0.0000 12.0110 + 143 CTL3 1 PII C730 143 -0.2700 12.0110 + 144 HAL3 1 PII H730 144 0.0900 1.0080 + 145 HAL3 1 PII H731 145 0.0900 1.0080 + 146 HAL3 1 PII H732 146 0.0900 1.0080 + 147 CTL2 1 PII C74 147 -0.1800 12.0110 + 148 HAL2 1 PII H741 148 0.0900 1.0080 + 149 HAL2 1 PII H742 149 0.0900 1.0080 + 150 CTL2 1 PII C75 150 -0.1800 12.0110 + 151 HAL2 1 PII H751 151 0.0900 1.0080 + 152 HAL2 1 PII H752 152 0.0900 1.0080 + 153 CEL1 1 PII C76 153 -0.1500 12.0110 + 154 HEL1 1 PII H761 154 0.1500 1.0080 + 155 CEL1 1 PII C77 155 0.0000 12.0110 + 156 CTL3 1 PII C770 156 -0.2700 12.0110 + 157 HAL3 1 PII H770 157 0.0900 1.0080 + 158 HAL3 1 PII H771 158 0.0900 1.0080 + 159 HAL3 1 PII H772 159 0.0900 1.0080 + 160 CTL2 1 PII C78 160 -0.1800 12.0110 + 161 HAL2 1 PII H781 161 0.0900 1.0080 + 162 HAL2 1 PII H782 162 0.0900 1.0080 + 163 CTL2 1 PII C79 163 -0.1800 12.0110 + 164 HAL2 1 PII H791 164 0.0900 1.0080 + 165 HAL2 1 PII H792 165 0.0900 1.0080 + 166 CEL1 1 PII C80 166 -0.1500 12.0110 + 167 HEL1 1 PII H801 167 0.1500 1.0080 + 168 CEL1 1 PII C81 168 0.0000 12.0110 + 169 CTL3 1 PII C810 169 -0.2700 12.0110 + 170 HAL3 1 PII H810 170 0.0900 1.0080 + 171 HAL3 1 PII H811 171 0.0900 1.0080 + 172 HAL3 1 PII H812 172 0.0900 1.0080 + 173 CTL2 1 PII C82 173 -0.1800 12.0110 + 174 HAL2 1 PII H821 174 0.0900 1.0080 + 175 HAL2 1 PII H822 175 0.0900 1.0080 + 176 CTL2 1 PII C83 176 -0.1800 12.0110 + 177 HAL2 1 PII H831 177 0.0900 1.0080 + 178 HAL2 1 PII H832 178 0.0900 1.0080 + 179 CEL1 1 PII C84 179 -0.1500 12.0110 + 180 HEL1 1 PII H841 180 0.1500 1.0080 + 181 CEL1 1 PII C85 181 0.0000 12.0110 + 182 CTL3 1 PII C850 182 -0.2700 12.0110 + 183 HAL3 1 PII H850 183 0.0900 1.0080 + 184 HAL3 1 PII H851 184 0.0900 1.0080 + 185 HAL3 1 PII H852 185 0.0900 1.0080 + 186 CTL2 1 PII C86 186 -0.1800 12.0110 + 187 HAL2 1 PII H861 187 0.0900 1.0080 + 188 HAL2 1 PII H862 188 0.0900 1.0080 + 189 CTL2 1 PII C87 189 -0.1800 12.0110 + 190 HAL2 1 PII H871 190 0.0900 1.0080 + 191 HAL2 1 PII H872 191 0.0900 1.0080 + 192 CEL1 1 PII C88 192 -0.1500 12.0110 + 193 HEL1 1 PII H881 193 0.1500 1.0080 + 194 CEL1 1 PII C89 194 0.0000 12.0110 + 195 CTL3 1 PII C890 195 -0.2700 12.0110 + 196 HAL3 1 PII H890 196 0.0900 1.0080 + 197 HAL3 1 PII H891 197 0.0900 1.0080 + 198 HAL3 1 PII H892 198 0.0900 1.0080 + 199 CTL2 1 PII C90 199 -0.1800 12.0110 + 200 HAL2 1 PII H901 200 0.0900 1.0080 + 201 HAL2 1 PII H902 201 0.0900 1.0080 + 202 CTL2 1 PII C91 202 -0.1800 12.0110 + 203 HAL2 1 PII H911 203 0.0900 1.0080 + 204 HAL2 1 PII H912 204 0.0900 1.0080 + 205 CEL1 1 PII C92 205 -0.1500 12.0110 + 206 HEL1 1 PII H921 206 0.1500 1.0080 + 207 CEL1 1 PII C93 207 0.0000 12.0110 + 208 CTL3 1 PII C94 208 -0.2700 12.0110 + 209 HAL3 1 PII H940 209 0.0900 1.0080 + 210 HAL3 1 PII H941 210 0.0900 1.0080 + 211 HAL3 1 PII H942 211 0.0900 1.0080 + 212 CTL3 1 PII C95 212 -0.2700 12.0110 + 213 HAL3 1 PII H950 213 0.0900 1.0080 + 214 HAL3 1 PII H951 214 0.0900 1.0080 + 215 HAL3 1 PII H952 215 0.0900 1.0080 + 216 NH1 1 PII N1 216 -0.4700 14.0070 + 217 H 1 PII HN1 217 0.3100 1.0080 + 218 CT1 1 PII CA1 218 0.0700 12.0110 + 219 HB1 1 PII HA1 219 0.0900 1.0080 + 220 CT3 1 PII CB1 220 -0.2700 12.0110 + 221 HA3 1 PII HB1 221 0.0900 1.0080 + 222 HA3 1 PII HB2 222 0.0900 1.0080 + 223 HA3 1 PII HB3 223 0.0900 1.0080 + 224 C 1 PII C1 224 0.5100 12.0110 + 225 O 1 PII O1 225 -0.5100 15.9990 + 226 CC 1 PII CD1 226 0.6200 12.0110 + 227 OC 1 PII OE1 227 -0.7600 15.9990 + 228 OC 1 PII OE2 228 -0.7600 15.9990 + 229 NH1 1 PII N2 229 -0.4700 14.0070 + 230 H 1 PII HN2 230 0.3100 1.0080 + 231 CT1 1 PII CA2 231 -0.0300 12.0110 + 232 HA1 1 PII HA2 232 0.0900 1.0080 + 233 CT2 1 PII CB2 233 -0.1800 12.0110 + 234 HA2 1 PII HB11 234 0.0900 1.0080 + 235 HA2 1 PII HB21 235 0.0900 1.0080 + 236 CT2 1 PII CG1 236 -0.1800 12.0110 + 237 HA2 1 PII HG11 237 0.0900 1.0080 + 238 HA2 1 PII HG21 238 0.0900 1.0080 + 239 C 1 PII C2 239 0.5100 12.0110 + 240 O 1 PII O2 240 -0.5100 15.9990 + 241 NH1 1 PII N3 241 -0.4700 14.0070 + 242 H 1 PII HN3 242 0.3100 1.0080 + 243 CT1 1 PII CA3 243 0.0700 12.0110 + 244 HB1 1 PII HA3 244 0.0900 1.0080 + 245 CT2 1 PII CB3 245 -0.1800 12.0110 + 246 HA2 1 PII HB13 246 0.0900 1.0080 + 247 HA2 1 PII HB23 247 0.0900 1.0080 + 248 CT2 1 PII CG2 248 -0.1800 12.0110 + 249 HA2 1 PII HG12 249 0.0900 1.0080 + 250 HA2 1 PII HG22 250 0.0900 1.0080 + 251 CT2 1 PII CD2 251 -0.1800 12.0110 + 252 HA2 1 PII HD12 252 0.0900 1.0080 + 253 HA2 1 PII HD22 253 0.0900 1.0080 + 254 CT2 1 PII CE 254 0.2100 12.0110 + 255 HA2 1 PII HE1 255 0.0500 1.0080 + 256 HA2 1 PII HE2 256 0.0500 1.0080 + 257 NH3 1 PII NZ 257 -0.3000 14.0070 + 258 HC 1 PII HZ1 258 0.3300 1.0080 + 259 HC 1 PII HZ2 259 0.3300 1.0080 + 260 HC 1 PII HZ3 260 0.3300 1.0080 + 261 C 1 PII C4 261 0.5100 12.0110 + 262 O 1 PII O4 262 -0.5100 15.9990 + 263 NH1 1 PII N4 263 -0.4700 14.0070 + 264 H 1 PII HN4 264 0.3100 1.0080 + 265 CT1 1 PII CA4 265 0.0700 12.0110 + 266 HB1 1 PII HA4 266 0.0900 1.0080 + 267 CT3 1 PII CB4 267 -0.2700 12.0110 + 268 HA3 1 PII HB14 268 0.0900 1.0080 + 269 HA3 1 PII HB24 269 0.0900 1.0080 + 270 HA3 1 PII HB34 270 0.0900 1.0080 + 271 C 1 PII C5 271 0.5100 12.0110 + 272 O 1 PII O5 272 -0.5100 15.9990 + 273 NH1 1 PII N5 273 -0.4700 14.0070 + 274 H 1 PII HN5 274 0.3100 1.0080 + 275 CT1 1 PII CA5 275 0.0700 12.0110 + 276 HB1 1 PII HA5 276 0.0900 1.0080 + 277 CT3 1 PII CB5 277 -0.2700 12.0110 + 278 HA3 1 PII HB15 278 0.0900 1.0080 + 279 HA3 1 PII HB25 279 0.0900 1.0080 + 280 HA3 1 PII HB35 280 0.0900 1.0080 + 281 CC 1 PII C6 281 0.3400 12.0110 + 282 OC 1 PII OT1 282 -0.6700 15.9990 + 283 OC 1 PII OT2 283 -0.6700 15.9990 + +[ bonds ] +; 284 bonds + 1 2 1 + 1 3 1 + 1 5 1 + 3 4 1 + 5 6 1 + 5 7 1 + 5 27 1 + 7 8 1 + 9 10 1 + 9 11 1 + 9 12 1 + 12 13 1 + 14 15 1 + 14 16 1 + 14 1 1 + 16 17 1 + 16 18 1 + 18 19 1 + 18 20 1 + 20 21 1 + 20 22 1 + 20 23 1 + 24 26 1 + 24 25 1 + 24 29 1 + 24 14 1 + 27 28 1 + 27 26 1 + 27 9 1 + 29 30 1 + 30 31 1 + 30 47 1 + 30 58 1 + 32 33 1 + 32 34 1 + 32 35 1 + 35 36 1 + 37 38 1 + 37 47 1 + 37 39 1 + 39 40 1 + 39 41 1 + 41 42 1 + 41 43 1 + 43 44 1 + 43 45 1 + 43 46 1 + 47 48 1 + 47 49 1 + 49 50 1 + 50 51 1 + 50 52 1 + 50 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9 +226 231 233 236 9 +226 231 233 234 9 +226 231 233 235 9 +227 226 231 229 9 +227 226 231 233 9 +227 226 231 232 9 +228 226 231 229 9 +228 226 231 233 9 +228 226 231 232 9 +229 231 233 236 9 +229 231 233 234 9 +229 231 233 235 9 +230 229 231 233 9 +230 229 231 232 9 +231 233 236 239 9 +231 233 236 237 9 +231 233 236 238 9 +232 231 233 236 9 +232 231 233 234 9 +232 231 233 235 9 +233 236 239 241 9 +233 236 239 240 9 +234 233 236 239 9 +234 233 236 237 9 +234 233 236 238 9 +235 233 236 239 9 +235 233 236 237 9 +235 233 236 238 9 +236 239 241 242 9 +236 239 241 243 9 +237 236 239 241 9 +237 236 239 240 9 +238 236 239 241 9 +238 236 239 240 9 +239 241 243 245 9 +239 241 243 261 9 +239 241 243 244 9 +240 239 241 242 9 +240 239 241 243 9 +241 243 245 248 9 +241 243 245 246 9 +241 243 245 247 9 +241 243 261 263 9 +241 243 261 262 9 +242 241 243 245 9 +242 241 243 261 9 +242 241 243 244 9 +243 261 263 264 9 +243 261 263 265 9 +243 245 248 251 9 +243 245 248 249 9 +243 245 248 250 9 +244 243 245 248 9 +244 243 245 246 9 +244 243 245 247 9 +244 243 261 263 9 +244 243 261 262 9 +245 248 251 254 9 +245 248 251 252 9 +245 248 251 253 9 +245 243 261 263 9 +245 243 261 262 9 +246 245 243 261 9 +246 245 248 251 9 +246 245 248 249 9 +246 245 248 250 9 +247 245 243 261 9 +247 245 248 251 9 +247 245 248 249 9 +247 245 248 250 9 +248 251 254 257 9 +248 251 254 255 9 +248 251 254 256 9 +248 245 243 261 9 +249 248 251 254 9 +249 248 251 252 9 +249 248 251 253 9 +250 248 251 254 9 +250 248 251 252 9 +250 248 251 253 9 +251 254 257 258 9 +251 254 257 259 9 +251 254 257 260 9 +252 251 254 257 9 +252 251 254 255 9 +252 251 254 256 9 +253 251 254 257 9 +253 251 254 255 9 +253 251 254 256 9 +255 254 257 258 9 +255 254 257 259 9 +255 254 257 260 9 +256 254 257 258 9 +256 254 257 259 9 +256 254 257 260 9 +261 263 265 267 9 +261 263 265 271 9 +261 263 265 266 9 +262 261 263 264 9 +262 261 263 265 9 +263 265 267 268 9 +263 265 267 269 9 +263 265 267 270 9 +263 265 271 273 9 +263 265 271 272 9 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+24 26 27 5 1 60 0 25000 +24 14 1 5 1 -60 0 25000 +26 27 5 1 1 -60 0 25000 + +#endif + +[ dihedrals ] +; 16 impropers + 16 18 14 17 2 + 18 20 16 19 2 + 39 41 37 40 2 + 41 43 39 42 2 + 56 50 216 57 2 +216 56 218 217 2 +224 218 229 225 2 +226 231 228 227 2 +229 224 231 230 2 +239 236 241 240 2 +241 239 243 242 2 +261 243 263 262 2 +263 261 265 264 2 +271 265 273 272 2 +273 271 275 274 2 +281 275 283 282 2 + +[ cmap ] +; 3 cmaps + 56 216 218 224 229 1 + 239 241 243 261 263 1 + 261 263 265 271 273 1 diff --git a/tests/data/membrane/TOCL2.itp b/tests/data/membrane/TOCL2.itp new file mode 100755 index 0000000..1e2a622 --- /dev/null +++ b/tests/data/membrane/TOCL2.itp @@ -0,0 +1,2321 @@ +;; +;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 +;; +;; psf2itp.py +;; +;; Correspondance: +;; jul316@lehigh.edu or wonpil@lehigh.edu +;; +;; GROMACS topology file for TOCL2 +;; + + +[ moleculetype ] +; name nrexcl +CDL2 3 + +[ atoms ] +; nr type resnr residu atom cgnr charge mass + 1 CTL2 1 CDL2 C3 1 -0.080 12.0110 ; qtot -0.080 + 2 HAL2 1 CDL2 HG31 2 0.090 1.0080 ; qtot 0.010 + 3 HAL2 1 CDL2 HG32 3 0.090 1.0080 ; qtot 0.100 + 4 PL 1 CDL2 P3 4 1.500 30.9740 ; qtot 1.600 + 5 O2L 1 CDL2 OP33 5 -0.780 15.9994 ; qtot 0.820 + 6 O2L 1 CDL2 OP34 6 -0.780 15.9994 ; qtot 0.040 + 7 OSLP 1 CDL2 OP31 7 -0.570 15.9994 ; qtot -0.530 + 8 OSLP 1 CDL2 OP32 8 -0.570 15.9994 ; qtot -1.100 + 9 CTL2 1 CDL2 C31 9 -0.080 12.0110 ; qtot -1.180 + 10 HAL2 1 CDL2 H31J 10 0.090 1.0080 ; qtot -1.090 + 11 HAL2 1 CDL2 H31K 11 0.090 1.0080 ; qtot -1.000 + 12 CTL1 1 CDL2 C2 12 0.140 12.0110 ; qtot -0.860 + 13 HAL1 1 CDL2 HG22 13 0.090 1.0080 ; qtot -0.770 + 14 OHL 1 CDL2 OG12 14 -0.650 15.9994 ; qtot -1.420 + 15 HOL 1 CDL2 HO12 15 0.420 1.0080 ; qtot -1.000 + 16 CTL2 1 CDL2 C1 16 -0.080 12.0110 ; qtot -1.080 + 17 HAL2 1 CDL2 HG11 17 0.090 1.0080 ; qtot -0.990 + 18 HAL2 1 CDL2 HG12 18 0.090 1.0080 ; qtot -0.900 + 19 PL 1 CDL2 P1 19 1.500 30.9740 ; qtot 0.600 + 20 O2L 1 CDL2 OP13 20 -0.780 15.9994 ; qtot -0.180 + 21 O2L 1 CDL2 OP14 21 -0.780 15.9994 ; qtot -0.960 + 22 OSLP 1 CDL2 OP11 22 -0.570 15.9994 ; qtot -1.530 + 23 OSLP 1 CDL2 OP12 23 -0.570 15.9994 ; qtot -2.100 + 24 CTL2 1 CDL2 C11 24 -0.080 12.0110 ; qtot -2.180 + 25 HAL2 1 CDL2 H11J 25 0.090 1.0080 ; qtot -2.090 + 26 HAL2 1 CDL2 H11K 26 0.090 1.0080 ; qtot -2.000 + 27 CTL1 1 CDL2 C12 27 0.170 12.0110 ; qtot -1.830 + 28 HAL1 1 CDL2 H12J 28 0.090 1.0080 ; qtot -1.740 + 29 OSL 1 CDL2 O12 29 -0.490 15.9994 ; qtot -2.230 + 30 CL 1 CDL2 CA1 30 0.900 12.0110 ; qtot -1.330 + 31 OBL 1 CDL2 OA1 31 -0.630 15.9994 ; qtot -1.960 + 32 CTL2 1 CDL2 CA2 32 -0.220 12.0110 ; qtot -2.180 + 33 HAL2 1 CDL2 H2A 33 0.090 1.0080 ; qtot -2.090 + 34 HAL2 1 CDL2 H2B 34 0.090 1.0080 ; qtot -2.000 + 35 CTL2 1 CDL2 C13 35 0.080 12.0110 ; qtot -1.920 + 36 HAL2 1 CDL2 H13J 36 0.090 1.0080 ; qtot -1.830 + 37 HAL2 1 CDL2 H13K 37 0.090 1.0080 ; qtot -1.740 + 38 OSL 1 CDL2 O13 38 -0.490 15.9994 ; qtot -2.230 + 39 CL 1 CDL2 CB1 39 0.900 12.0110 ; qtot -1.330 + 40 OBL 1 CDL2 OB1 40 -0.630 15.9994 ; qtot -1.960 + 41 CTL2 1 CDL2 CB2 41 -0.220 12.0110 ; qtot -2.180 + 42 HAL2 1 CDL2 H2D 42 0.090 1.0080 ; qtot -2.090 + 43 HAL2 1 CDL2 H2E 43 0.090 1.0080 ; qtot -2.000 + 44 CTL1 1 CDL2 C32 44 0.170 12.0110 ; qtot -1.830 + 45 HAL1 1 CDL2 H32J 45 0.090 1.0080 ; qtot -1.740 + 46 OSL 1 CDL2 O32 46 -0.490 15.9994 ; qtot -2.230 + 47 CL 1 CDL2 CC1 47 0.900 12.0110 ; qtot -1.330 + 48 OBL 1 CDL2 OC1 48 -0.630 15.9994 ; qtot -1.960 + 49 CTL2 1 CDL2 CC2 49 -0.220 12.0110 ; qtot -2.180 + 50 HAL2 1 CDL2 H2R 50 0.090 1.0080 ; qtot -2.090 + 51 HAL2 1 CDL2 H2S 51 0.090 1.0080 ; qtot -2.000 + 52 CTL2 1 CDL2 C33 52 0.080 12.0110 ; qtot -1.920 + 53 HAL2 1 CDL2 H33J 53 0.090 1.0080 ; qtot -1.830 + 54 HAL2 1 CDL2 H33K 54 0.090 1.0080 ; qtot -1.740 + 55 OSL 1 CDL2 O33 55 -0.490 15.9994 ; qtot -2.230 + 56 CL 1 CDL2 CD1 56 0.900 12.0110 ; qtot -1.330 + 57 OBL 1 CDL2 OD1 57 -0.630 15.9994 ; qtot -1.960 + 58 CTL2 1 CDL2 CD2 58 -0.220 12.0110 ; qtot -2.180 + 59 HAL2 1 CDL2 H2X 59 0.090 1.0080 ; qtot -2.090 + 60 HAL2 1 CDL2 H2Y 60 0.090 1.0080 ; qtot -2.000 + 61 CTL2 1 CDL2 CA3 61 -0.180 12.0110 ; qtot -2.180 + 62 HAL2 1 CDL2 H3A 62 0.090 1.0080 ; qtot -2.090 + 63 HAL2 1 CDL2 H3B 63 0.090 1.0080 ; qtot -2.000 + 64 CTL2 1 CDL2 CA4 64 -0.180 12.0110 ; qtot -2.180 + 65 HAL2 1 CDL2 H4A 65 0.090 1.0080 ; qtot -2.090 + 66 HAL2 1 CDL2 H4B 66 0.090 1.0080 ; qtot -2.000 + 67 CTL2 1 CDL2 CA5 67 -0.180 12.0110 ; qtot -2.180 + 68 HAL2 1 CDL2 H5A 68 0.090 1.0080 ; qtot -2.090 + 69 HAL2 1 CDL2 H5B 69 0.090 1.0080 ; qtot -2.000 + 70 CTL2 1 CDL2 CA6 70 -0.180 12.0110 ; qtot -2.180 + 71 HAL2 1 CDL2 H6A 71 0.090 1.0080 ; qtot -2.090 + 72 HAL2 1 CDL2 H6B 72 0.090 1.0080 ; qtot -2.000 + 73 CTL2 1 CDL2 CA7 73 -0.180 12.0110 ; qtot -2.180 + 74 HAL2 1 CDL2 H7A 74 0.090 1.0080 ; qtot -2.090 + 75 HAL2 1 CDL2 H7B 75 0.090 1.0080 ; qtot -2.000 + 76 CTL2 1 CDL2 CA8 76 -0.180 12.0110 ; qtot -2.180 + 77 HAL2 1 CDL2 H8A 77 0.090 1.0080 ; qtot -2.090 + 78 HAL2 1 CDL2 H8B 78 0.090 1.0080 ; qtot -2.000 + 79 CEL1 1 CDL2 CA9 79 -0.150 12.0110 ; qtot -2.150 + 80 HEL1 1 CDL2 H9A 80 0.150 1.0080 ; qtot -2.000 + 81 CEL1 1 CDL2 CA10 81 -0.150 12.0110 ; qtot -2.150 + 82 HEL1 1 CDL2 H10A 82 0.150 1.0080 ; qtot -2.000 + 83 CTL2 1 CDL2 CA11 83 -0.180 12.0110 ; qtot -2.180 + 84 HAL2 1 CDL2 H11A 84 0.090 1.0080 ; qtot -2.090 + 85 HAL2 1 CDL2 H11B 85 0.090 1.0080 ; qtot -2.000 + 86 CTL2 1 CDL2 CA12 86 -0.180 12.0110 ; qtot -2.180 + 87 HAL2 1 CDL2 H12A 87 0.090 1.0080 ; qtot -2.090 + 88 HAL2 1 CDL2 H12B 88 0.090 1.0080 ; qtot -2.000 + 89 CTL2 1 CDL2 CA13 89 -0.180 12.0110 ; qtot -2.180 + 90 HAL2 1 CDL2 H13A 90 0.090 1.0080 ; qtot -2.090 + 91 HAL2 1 CDL2 H13B 91 0.090 1.0080 ; qtot -2.000 + 92 CTL2 1 CDL2 CA14 92 -0.180 12.0110 ; qtot -2.180 + 93 HAL2 1 CDL2 H14A 93 0.090 1.0080 ; qtot -2.090 + 94 HAL2 1 CDL2 H14B 94 0.090 1.0080 ; qtot -2.000 + 95 CTL2 1 CDL2 CA15 95 -0.180 12.0110 ; qtot -2.180 + 96 HAL2 1 CDL2 H15A 96 0.090 1.0080 ; qtot -2.090 + 97 HAL2 1 CDL2 H15B 97 0.090 1.0080 ; qtot -2.000 + 98 CTL2 1 CDL2 CA16 98 -0.180 12.0110 ; qtot -2.180 + 99 HAL2 1 CDL2 H16A 99 0.090 1.0080 ; qtot -2.090 + 100 HAL2 1 CDL2 H16B 100 0.090 1.0080 ; qtot -2.000 + 101 CTL2 1 CDL2 CA17 101 -0.180 12.0110 ; qtot -2.180 + 102 HAL2 1 CDL2 H17A 102 0.090 1.0080 ; qtot -2.090 + 103 HAL2 1 CDL2 H17B 103 0.090 1.0080 ; qtot -2.000 + 104 CTL3 1 CDL2 CA18 104 -0.270 12.0110 ; qtot -2.270 + 105 HAL3 1 CDL2 H18A 105 0.090 1.0080 ; qtot -2.180 + 106 HAL3 1 CDL2 H18B 106 0.090 1.0080 ; qtot -2.090 + 107 HAL3 1 CDL2 H18C 107 0.090 1.0080 ; qtot -2.000 + 108 CTL2 1 CDL2 CB3 108 -0.180 12.0110 ; qtot -2.180 + 109 HAL2 1 CDL2 H3D 109 0.090 1.0080 ; qtot -2.090 + 110 HAL2 1 CDL2 H3E 110 0.090 1.0080 ; qtot -2.000 + 111 CTL2 1 CDL2 CB4 111 -0.180 12.0110 ; qtot -2.180 + 112 HAL2 1 CDL2 H4D 112 0.090 1.0080 ; qtot -2.090 + 113 HAL2 1 CDL2 H4E 113 0.090 1.0080 ; qtot -2.000 + 114 CTL2 1 CDL2 CB5 114 -0.180 12.0110 ; qtot -2.180 + 115 HAL2 1 CDL2 H5D 115 0.090 1.0080 ; qtot -2.090 + 116 HAL2 1 CDL2 H5E 116 0.090 1.0080 ; qtot -2.000 + 117 CTL2 1 CDL2 CB6 117 -0.180 12.0110 ; qtot -2.180 + 118 HAL2 1 CDL2 H6D 118 0.090 1.0080 ; qtot -2.090 + 119 HAL2 1 CDL2 H6E 119 0.090 1.0080 ; qtot -2.000 + 120 CTL2 1 CDL2 CB7 120 -0.180 12.0110 ; qtot -2.180 + 121 HAL2 1 CDL2 H7D 121 0.090 1.0080 ; qtot -2.090 + 122 HAL2 1 CDL2 H7E 122 0.090 1.0080 ; qtot -2.000 + 123 CTL2 1 CDL2 CB8 123 -0.180 12.0110 ; qtot -2.180 + 124 HAL2 1 CDL2 H8D 124 0.090 1.0080 ; qtot -2.090 + 125 HAL2 1 CDL2 H8E 125 0.090 1.0080 ; qtot -2.000 + 126 CEL1 1 CDL2 CB9 126 -0.150 12.0110 ; qtot -2.150 + 127 HEL1 1 CDL2 H9D 127 0.150 1.0080 ; qtot -2.000 + 128 CEL1 1 CDL2 CB10 128 -0.150 12.0110 ; qtot -2.150 + 129 HEL1 1 CDL2 H10D 129 0.150 1.0080 ; qtot -2.000 + 130 CTL2 1 CDL2 CB11 130 -0.180 12.0110 ; qtot -2.180 + 131 HAL2 1 CDL2 H11D 131 0.090 1.0080 ; qtot -2.090 + 132 HAL2 1 CDL2 H11E 132 0.090 1.0080 ; qtot -2.000 + 133 CTL2 1 CDL2 CB12 133 -0.180 12.0110 ; qtot -2.180 + 134 HAL2 1 CDL2 H12D 134 0.090 1.0080 ; qtot -2.090 + 135 HAL2 1 CDL2 H12E 135 0.090 1.0080 ; qtot -2.000 + 136 CTL2 1 CDL2 CB13 136 -0.180 12.0110 ; qtot -2.180 + 137 HAL2 1 CDL2 H13D 137 0.090 1.0080 ; qtot -2.090 + 138 HAL2 1 CDL2 H13E 138 0.090 1.0080 ; qtot -2.000 + 139 CTL2 1 CDL2 CB14 139 -0.180 12.0110 ; qtot -2.180 + 140 HAL2 1 CDL2 H14D 140 0.090 1.0080 ; qtot -2.090 + 141 HAL2 1 CDL2 H14E 141 0.090 1.0080 ; qtot -2.000 + 142 CTL2 1 CDL2 CB15 142 -0.180 12.0110 ; qtot -2.180 + 143 HAL2 1 CDL2 H15D 143 0.090 1.0080 ; qtot -2.090 + 144 HAL2 1 CDL2 H15E 144 0.090 1.0080 ; qtot -2.000 + 145 CTL2 1 CDL2 CB16 145 -0.180 12.0110 ; qtot -2.180 + 146 HAL2 1 CDL2 H16D 146 0.090 1.0080 ; qtot -2.090 + 147 HAL2 1 CDL2 H16E 147 0.090 1.0080 ; qtot -2.000 + 148 CTL2 1 CDL2 CB17 148 -0.180 12.0110 ; qtot -2.180 + 149 HAL2 1 CDL2 H17D 149 0.090 1.0080 ; qtot -2.090 + 150 HAL2 1 CDL2 H17E 150 0.090 1.0080 ; qtot -2.000 + 151 CTL3 1 CDL2 CB18 151 -0.270 12.0110 ; qtot -2.270 + 152 HAL3 1 CDL2 H18D 152 0.090 1.0080 ; qtot -2.180 + 153 HAL3 1 CDL2 H18E 153 0.090 1.0080 ; qtot -2.090 + 154 HAL3 1 CDL2 H18F 154 0.090 1.0080 ; qtot -2.000 + 155 CTL2 1 CDL2 CC3 155 -0.180 12.0110 ; qtot -2.180 + 156 HAL2 1 CDL2 H3R 156 0.090 1.0080 ; qtot -2.090 + 157 HAL2 1 CDL2 H3S 157 0.090 1.0080 ; qtot -2.000 + 158 CTL2 1 CDL2 CC4 158 -0.180 12.0110 ; qtot -2.180 + 159 HAL2 1 CDL2 H4R 159 0.090 1.0080 ; qtot -2.090 + 160 HAL2 1 CDL2 H4S 160 0.090 1.0080 ; qtot -2.000 + 161 CTL2 1 CDL2 CC5 161 -0.180 12.0110 ; qtot -2.180 + 162 HAL2 1 CDL2 H5R 162 0.090 1.0080 ; qtot -2.090 + 163 HAL2 1 CDL2 H5S 163 0.090 1.0080 ; qtot -2.000 + 164 CTL2 1 CDL2 CC6 164 -0.180 12.0110 ; qtot -2.180 + 165 HAL2 1 CDL2 H6R 165 0.090 1.0080 ; qtot -2.090 + 166 HAL2 1 CDL2 H6S 166 0.090 1.0080 ; qtot -2.000 + 167 CTL2 1 CDL2 CC7 167 -0.180 12.0110 ; qtot -2.180 + 168 HAL2 1 CDL2 H7R 168 0.090 1.0080 ; qtot -2.090 + 169 HAL2 1 CDL2 H7S 169 0.090 1.0080 ; qtot -2.000 + 170 CTL2 1 CDL2 CC8 170 -0.180 12.0110 ; qtot -2.180 + 171 HAL2 1 CDL2 H8R 171 0.090 1.0080 ; qtot -2.090 + 172 HAL2 1 CDL2 H8S 172 0.090 1.0080 ; qtot -2.000 + 173 CEL1 1 CDL2 CC9 173 -0.150 12.0110 ; qtot -2.150 + 174 HEL1 1 CDL2 H9R 174 0.150 1.0080 ; qtot -2.000 + 175 CEL1 1 CDL2 CC10 175 -0.150 12.0110 ; qtot -2.150 + 176 HEL1 1 CDL2 H10R 176 0.150 1.0080 ; qtot -2.000 + 177 CTL2 1 CDL2 CC11 177 -0.180 12.0110 ; qtot -2.180 + 178 HAL2 1 CDL2 H11R 178 0.090 1.0080 ; qtot -2.090 + 179 HAL2 1 CDL2 H11S 179 0.090 1.0080 ; qtot -2.000 + 180 CTL2 1 CDL2 CC12 180 -0.180 12.0110 ; qtot -2.180 + 181 HAL2 1 CDL2 H12R 181 0.090 1.0080 ; qtot -2.090 + 182 HAL2 1 CDL2 H12S 182 0.090 1.0080 ; qtot -2.000 + 183 CTL2 1 CDL2 CC13 183 -0.180 12.0110 ; qtot -2.180 + 184 HAL2 1 CDL2 H13R 184 0.090 1.0080 ; qtot -2.090 + 185 HAL2 1 CDL2 H13S 185 0.090 1.0080 ; qtot -2.000 + 186 CTL2 1 CDL2 CC14 186 -0.180 12.0110 ; qtot -2.180 + 187 HAL2 1 CDL2 H14R 187 0.090 1.0080 ; qtot -2.090 + 188 HAL2 1 CDL2 H14S 188 0.090 1.0080 ; qtot -2.000 + 189 CTL2 1 CDL2 CC15 189 -0.180 12.0110 ; qtot -2.180 + 190 HAL2 1 CDL2 H15R 190 0.090 1.0080 ; qtot -2.090 + 191 HAL2 1 CDL2 H15S 191 0.090 1.0080 ; qtot -2.000 + 192 CTL2 1 CDL2 CC16 192 -0.180 12.0110 ; qtot -2.180 + 193 HAL2 1 CDL2 H16R 193 0.090 1.0080 ; qtot -2.090 + 194 HAL2 1 CDL2 H16S 194 0.090 1.0080 ; qtot -2.000 + 195 CTL2 1 CDL2 CC17 195 -0.180 12.0110 ; qtot -2.180 + 196 HAL2 1 CDL2 H17R 196 0.090 1.0080 ; qtot -2.090 + 197 HAL2 1 CDL2 H17S 197 0.090 1.0080 ; qtot -2.000 + 198 CTL3 1 CDL2 CC18 198 -0.270 12.0110 ; qtot -2.270 + 199 HAL3 1 CDL2 H18R 199 0.090 1.0080 ; qtot -2.180 + 200 HAL3 1 CDL2 H18S 200 0.090 1.0080 ; qtot -2.090 + 201 HAL3 1 CDL2 H18T 201 0.090 1.0080 ; qtot -2.000 + 202 CTL2 1 CDL2 CD3 202 -0.180 12.0110 ; qtot -2.180 + 203 HAL2 1 CDL2 H3X 203 0.090 1.0080 ; qtot -2.090 + 204 HAL2 1 CDL2 H3Y 204 0.090 1.0080 ; qtot -2.000 + 205 CTL2 1 CDL2 CD4 205 -0.180 12.0110 ; qtot -2.180 + 206 HAL2 1 CDL2 H4X 206 0.090 1.0080 ; qtot -2.090 + 207 HAL2 1 CDL2 H4Y 207 0.090 1.0080 ; qtot -2.000 + 208 CTL2 1 CDL2 CD5 208 -0.180 12.0110 ; qtot -2.180 + 209 HAL2 1 CDL2 H5X 209 0.090 1.0080 ; qtot -2.090 + 210 HAL2 1 CDL2 H5Y 210 0.090 1.0080 ; qtot -2.000 + 211 CTL2 1 CDL2 CD6 211 -0.180 12.0110 ; qtot -2.180 + 212 HAL2 1 CDL2 H6X 212 0.090 1.0080 ; qtot -2.090 + 213 HAL2 1 CDL2 H6Y 213 0.090 1.0080 ; qtot -2.000 + 214 CTL2 1 CDL2 CD7 214 -0.180 12.0110 ; qtot -2.180 + 215 HAL2 1 CDL2 H7X 215 0.090 1.0080 ; qtot -2.090 + 216 HAL2 1 CDL2 H7Y 216 0.090 1.0080 ; qtot -2.000 + 217 CTL2 1 CDL2 CD8 217 -0.180 12.0110 ; qtot -2.180 + 218 HAL2 1 CDL2 H8X 218 0.090 1.0080 ; qtot -2.090 + 219 HAL2 1 CDL2 H8Y 219 0.090 1.0080 ; qtot -2.000 + 220 CEL1 1 CDL2 CD9 220 -0.150 12.0110 ; qtot -2.150 + 221 HEL1 1 CDL2 H9X 221 0.150 1.0080 ; qtot -2.000 + 222 CEL1 1 CDL2 CD10 222 -0.150 12.0110 ; qtot -2.150 + 223 HEL1 1 CDL2 H10X 223 0.150 1.0080 ; qtot -2.000 + 224 CTL2 1 CDL2 CD11 224 -0.180 12.0110 ; qtot -2.180 + 225 HAL2 1 CDL2 H11X 225 0.090 1.0080 ; qtot -2.090 + 226 HAL2 1 CDL2 H11Y 226 0.090 1.0080 ; qtot -2.000 + 227 CTL2 1 CDL2 CD12 227 -0.180 12.0110 ; qtot -2.180 + 228 HAL2 1 CDL2 H12X 228 0.090 1.0080 ; qtot -2.090 + 229 HAL2 1 CDL2 H12Y 229 0.090 1.0080 ; qtot -2.000 + 230 CTL2 1 CDL2 CD13 230 -0.180 12.0110 ; qtot -2.180 + 231 HAL2 1 CDL2 H13X 231 0.090 1.0080 ; qtot -2.090 + 232 HAL2 1 CDL2 H13Y 232 0.090 1.0080 ; qtot -2.000 + 233 CTL2 1 CDL2 CD14 233 -0.180 12.0110 ; qtot -2.180 + 234 HAL2 1 CDL2 H14X 234 0.090 1.0080 ; qtot -2.090 + 235 HAL2 1 CDL2 H14Y 235 0.090 1.0080 ; qtot -2.000 + 236 CTL2 1 CDL2 CD15 236 -0.180 12.0110 ; qtot -2.180 + 237 HAL2 1 CDL2 H15X 237 0.090 1.0080 ; qtot -2.090 + 238 HAL2 1 CDL2 H15Y 238 0.090 1.0080 ; qtot -2.000 + 239 CTL2 1 CDL2 CD16 239 -0.180 12.0110 ; qtot -2.180 + 240 HAL2 1 CDL2 H16X 240 0.090 1.0080 ; qtot -2.090 + 241 HAL2 1 CDL2 H16Y 241 0.090 1.0080 ; qtot -2.000 + 242 CTL2 1 CDL2 CD17 242 -0.180 12.0110 ; qtot -2.180 + 243 HAL2 1 CDL2 H17X 243 0.090 1.0080 ; qtot -2.090 + 244 HAL2 1 CDL2 H17Y 244 0.090 1.0080 ; qtot -2.000 + 245 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-0.8328 0.7137 1.2627 + 1PII HE2 256 0.175 7.307 2.336 -0.6619 -0.3099 -0.6725 + 1PII NZ 257 0.057 7.381 2.492 -0.0135 -0.1110 -0.1137 + 1PII HZ1 258 -0.042 7.363 2.466 0.0278 0.8941 -0.9458 + 1PII HZ2 259 0.056 7.395 2.595 -2.9082 -0.8299 -0.0159 + 1PII HZ3 260 0.089 7.467 2.444 0.2059 0.4108 0.9831 + 1PII C4 261 0.346 7.760 2.643 0.5190 0.8471 0.5368 + 1PII O4 262 0.256 7.762 2.726 0.0065 -0.6398 0.0188 + 1PII N4 263 0.379 7.872 2.576 -0.3038 0.8246 0.0951 + 1PII HN4 264 0.458 7.862 2.516 -0.0581 -0.7093 0.6751 + 1PII CA4 265 0.320 8.001 2.598 -0.7054 0.5917 0.3863 + 1PII HA4 266 0.235 7.999 2.665 -0.7318 -0.8837 0.3126 + 1PII CB4 267 0.290 8.071 2.465 -0.0594 0.2816 0.0785 + 1PII HB14 268 0.220 7.998 2.420 0.6908 0.0537 -0.7300 + 1PII HB24 269 0.237 8.168 2.480 -0.3038 0.4274 -1.6872 + 1PII HB34 270 0.377 8.092 2.399 -0.2198 1.7246 0.3114 + 1PII C5 271 0.418 8.084 2.674 -0.2196 0.5531 -0.1983 + 1PII O5 272 0.525 8.110 2.620 0.0003 -0.3957 -0.2233 + 1PII N5 273 0.388 8.118 2.801 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-0.0727 + 6PII HG11 1652 4.644 14.033 7.863 -0.9399 1.1577 1.3281 + 6PII HG21 1653 4.775 14.128 7.936 -1.4510 0.4207 0.8137 + 6PII C2 1654 4.808 14.069 7.736 0.4358 -0.2422 0.3935 + 6PII O2 1655 4.867 14.147 7.661 -0.2892 -0.1082 -0.0420 + 6PII N3 1656 4.830 13.937 7.744 -0.2834 -0.3911 0.0608 + 6PII HN3 1657 4.757 13.891 7.794 0.0874 -0.7137 0.3019 + 6PII CA3 1658 4.962 13.882 7.754 -0.3288 -0.6098 -0.5838 + 6PII HA3 1659 5.004 13.941 7.833 -0.5616 -0.4504 -0.5885 + 6PII CB3 1660 5.038 13.885 7.620 0.1735 -0.2988 -0.2916 + 6PII HB13 1661 4.966 13.849 7.543 0.5802 2.0240 -1.7647 + 6PII HB23 1662 5.057 13.992 7.596 0.9787 -0.6534 -1.2449 + 6PII CG2 1663 5.175 13.817 7.614 0.2002 -0.2810 -0.0642 + 6PII HG12 1664 5.219 13.851 7.518 0.0794 0.5969 0.1907 + 6PII HG22 1665 5.165 13.706 7.608 2.5872 -0.4834 -0.0689 + 6PII CD2 1666 5.270 13.851 7.728 0.4604 -0.2256 -0.2963 + 6PII HD12 1667 5.235 13.945 7.774 -3.0344 -1.4133 -0.5325 + 6PII HD22 1668 5.366 13.882 7.681 -0.2995 0.0039 -1.7151 + 6PII CE 1669 5.296 13.739 7.829 -0.6274 -0.0645 0.1716 + 6PII HE1 1670 5.374 13.667 7.796 -0.0221 0.4523 0.4792 + 6PII HE2 1671 5.203 13.682 7.845 -0.0237 -0.5156 2.1097 + 6PII NZ 1672 5.344 13.788 7.960 -0.7397 -0.2404 0.2773 + 6PII HZ1 1673 5.435 13.837 7.953 -0.9027 0.3021 1.8488 + 6PII HZ2 1674 5.365 13.703 8.016 -0.2137 -0.7826 -0.7639 + 6PII HZ3 1675 5.287 13.858 8.012 0.0366 -0.0512 0.8935 + 6PII C4 1676 4.955 13.747 7.817 0.7138 -0.2595 0.2945 + 6PII O4 1677 4.961 13.739 7.940 0.1803 -0.5633 0.2993 + 6PII N4 1678 4.948 13.634 7.744 -0.3130 0.0444 -0.0667 + 6PII HN4 1679 4.947 13.663 7.649 1.9663 -0.1849 -0.1813 + 6PII CA4 1680 4.932 13.499 7.789 0.1615 0.1802 0.5275 + 6PII HA4 1681 4.978 13.438 7.713 0.7405 0.6172 0.5263 + 6PII CB4 1682 4.781 13.467 7.780 0.1590 0.1807 0.4768 + 6PII HB14 1683 4.748 13.523 7.689 -0.2178 -1.0793 -0.1565 + 6PII HB24 1684 4.755 13.361 7.762 -1.0822 1.1858 -3.7764 + 6PII HB34 1685 4.722 13.505 7.866 -1.2186 -0.5080 -0.1770 + 6PII C5 1686 5.000 13.453 7.913 0.0181 -0.0532 0.5210 + 6PII O5 1687 5.104 13.388 7.906 -0.2315 -0.3025 -0.7586 + 6PII N5 1688 4.936 13.476 8.029 0.0618 0.8770 0.3590 + 6PII HN5 1689 4.851 13.527 8.020 -1.1513 -1.1702 0.2813 + 6PII CA5 1690 4.993 13.481 8.160 0.5058 -0.1883 0.2024 + 6PII HA5 1691 4.917 13.527 8.221 -0.3993 0.7865 -1.6832 + 6PII CB5 1692 5.108 13.581 8.179 0.6633 -0.3666 0.1742 + 6PII HB15 1693 5.184 13.567 8.099 0.2407 -0.4489 -0.2191 + 6PII HB25 1694 5.072 13.686 8.169 -1.7080 -1.1146 0.9385 + 6PII HB35 1695 5.160 13.565 8.276 -0.4705 -1.6988 0.5680 + 6PII C6 1696 5.012 13.342 8.221 -0.1732 -0.1788 0.4457 + 6PII OT1 1697 5.122 13.281 8.222 0.2060 0.5027 -0.1965 + 6PII OT2 1698 4.912 13.298 8.284 -0.2784 -0.2660 0.2108 + 7PII C13 1699 1.932 4.747 2.580 0.5339 -0.2676 -0.1077 + 7PII H13 1700 1.897 4.826 2.650 -1.1797 -1.5834 0.5361 + 7PII O13 1701 1.859 4.746 2.459 0.1855 0.5065 0.1000 + 7PII HO13 1702 1.886 4.681 2.394 -0.3885 -0.4577 0.8309 + 7PII C14 1703 1.910 4.615 2.645 0.2348 -0.1547 0.0248 + 7PII H14 1704 1.949 4.537 2.577 0.1150 -0.0639 -0.1485 + 7PII O14 1705 1.773 4.588 2.666 0.1880 0.1724 0.1385 + 7PII HO14 1706 1.732 4.661 2.713 -1.1893 -1.2728 1.2028 + 7PII C16 1707 2.003 4.469 2.827 0.1546 -0.2053 0.2359 + 7PII H161 1708 2.021 4.399 2.743 -1.5012 -1.3640 0.8405 + 7PII H162 1709 2.091 4.468 2.895 -1.0455 0.8739 1.7997 + 7PII O16 1710 1.896 4.433 2.914 -0.2033 0.6744 0.1564 + 7PII HO16 1711 1.841 4.368 2.870 -0.2554 0.2094 0.9200 + 7PII C12 1712 2.076 4.772 2.556 0.4695 0.2440 0.0368 + 7PII H12 1713 2.117 4.683 2.502 1.1567 0.8278 -0.3913 + 7PII N17 1714 2.109 4.879 2.468 1.0752 -0.0399 -0.0863 + 7PII H17 1715 2.156 4.851 2.384 -1.1826 0.6296 -1.6038 + 7PII C18 1716 2.067 5.007 2.477 0.1616 -0.3472 0.0925 + 7PII O18 1717 1.995 5.059 2.562 0.0404 0.2354 -0.3750 + 7PII C19 1718 2.136 5.096 2.375 -0.4950 0.2364 0.1686 + 7PII H191 1719 2.154 5.193 2.425 0.4250 0.0450 0.1984 + 7PII H192 1720 2.224 5.043 2.333 0.0543 1.9087 -0.8285 + 7PII H193 1721 2.061 5.115 2.294 1.0388 0.2573 -1.2495 + 7PII C11 1722 2.147 4.777 2.685 0.2445 -0.2536 0.1828 + 7PII H11 1723 2.111 4.858 2.752 -0.8792 0.9471 -1.8769 + 7PII O15 1724 2.128 4.650 2.747 -0.3064 0.1691 0.8684 + 7PII C15 1725 1.994 4.606 2.769 -0.2716 -0.1804 0.3678 + 7PII H15 1726 1.951 4.675 2.844 -0.7779 0.7358 -0.7501 + 7PII O24 1727 2.280 4.795 2.646 0.0981 0.0124 -0.1944 + 7PII C24 1728 2.379 4.720 2.714 0.1310 -0.0310 -0.2953 + 7PII H24 1729 2.340 4.617 2.702 -1.2731 0.5183 -0.4998 + 7PII C26 1730 2.429 4.620 2.940 -0.5403 0.3127 0.4333 + 7PII H261 1731 2.392 4.531 2.884 1.8256 0.7704 -1.8981 + 7PII H262 1732 2.539 4.609 2.940 -0.5528 0.1825 0.6007 + 7PII O26 1733 2.379 4.620 3.073 -0.1879 0.2984 0.5625 + 7PII HO26 1734 2.454 4.666 3.111 0.9863 -0.7103 -0.4862 + 7PII C22 1735 2.600 4.841 2.721 -0.2881 0.3505 0.2413 + 7PII H22 1736 2.670 4.775 2.777 -1.0980 -0.8349 -0.1309 + 7PII N27 1737 2.671 4.937 2.643 -0.1384 0.0602 0.0167 + 7PII H27 1738 2.629 5.027 2.640 2.9642 1.4859 -0.4882 + 7PII C28 1739 2.782 4.927 2.567 0.2064 0.1273 0.5058 + 7PII O28 1740 2.816 5.021 2.496 0.1315 -0.1614 0.0927 + 7PII C29 1741 2.868 4.802 2.576 0.1317 0.0695 0.3720 + 7PII H291 1742 2.964 4.808 2.631 0.0432 0.1901 0.5137 + 7PII H292 1743 2.814 4.725 2.636 -0.3693 0.4944 0.4683 + 7PII H293 1744 2.899 4.759 2.479 4.1432 0.0584 1.6529 + 7PII C23 1745 2.508 4.751 2.648 0.1409 0.2270 -0.1528 + 7PII H23 1746 2.501 4.797 2.548 0.5788 0.5050 -0.0509 + 7PII O23 1747 2.574 4.627 2.632 0.3187 0.2615 0.3175 + 7PII C31 1748 2.534 4.541 2.526 -0.1666 0.4361 0.3570 + 7PII H31 1749 2.621 4.545 2.458 -0.9497 -0.7455 -0.7256 + 7PII C32 1750 2.414 4.588 2.441 0.3181 0.0239 -0.5496 + 7PII H321 1751 2.319 4.615 2.490 0.7128 -2.8389 1.8247 + 7PII H322 1752 2.388 4.519 2.358 -0.5282 -1.0633 0.6154 + 7PII H323 1753 2.447 4.687 2.403 1.2988 1.5943 4.2182 + 7PII C 1754 2.532 4.400 2.575 -0.1534 0.2996 -0.0263 + 7PII O33 1755 2.630 4.339 2.619 -0.5518 -0.1591 0.2266 + 7PII C25 1756 2.377 4.737 2.863 0.1802 0.1446 -0.3132 + 7PII H25 1757 2.272 4.759 2.893 0.0254 1.0455 -1.5197 + 7PII O25 1758 2.453 4.848 2.911 0.2612 -0.4880 1.0224 + 7PII C21 1759 2.530 4.926 2.819 -0.5263 -0.2327 0.5830 + 7PII H21 1760 2.608 4.965 2.888 0.3746 0.0329 -0.5974 + 7PII O41 1761 2.458 5.033 2.758 -0.2873 -0.3789 0.0483 + 7PII O42 1762 2.338 5.256 2.813 0.1000 -0.0286 -0.0704 + 7PII O43 1763 2.228 5.046 2.885 -0.0295 -0.4979 -0.8754 + 7PII P44 1764 2.360 5.116 2.866 -0.1425 -0.0619 -0.0643 + 7PII O45 1765 2.452 5.125 3.006 0.1802 0.3388 -0.3008 + 7PII O46 1766 2.461 5.343 3.149 0.0412 0.1905 -0.1807 + 7PII O47 1767 2.254 5.190 3.153 0.2740 -0.1320 0.1680 + 7PII P48 1768 2.404 5.203 3.146 0.2377 0.1125 -0.1553 + 7PII O49 1769 2.466 5.100 3.258 0.3668 0.3618 0.0014 + 7PII C51 1770 2.485 5.151 3.391 0.1824 0.0848 0.1344 + 7PII H511 1771 2.488 5.060 3.454 -1.0428 0.1082 0.2459 + 7PII H512 1772 2.393 5.205 3.422 -0.8636 -2.0807 0.8252 + 7PII C52 1773 2.601 5.246 3.397 0.0661 0.2379 -0.0302 + 7PII H521 1774 2.616 5.322 3.319 -0.1453 -0.4370 -0.7380 + 7PII C53 1775 2.707 5.237 3.479 0.3173 -0.3002 -0.4118 + 7PII C530 1776 2.825 5.327 3.451 0.2977 -0.3409 -0.6398 + 7PII H530 1777 2.915 5.262 3.448 0.0485 -0.8880 2.9009 + 7PII H531 1778 2.832 5.397 3.537 2.1404 -1.7442 0.3610 + 7PII H532 1779 2.820 5.380 3.354 0.1538 0.7317 -0.0441 + 7PII C54 1780 2.705 5.137 3.590 0.0358 0.1635 -0.0015 + 7PII H541 1781 2.790 5.069 3.568 -0.5824 -0.1471 -1.4483 + 7PII H542 1782 2.614 5.072 3.590 -2.0259 3.0478 -0.6493 + 7PII C55 1783 2.721 5.200 3.729 -0.1310 0.2632 -0.0239 + 7PII H551 1784 2.651 5.285 3.739 0.8255 1.4698 -3.4421 + 7PII H552 1785 2.826 5.237 3.727 0.0013 -0.0167 1.7223 + 7PII C56 1786 2.701 5.097 3.836 -0.1720 0.2020 -0.0901 + 7PII H561 1787 2.697 4.993 3.801 0.5045 -0.5231 1.9393 + 7PII C57 1788 2.704 5.123 3.968 -0.7595 0.3351 -0.0996 + 7PII C570 1789 2.688 5.005 4.061 -0.6593 0.1301 -0.3354 + 7PII H570 1790 2.674 4.909 4.007 -1.6680 -1.0742 2.0684 + 7PII H571 1791 2.593 5.024 4.115 0.0335 0.3019 0.8163 + 7PII H572 1792 2.770 5.003 4.135 -0.4747 -1.2369 -0.5821 + 7PII C58 1793 2.732 5.256 4.030 -0.5385 0.3066 -0.1358 + 7PII H581 1794 2.831 5.241 4.077 -1.8096 -0.4572 2.3320 + 7PII H582 1795 2.761 5.334 3.956 -0.3725 0.5683 0.1957 + 7PII C59 1796 2.620 5.312 4.118 -0.1560 -0.4023 0.7912 + 7PII H591 1797 2.594 5.232 4.191 -3.0564 -0.3729 -0.1884 + 7PII H592 1798 2.526 5.328 4.060 0.7896 -1.0742 -0.9083 + 7PII C60 1799 2.648 5.428 4.210 0.1902 0.0819 0.0796 + 7PII H601 1800 2.754 5.453 4.222 0.1132 -0.2845 1.4643 + 7PII C61 1801 2.563 5.498 4.287 -0.2437 -0.4194 0.0532 + 7PII C610 1802 2.611 5.614 4.371 -1.0084 0.1725 -0.3247 + 7PII H610 1803 2.639 5.700 4.306 -0.9017 -0.3988 -1.0462 + 7PII H611 1804 2.527 5.642 4.438 -1.2000 -0.7426 -0.1779 + 7PII H612 1805 2.702 5.589 4.429 -1.0543 -0.4182 -0.5054 + 7PII C62 1806 2.419 5.458 4.294 -0.2982 -0.1970 0.2262 + 7PII H621 1807 2.401 5.362 4.240 -0.0513 -0.5540 0.7730 + 7PII H622 1808 2.371 5.530 4.225 0.0958 0.3375 0.5246 + 7PII C63 1809 2.338 5.461 4.424 0.0141 0.3981 0.4042 + 7PII H631 1810 2.396 5.397 4.493 -0.3290 0.0446 0.3609 + 7PII H632 1811 2.326 5.564 4.464 1.9220 0.6394 0.3935 + 7PII C64 1812 2.202 5.401 4.403 -0.3365 1.0246 0.8964 + 7PII H641 1813 2.163 5.413 4.301 -0.2305 1.5390 0.9143 + 7PII C65 1814 2.119 5.361 4.500 -0.5540 0.3421 0.4275 + 7PII C650 1815 1.989 5.306 4.450 -0.3782 0.4424 -0.1413 + 7PII H650 1816 1.999 5.262 4.348 1.0343 1.5416 -0.4657 + 7PII H651 1817 1.897 5.367 4.463 -1.2364 -0.5388 -1.4837 + 7PII H652 1818 1.982 5.210 4.506 -0.7593 -0.0330 -0.9941 + 7PII C66 1819 2.167 5.355 4.643 0.0562 -1.0987 0.1613 + 7PII H661 1820 2.233 5.265 4.643 0.5287 -0.7525 -0.6220 + 7PII H662 1821 2.231 5.440 4.672 0.0486 -0.5235 -1.5094 + 7PII C67 1822 2.059 5.330 4.748 -0.3870 0.4029 0.0562 + 7PII H671 1823 1.977 5.405 4.739 -0.0675 0.6865 -0.4674 + 7PII H672 1824 2.017 5.229 4.726 -0.0755 0.2662 0.0955 + 7PII C68 1825 2.108 5.335 4.889 0.0414 -0.0031 -0.0815 + 7PII H681 1826 2.218 5.335 4.895 0.0673 0.3025 -0.6422 + 7PII C69 1827 2.034 5.323 5.000 0.2710 0.0067 0.0739 + 7PII C690 1828 2.095 5.342 5.137 -0.0981 0.2690 0.2011 + 7PII H690 1829 2.052 5.427 5.193 -0.4563 0.9365 -1.0723 + 7PII H691 1830 2.206 5.348 5.131 -0.1321 1.3215 0.8304 + 7PII H692 1831 2.076 5.255 5.203 -2.2117 0.5812 0.0005 + 7PII C70 1832 1.885 5.314 4.985 0.2989 -0.2200 -0.0763 + 7PII H701 1833 1.863 5.423 4.978 1.2165 -0.0124 0.2391 + 7PII H702 1834 1.846 5.280 4.887 -0.5305 0.8456 -0.1173 + 7PII C71 1835 1.796 5.253 5.094 -0.1116 -0.6179 -0.6402 + 7PII H711 1836 1.694 5.286 5.063 -1.1429 -1.0733 2.2401 + 7PII H712 1837 1.797 5.303 5.193 -2.0121 -0.6530 -0.5850 + 7PII C72 1838 1.794 5.104 5.110 0.0535 -0.5090 0.3840 + 7PII H721 1839 1.861 5.054 5.039 0.1511 -0.1993 0.2555 + 7PII C73 1840 1.720 5.031 5.195 -0.4251 -0.6025 -0.1128 + 7PII C730 1841 1.626 5.096 5.293 0.4503 0.1336 0.2450 + 7PII H730 1842 1.523 5.056 5.279 -0.1374 1.5715 0.4316 + 7PII H731 1843 1.656 5.078 5.398 -0.5640 -0.7419 0.3827 + 7PII H732 1844 1.618 5.204 5.270 0.5733 -0.2008 -1.4094 + 7PII C74 1845 1.718 4.881 5.201 -0.2459 -0.5938 0.1772 + 7PII H741 1846 1.639 4.855 5.274 0.4002 -1.1901 0.6769 + 7PII H742 1847 1.685 4.836 5.105 0.1619 0.4970 -0.4782 + 7PII C75 1848 1.854 4.816 5.231 0.0989 -0.0605 -0.2219 + 7PII H751 1849 1.836 4.708 5.216 -3.6413 0.5450 -0.2442 + 7PII H752 1850 1.919 4.859 5.153 0.8339 -0.5064 0.1470 + 7PII C76 1851 1.909 4.852 5.366 -0.3528 0.0786 -0.0716 + 7PII H761 1852 1.878 4.949 5.408 0.3457 -0.4809 1.7922 + 7PII C77 1853 1.996 4.778 5.437 -0.0354 0.4205 -0.1080 + 7PII C770 1854 2.024 4.811 5.581 -0.1299 0.6639 -0.1478 + 7PII H770 1855 2.133 4.810 5.602 0.2734 -1.3034 -2.3032 + 7PII H771 1856 1.982 4.726 5.639 -0.2806 0.4819 -0.5229 + 7PII H772 1857 1.989 4.911 5.616 0.9770 1.1785 -0.4911 + 7PII C78 1858 2.052 4.648 5.385 -0.5022 -0.0995 0.6617 + 7PII H781 1859 2.039 4.653 5.275 1.1394 1.4732 0.5274 + 7PII H782 1860 2.162 4.657 5.382 -0.5834 0.6601 -0.3412 + 7PII C79 1861 1.994 4.521 5.447 -0.5443 -0.4338 -0.0857 + 7PII H791 1862 1.888 4.531 5.416 -0.3067 -0.6077 -0.9751 + 7PII H792 1863 1.986 4.520 5.557 1.2840 -0.0799 0.0638 + 7PII C80 1864 2.037 4.393 5.379 -0.3382 -0.1365 -0.5167 + 7PII H801 1865 2.001 4.373 5.278 0.0278 0.2427 -0.7250 + 7PII C81 1866 2.119 4.307 5.440 -0.4491 0.0948 -0.0344 + 7PII C810 1867 2.186 4.338 5.571 -0.6091 0.0136 0.0643 + 7PII H810 1868 2.161 4.433 5.623 1.7749 -0.4544 2.0825 + 7PII H811 1869 2.296 4.337 5.557 -0.8191 0.3232 -1.6191 + 7PII H812 1870 2.146 4.261 5.640 -0.9745 0.0336 -0.1187 + 7PII C82 1871 2.159 4.176 5.378 -0.4499 -0.2796 0.7521 + 7PII H821 1872 2.249 4.197 5.316 -0.3244 -1.0675 0.6612 + 7PII H822 1873 2.187 4.107 5.460 -0.0123 0.2189 1.0234 + 7PII C83 1874 2.055 4.097 5.298 -0.0372 -0.4906 0.4239 + 7PII H831 1875 1.965 4.059 5.352 1.9122 -1.8153 2.7545 + 7PII H832 1876 2.013 4.172 5.228 -0.9263 -1.7106 -0.3649 + 7PII C84 1877 2.109 3.979 5.222 -0.1256 0.0012 -0.3997 + 7PII H841 1878 2.201 3.934 5.261 0.0114 2.4025 2.0643 + 7PII C85 1879 2.058 3.940 5.104 -0.0607 -0.4898 -0.2694 + 7PII C850 1880 1.935 4.004 5.045 -0.0625 0.1689 0.4560 + 7PII H850 1881 1.871 3.919 5.013 -0.2662 -0.0160 1.3480 + 7PII H851 1882 1.878 4.069 5.115 0.1325 1.1616 -0.3116 + 7PII H852 1883 1.952 4.057 4.950 -0.3928 -0.6293 -0.0466 + 7PII C86 1884 2.136 3.839 5.025 0.7829 -0.1851 0.1710 + 7PII H861 1885 2.132 3.879 4.921 0.7408 1.1732 0.6904 + 7PII H862 1886 2.244 3.836 5.051 0.8063 0.5591 0.1574 + 7PII C87 1887 2.085 3.695 5.039 -0.1320 0.1212 -0.0073 + 7PII H871 1888 1.979 3.695 5.006 -0.1662 -0.5518 0.0936 + 7PII H872 1889 2.074 3.652 5.141 0.0513 0.4223 0.1376 + 7PII C88 1890 2.161 3.590 4.964 -0.0640 -0.1658 0.4641 + 7PII H881 1891 2.124 3.559 4.865 0.4742 0.1817 0.1503 + 7PII C89 1892 2.269 3.525 5.010 0.1727 0.0160 0.1674 + 7PII C890 1893 2.319 3.416 4.919 -0.1905 0.7534 -0.9203 + 7PII H890 1894 2.421 3.438 4.879 -0.3763 -0.2332 -1.9137 + 7PII H891 1895 2.255 3.393 4.831 -1.8595 0.3609 0.3923 + 7PII H892 1896 2.326 3.317 4.969 -2.4307 -0.6546 -3.3788 + 7PII C90 1897 2.335 3.553 5.142 0.0404 0.3652 0.1578 + 7PII H901 1898 2.286 3.629 5.206 -1.2575 -0.7316 0.4661 + 7PII H902 1899 2.342 3.458 5.199 0.1011 2.1021 3.0553 + 7PII C91 1900 2.482 3.590 5.115 0.2290 -0.3509 0.2089 + 7PII H911 1901 2.544 3.506 5.077 -2.2713 -1.9389 -0.4639 + 7PII H912 1902 2.496 3.665 5.034 -2.5874 -1.5146 -1.3731 + 7PII C92 1903 2.531 3.655 5.241 -0.0494 0.0439 0.1103 + 7PII H921 1904 2.506 3.762 5.249 -0.4605 -0.0993 0.7430 + 7PII C93 1905 2.602 3.604 5.342 -0.3005 -0.3492 0.0892 + 7PII C94 1906 2.639 3.458 5.342 0.1572 -0.2363 -0.0513 + 7PII H940 1907 2.640 3.416 5.239 0.1813 -0.5693 0.0831 + 7PII H941 1908 2.558 3.402 5.393 0.7215 -0.3522 0.7089 + 7PII H942 1909 2.738 3.431 5.385 -0.8567 -1.0691 1.7545 + 7PII C95 1910 2.639 3.699 5.452 -0.8803 0.2283 -0.2175 + 7PII H950 1911 2.584 3.796 5.447 -0.8570 0.2881 0.6876 + 7PII H951 1912 2.748 3.711 5.467 -0.6112 -0.1132 -1.8702 + 7PII H952 1913 2.604 3.649 5.545 0.2134 0.6573 0.4273 + 7PII N1 1914 2.413 4.338 2.581 0.1518 -0.2482 0.4004 + 7PII HN1 1915 2.330 4.385 2.554 -0.2937 -1.5570 -0.4896 + 7PII CA1 1916 2.393 4.214 2.649 0.0122 -0.1256 0.5872 + 7PII HA1 1917 2.388 4.231 2.755 5.0352 -0.8673 0.9712 + 7PII CB1 1918 2.249 4.173 2.611 0.2531 0.2289 -0.7118 + 7PII HB1 1919 2.240 4.168 2.501 0.2916 1.4729 -0.7798 + 7PII HB2 1920 2.211 4.081 2.659 -0.3666 0.6346 -0.4256 + 7PII HB3 1921 2.169 4.245 2.637 -2.2396 -3.6954 2.5121 + 7PII C1 1922 2.478 4.094 2.623 0.1302 0.1155 -0.1320 + 7PII O1 1923 2.505 4.018 2.716 0.2608 -0.0195 -0.2760 + 7PII CD1 1924 2.506 3.893 2.323 -0.4571 0.2106 -0.1719 + 7PII OE1 1925 2.452 3.779 2.309 -0.2207 0.1271 -0.4013 + 7PII OE2 1926 2.493 3.972 2.226 -0.0292 0.2935 -0.1599 + 7PII N2 1927 2.515 4.070 2.496 0.5660 0.6760 -0.1099 + 7PII HN2 1928 2.498 4.136 2.423 0.6523 -1.1738 -1.8272 + 7PII CA2 1929 2.573 3.949 2.448 -0.3126 0.3318 -0.3032 + 7PII HA2 1930 2.574 3.870 2.526 -2.8509 3.1615 2.5895 + 7PII CB2 1931 2.724 3.968 2.424 -0.2839 -0.4438 -0.7447 + 7PII HB11 1932 2.770 4.002 2.519 -0.1553 -0.1955 -0.8984 + 7PII HB21 1933 2.733 4.055 2.357 0.2069 -1.1439 -1.5921 + 7PII CG1 1934 2.801 3.847 2.372 0.6149 -0.3288 0.3254 + 7PII HG11 1935 2.800 3.768 2.451 -3.8816 -0.4763 0.1410 + 7PII HG21 1936 2.758 3.788 2.289 0.4309 0.7207 -0.3135 + 7PII C2 1937 2.938 3.882 2.323 0.6207 -0.0733 0.5257 + 7PII O2 1938 2.994 3.808 2.243 0.6232 0.2847 0.1970 + 7PII N3 1939 2.997 3.995 2.364 0.2010 0.2709 0.1740 + 7PII HN3 1940 2.966 4.050 2.442 -0.8410 0.4526 -0.3698 + 7PII CA3 1941 3.083 4.073 2.281 0.4281 -0.2626 -0.0885 + 7PII HA3 1942 3.156 4.000 2.247 -0.3250 -1.4319 0.7813 + 7PII CB3 1943 3.157 4.176 2.368 0.1640 -0.6348 0.5743 + 7PII HB13 1944 3.221 4.250 2.316 0.6157 -0.9359 0.6992 + 7PII HB23 1945 3.206 4.102 2.435 1.4915 -0.6508 -0.3994 + 7PII CG2 1946 3.086 4.268 2.467 0.5414 0.3822 -0.1012 + 7PII HG12 1947 3.030 4.197 2.531 2.4024 -1.2373 -0.2491 + 7PII HG22 1948 3.167 4.324 2.519 -1.0520 0.5486 2.2354 + 7PII CD2 1949 2.986 4.365 2.404 -0.3453 -0.3779 0.1283 + 7PII HD12 1950 3.040 4.411 2.318 -0.0344 -0.0167 0.5156 + 7PII HD22 1951 2.898 4.307 2.372 -0.1395 -0.0760 -1.0013 + 7PII CE 1952 2.939 4.474 2.500 -0.0594 0.0619 -0.2217 + 7PII HE1 1953 3.020 4.541 2.538 1.4525 -2.2085 0.5905 + 7PII HE2 1954 2.865 4.542 2.454 -0.0044 2.2909 2.9100 + 7PII NZ 1955 2.877 4.420 2.623 0.0854 0.3304 -0.0264 + 7PII HZ1 1956 2.930 4.333 2.645 -1.1727 -0.0413 1.6105 + 7PII HZ2 1957 2.896 4.488 2.699 1.0365 0.8920 -0.7646 + 7PII HZ3 1958 2.777 4.394 2.619 0.7711 -2.3777 -0.0437 + 7PII C4 1959 3.025 4.129 2.156 -0.3227 -0.6735 0.0781 + 7PII O4 1960 2.904 4.116 2.140 -0.4031 0.0654 0.0789 + 7PII N4 1961 3.110 4.191 2.072 -0.4434 -0.2953 0.2273 + 7PII HN4 1962 3.200 4.218 2.106 -0.5108 -0.9623 0.9315 + 7PII CA4 1963 3.062 4.252 1.952 0.3829 -0.4891 -0.2030 + 7PII HA4 1964 2.960 4.282 1.970 0.3992 -0.7133 0.2771 + 7PII CB4 1965 3.066 4.147 1.840 0.1202 -0.4606 -0.2407 + 7PII HB14 1966 3.025 4.051 1.877 -3.0643 0.9687 -0.0023 + 7PII HB24 1967 3.021 4.180 1.743 -0.5644 -0.3257 0.1276 + 7PII HB34 1968 3.167 4.113 1.808 -0.2923 -0.1791 -1.8664 + 7PII C5 1969 3.132 4.381 1.928 0.1101 -0.3354 -0.1697 + 7PII O5 1970 3.217 4.414 2.011 -0.0147 0.4196 -0.3382 + 7PII N5 1971 3.092 4.457 1.825 0.0938 -0.5350 -0.3124 + 7PII HN5 1972 3.008 4.423 1.783 1.0089 -0.9161 -1.8321 + 7PII CA5 1973 3.148 4.586 1.796 -0.3041 -0.2932 -0.0025 + 7PII HA5 1974 3.110 4.613 1.699 -0.9339 1.5783 0.7586 + 7PII CB5 1975 3.301 4.579 1.787 -0.3134 0.3115 -0.6153 + 7PII HB15 1976 3.328 4.496 1.718 -1.1563 -0.4871 0.0202 + 7PII HB25 1977 3.346 4.565 1.888 0.8672 1.4251 -0.9923 + 7PII HB35 1978 3.342 4.676 1.751 -1.4521 -0.8603 -5.1252 + 7PII C6 1979 3.114 4.702 1.889 -0.3474 0.0997 -0.5071 + 7PII OT1 1980 3.134 4.818 1.844 0.6609 0.0375 -0.2052 + 7PII OT2 1981 3.062 4.678 2.001 -0.4243 0.1680 -0.5283 + 8PII C13 1982 12.114 3.818 8.962 0.3572 -0.0509 -0.0910 + 8PII H13 1983 12.133 3.921 8.999 0.6371 -1.2695 3.1742 + 8PII O13 1984 11.986 3.826 8.904 0.1598 -0.5477 0.2879 + 8PII HO13 1985 11.949 3.911 8.927 -0.4474 -0.5889 -0.5367 + 8PII C14 1986 12.113 3.718 9.071 -0.1613 -0.1232 -0.1637 + 8PII H14 1987 12.053 3.629 9.040 0.3322 -0.3902 -0.3258 + 8PII O14 1988 12.044 3.773 9.181 0.3789 -0.0327 0.1229 + 8PII HO14 1989 12.109 3.829 9.222 0.6582 0.8775 -1.5476 + 8PII C16 1990 12.257 3.565 9.218 0.0562 0.4070 -0.6487 + 8PII H161 1991 12.199 3.599 9.307 -1.1098 -1.0311 -0.8621 + 8PII H162 1992 12.206 3.469 9.195 1.8259 -0.8964 0.8560 + 8PII O16 1993 12.390 3.532 9.252 -0.2387 -0.1395 0.0012 + 8PII HO16 1994 12.450 3.541 9.177 0.2686 0.7035 0.4834 + 8PII C12 1995 12.215 3.779 8.861 0.0938 0.1137 -0.4089 + 8PII H12 1996 12.173 3.798 8.760 1.1434 -1.0462 -1.0639 + 8PII N17 1997 12.336 3.853 8.875 0.0267 0.1957 -0.2171 + 8PII H17 1998 12.410 3.798 8.914 -1.0755 -0.8583 0.3753 + 8PII C18 1999 12.345 3.983 8.842 0.5628 0.2388 0.1002 + 8PII O18 2000 12.244 4.034 8.796 0.4349 -0.1108 -0.0093 + 8PII C19 2001 12.472 4.061 8.873 0.4754 0.1714 0.6445 + 8PII H191 2002 12.475 4.091 8.980 0.2080 2.3349 0.0375 + 8PII H192 2003 12.558 4.003 8.834 0.0680 -0.5207 0.7610 + 8PII H193 2004 12.472 4.158 8.817 2.1304 0.0286 0.4006 + 8PII C11 2005 12.261 3.638 8.870 0.0817 0.1204 -0.2551 + 8PII H11 2006 12.334 3.632 8.786 -1.4578 -2.8467 -1.3787 + 8PII O15 2007 12.320 3.621 8.999 0.0853 -0.0981 -0.2887 + 8PII C15 2008 12.249 3.670 9.112 0.1897 0.5634 -0.5003 + 8PII H15 2009 12.305 3.758 9.151 0.7630 0.3660 -0.8944 + 8PII O24 2010 12.156 3.549 8.849 -0.2715 0.5543 -0.3072 + 8PII C24 2011 12.148 3.486 8.723 0.1197 -0.1515 0.0179 + 8PII H24 2012 12.189 3.560 8.651 -0.4399 -1.3057 -1.4998 + 8PII C26 2013 11.913 3.556 8.710 0.0689 0.2553 -0.4369 + 8PII H261 2014 11.902 3.560 8.820 -1.3853 -2.0040 -0.4860 + 8PII H262 2015 11.817 3.524 8.666 -1.3593 0.3934 2.5774 + 8PII O26 2016 11.958 3.680 8.656 0.4009 0.4927 0.3799 + 8PII HO26 2017 11.954 3.738 8.733 -2.7862 -1.2145 1.5254 + 8PII C22 2018 12.232 3.343 8.559 0.0647 0.3389 0.1367 + 8PII H22 2019 12.257 3.442 8.516 -0.5773 0.4499 0.0162 + 8PII N27 2020 12.328 3.242 8.525 0.2221 0.3321 0.5943 + 8PII H27 2021 12.298 3.147 8.525 -1.1739 0.7720 -0.2780 + 8PII C28 2022 12.458 3.259 8.492 0.1707 -0.2981 0.1051 + 8PII O28 2023 12.525 3.164 8.451 0.0595 -0.0883 -0.5574 + 8PII C29 2024 12.524 3.395 8.507 -0.3143 -0.0094 -0.3682 + 8PII H291 2025 12.495 3.456 8.419 -1.3292 1.4466 0.9844 + 8PII H292 2026 12.634 3.383 8.518 -0.0320 0.5157 -2.4951 + 8PII H293 2027 12.491 3.438 8.604 -0.3778 2.4708 -1.4869 + 8PII C23 2028 12.239 3.371 8.704 0.8928 0.4599 0.0627 + 8PII H23 2029 12.340 3.416 8.719 -0.4100 3.0538 1.2041 + 8PII O23 2030 12.222 3.257 8.786 -0.0156 0.2906 -0.3583 + 8PII C31 2031 12.272 3.268 8.919 -0.1847 0.3387 -0.3034 + 8PII H31 2032 12.278 3.376 8.944 1.1359 0.7745 -2.4303 + 8PII C32 2033 12.412 3.206 8.910 -0.3751 -0.0776 -0.3573 + 8PII H321 2034 12.474 3.230 8.999 -1.3987 0.0523 0.3106 + 8PII H322 2035 12.404 3.097 8.891 4.7464 0.0630 -3.3963 + 8PII H323 2036 12.467 3.231 8.817 0.4567 -0.8269 -0.0734 + 8PII C 2037 12.182 3.200 9.016 0.3227 -0.5768 -0.4742 + 8PII O33 2038 12.059 3.200 9.002 0.1774 0.8434 0.7448 + 8PII C25 2039 12.008 3.443 8.691 0.0644 0.2292 -0.2744 + 8PII H25 2040 11.969 3.365 8.761 0.9641 2.0988 2.3063 + 8PII O25 2041 11.992 3.397 8.557 0.2304 0.1433 -0.2597 + 8PII C21 2042 12.096 3.312 8.509 0.0801 -0.5164 0.5943 + 8PII H21 2043 12.104 3.320 8.399 -2.1352 1.8900 0.5931 + 8PII O41 2044 12.067 3.177 8.546 0.2063 -0.7229 -0.0517 + 8PII O42 2045 11.905 2.981 8.516 -0.2725 0.2367 0.5445 + 8PII O43 2046 11.858 3.196 8.388 -0.0641 0.1537 0.0503 + 8PII P44 2047 11.961 3.100 8.442 -0.2766 -0.1049 -0.0109 + 8PII O45 2048 12.066 3.042 8.325 0.3185 0.9014 0.0158 + 8PII O46 2049 11.989 3.190 8.122 0.0908 0.0265 0.3259 + 8PII O47 2050 11.900 2.950 8.137 -0.4534 0.3658 0.3405 + 8PII P48 2051 12.012 3.047 8.166 -0.0214 -0.0611 0.0950 + 8PII O49 2052 12.146 2.978 8.099 0.1276 0.2626 0.0662 + 8PII C51 2053 12.177 3.007 7.962 0.1549 0.2422 0.0739 + 8PII H511 2054 12.207 3.113 7.954 0.6907 0.1215 0.4359 + 8PII H512 2055 12.100 2.971 7.890 0.4258 1.1953 -0.6845 + 8PII C52 2056 12.298 2.920 7.946 -0.0012 -0.1126 0.8376 + 8PII H521 2057 12.305 2.838 8.020 0.8854 -1.1472 -0.3939 + 8PII C53 2058 12.402 2.922 7.862 -0.6083 0.2403 0.0939 + 8PII C530 2059 12.513 2.822 7.881 -1.1105 -0.3102 0.1206 + 8PII H530 2060 12.497 2.748 7.962 -0.8581 -0.3470 0.1347 + 8PII H531 2061 12.525 2.769 7.784 -2.1421 -0.9923 0.3551 + 8PII H532 2062 12.604 2.877 7.910 -0.9116 -1.1745 1.1358 + 8PII C54 2063 12.432 3.030 7.762 0.3036 0.1522 0.2615 + 8PII H541 2064 12.338 3.089 7.752 0.0524 -0.3525 -0.3985 + 8PII H542 2065 12.513 3.098 7.796 0.2526 -0.5305 1.7359 + 8PII C55 2066 12.471 2.971 7.627 0.6070 0.2447 0.3120 + 8PII H551 2067 12.571 2.922 7.626 0.7468 0.5217 0.1976 + 8PII H552 2068 12.397 2.901 7.583 0.1820 1.7828 -1.3882 + 8PII C56 2069 12.497 3.086 7.535 0.0703 0.2261 0.1330 + 8PII H561 2070 12.500 3.187 7.579 0.8461 1.8293 -3.5841 + 8PII C57 2071 12.524 3.077 7.404 0.8744 -0.4397 0.3452 + 8PII C570 2072 12.562 3.205 7.336 0.2332 -0.3430 0.1592 + 8PII H570 2073 12.647 3.186 7.266 2.2522 3.1633 1.6018 + 8PII H571 2074 12.590 3.292 7.399 -0.7746 0.6647 -0.7644 + 8PII H572 2075 12.476 3.250 7.281 -1.5674 -2.0694 1.5769 + 8PII C58 2076 12.536 2.954 7.318 0.0010 -0.3826 0.1468 + 8PII H581 2077 12.645 2.935 7.315 0.0580 -0.4056 2.0670 + 8PII H582 2078 12.499 2.865 7.374 -1.2417 0.3143 0.4406 + 8PII C59 2079 12.491 2.952 7.172 0.2449 0.1015 0.0683 + 8PII H591 2080 12.517 2.847 7.147 -1.3484 -0.3427 0.2722 + 8PII H592 2081 12.559 3.022 7.118 1.7587 -0.7854 0.8175 + 8PII C60 2082 12.346 2.985 7.154 0.0221 -1.0352 -0.1981 + 8PII H601 2083 12.279 2.974 7.241 1.5877 0.3330 1.1649 + 8PII C61 2084 12.276 2.983 7.040 0.0059 0.2605 -0.2092 + 8PII C610 2085 12.132 3.024 7.058 -0.1539 -0.0967 -0.6760 + 8PII H610 2086 12.061 2.964 6.998 -0.7008 0.1265 -0.2475 + 8PII H611 2087 12.124 3.128 7.020 -0.5426 0.6041 1.3005 + 8PII H612 2088 12.097 3.016 7.164 0.1044 -1.4235 -0.6928 + 8PII C62 2089 12.339 2.967 6.905 -0.8356 -0.5758 -0.5000 + 8PII H621 2090 12.442 2.926 6.915 -0.2384 0.7858 -1.1161 + 8PII H622 2091 12.292 2.881 6.851 -0.4405 -0.9433 -0.2568 + 8PII C63 2092 12.336 3.090 6.814 0.3602 0.0162 0.2685 + 8PII H631 2093 12.409 3.165 6.850 -0.3049 0.3225 0.9796 + 8PII H632 2094 12.230 3.123 6.808 0.9088 1.7964 0.5188 + 8PII C64 2095 12.360 3.054 6.670 -0.2017 0.2623 0.1123 + 8PII H641 2096 12.334 2.951 6.642 -1.2784 0.4228 0.5238 + 8PII C65 2097 12.415 3.141 6.584 0.5764 0.0463 0.4036 + 8PII C650 2098 12.464 3.102 6.447 -0.3711 0.3679 -0.0308 + 8PII H650 2099 12.427 3.187 6.386 -3.0001 -0.2481 0.7279 + 8PII H651 2100 12.429 3.001 6.418 -0.5384 0.4990 -0.2934 + 8PII H652 2101 12.575 3.094 6.440 -0.3062 2.1136 -1.1949 + 8PII C66 2102 12.444 3.280 6.633 0.0119 0.1462 0.4439 + 8PII H661 2103 12.529 3.289 6.704 -1.9793 -1.4973 3.0754 + 8PII H662 2104 12.360 3.309 6.700 0.2935 -2.1925 1.8507 + 8PII C67 2105 12.448 3.387 6.524 0.1028 0.2080 0.5078 + 8PII H671 2106 12.543 3.394 6.467 -0.6961 -1.7093 -1.0929 + 8PII H672 2107 12.369 3.368 6.449 0.0692 0.4708 0.4765 + 8PII C68 2108 12.447 3.529 6.571 0.3675 0.1545 0.6689 + 8PII H681 2109 12.509 3.540 6.662 -0.6924 -0.7936 1.5007 + 8PII C69 2110 12.377 3.637 6.535 -0.0939 -0.2288 0.4324 + 8PII C690 2111 12.394 3.761 6.618 -0.2081 0.2234 -0.2249 + 8PII H690 2112 12.430 3.843 6.552 -0.8725 1.1637 0.5756 + 8PII H691 2113 12.298 3.793 6.665 -0.5154 -0.2335 -0.5443 + 8PII H692 2114 12.476 3.751 6.692 -0.4521 -0.6751 -0.0779 + 8PII C70 2115 12.294 3.651 6.410 0.9457 0.7337 -0.1587 + 8PII H701 2116 12.285 3.557 6.352 1.2924 1.1132 -0.8287 + 8PII H702 2117 12.344 3.724 6.343 -0.6502 1.9790 -0.0116 + 8PII C71 2118 12.150 3.697 6.433 0.6658 -0.1532 -0.1844 + 8PII H711 2119 12.073 3.628 6.474 1.2012 -1.1058 -0.7806 + 8PII H712 2120 12.164 3.773 6.513 1.7468 -0.2516 -0.2816 + 8PII C72 2121 12.106 3.755 6.302 0.7115 -0.3515 -0.2870 + 8PII H721 2122 12.075 3.680 6.227 -0.1160 1.4398 -1.7446 + 8PII C73 2123 12.119 3.878 6.250 -0.1812 -0.0493 0.2205 + 8PII C730 2124 12.183 3.987 6.331 0.2501 -0.3492 0.2911 + 8PII H730 2125 12.272 4.027 6.278 -0.0197 0.3373 0.3309 + 8PII H731 2126 12.222 3.963 6.432 2.3056 1.0133 -0.1742 + 8PII H732 2127 12.108 4.064 6.359 -1.7465 -2.0923 -0.2524 + 8PII C74 2128 12.066 3.911 6.113 0.3981 0.2197 0.0660 + 8PII H741 2129 12.032 3.826 6.051 0.8370 1.1013 -1.3719 + 8PII H742 2130 12.159 3.950 6.065 0.5816 0.1479 0.3621 + 8PII C75 2131 11.949 4.007 6.098 0.1819 -0.0055 0.2784 + 8PII H751 2132 11.940 4.049 5.995 -4.0360 -1.4297 0.0474 + 8PII H752 2133 11.969 4.087 6.173 -1.0803 -0.0676 0.6832 + 8PII C76 2134 11.811 3.954 6.125 0.3246 -0.5048 -0.0247 + 8PII H761 2135 11.780 3.857 6.085 1.0479 -0.7375 -0.0161 + 8PII C77 2136 11.714 4.033 6.174 0.4941 -0.0841 -0.3517 + 8PII C770 2137 11.571 3.985 6.167 0.3519 0.2963 -0.1198 + 8PII H770 2138 11.532 3.959 6.268 1.6784 2.4435 0.9539 + 8PII H771 2139 11.555 3.899 6.099 -1.0158 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H31J 122 7.567 4.737 3.343 -0.7042 0.3728 0.4059 + 715CDL2 H31K 123 7.484 4.900 3.343 -0.6995 0.5715 0.7284 + 715CDL2 C2 124 7.722 4.459 3.164 -0.2582 0.0745 -0.0275 + 715CDL2 HG22 125 7.776 4.372 3.120 -0.7305 0.8618 -2.1960 + 715CDL2 OG12 126 7.660 4.534 3.061 -0.1204 0.6035 0.2766 + 715CDL2 HO12 127 7.697 4.623 3.065 2.1614 -0.3601 0.6251 + 715CDL2 C1 128 7.631 4.401 3.273 -0.1678 0.0883 0.0581 + 715CDL2 HG11 129 7.696 4.344 3.343 -0.0399 0.4018 0.2000 + 715CDL2 HG12 130 7.606 4.488 3.337 0.4276 -0.8233 1.5190 + 715CDL2 P1 131 7.412 4.281 3.332 -0.0998 -0.3075 0.0297 + 715CDL2 OP13 132 7.462 4.159 3.401 0.4699 0.0053 0.1717 + 715CDL2 OP14 133 7.281 4.281 3.264 0.2870 -0.1729 -0.7146 + 715CDL2 OP11 134 7.517 4.330 3.222 -0.0259 -0.1984 0.1492 + 715CDL2 OP12 135 7.408 4.404 3.435 -0.6032 0.1999 -0.5986 + 715CDL2 C11 136 7.462 4.398 3.567 -0.1830 -0.4823 -0.7994 + 715CDL2 H11J 137 7.513 4.304 3.598 0.8713 0.5449 0.5758 + 715CDL2 H11K 138 7.533 4.483 3.569 -1.7749 0.8649 -0.8817 + 715CDL2 C12 139 7.347 4.432 3.664 0.3166 0.1774 -0.4418 + 715CDL2 H12J 140 7.306 4.531 3.636 0.2402 -0.1320 -1.4451 + 715CDL2 O12 141 7.391 4.452 3.798 -0.0852 -0.3721 -0.2225 + 715CDL2 CA1 142 7.428 4.350 3.876 -0.3237 0.2868 0.7476 + 715CDL2 OA1 143 7.415 4.232 3.852 -0.1610 0.3561 0.3107 + 715CDL2 CA2 144 7.470 4.410 4.010 0.2521 0.7193 0.3748 + 715CDL2 H2A 145 7.559 4.472 3.986 1.0716 -1.2132 -1.5976 + 715CDL2 H2B 146 7.384 4.468 4.051 -0.1916 1.3425 -1.4414 + 715CDL2 C13 147 7.228 4.337 3.640 0.2633 0.1880 -0.2209 + 715CDL2 H13J 148 7.212 4.328 3.530 0.8459 0.9757 -0.3697 + 715CDL2 H13K 149 7.255 4.231 3.664 0.9779 0.9463 2.4104 + 715CDL2 O13 150 7.118 4.384 3.718 0.0820 -0.1318 -0.2770 + 715CDL2 CB1 151 7.033 4.464 3.653 0.4062 0.6040 0.2076 + 715CDL2 OB1 152 7.035 4.491 3.534 -0.3402 -0.2673 -0.0038 + 715CDL2 CB2 153 6.932 4.518 3.753 0.0665 0.8113 -0.2447 + 715CDL2 H2D 154 6.885 4.598 3.693 -1.8645 -0.6637 -0.7305 + 715CDL2 H2E 155 6.860 4.438 3.780 1.2069 -0.0243 0.3217 + 715CDL2 C32 156 7.604 4.846 3.519 0.2835 -0.1090 -0.1643 + 715CDL2 H32J 157 7.592 4.738 3.539 -0.2555 0.4416 2.4393 + 715CDL2 O32 158 7.511 4.934 3.582 0.0365 -0.1441 -0.4735 + 715CDL2 CC1 159 7.389 4.886 3.608 0.2948 -0.1896 0.6668 + 715CDL2 OC1 160 7.351 4.778 3.566 -0.5542 0.1264 0.6321 + 715CDL2 CC2 161 7.313 4.978 3.701 -0.5223 0.2157 -0.3996 + 715CDL2 H2R 162 7.377 5.052 3.753 -2.7166 2.6580 -1.1165 + 715CDL2 H2S 163 7.248 5.041 3.636 -0.4079 0.5609 -0.1823 + 715CDL2 C33 164 7.749 4.873 3.563 0.2056 0.1076 -0.0376 + 715CDL2 H33J 165 7.781 4.978 3.543 0.8627 0.3813 2.4549 + 715CDL2 H33K 166 7.818 4.814 3.499 -0.6527 0.0458 -0.9046 + 715CDL2 O33 167 7.769 4.856 3.703 0.4582 0.1935 -0.0636 + 715CDL2 CD1 168 7.773 4.727 3.738 -0.1271 0.1095 -0.3165 + 715CDL2 OD1 169 7.771 4.630 3.664 -0.1954 0.0867 -0.2885 + 715CDL2 CD2 170 7.739 4.722 3.886 -0.1095 0.0658 -0.3160 + 715CDL2 H2X 171 7.632 4.690 3.892 0.1774 -1.0342 -1.0870 + 715CDL2 H2Y 172 7.750 4.823 3.931 -0.8273 -0.1425 0.3368 + 715CDL2 CA3 173 7.509 4.306 4.115 0.2982 0.7392 0.3797 + 715CDL2 H3A 174 7.545 4.366 4.201 0.9236 -0.0778 0.6848 + 715CDL2 H3B 175 7.600 4.250 4.084 0.9902 0.3557 3.0862 + 715CDL2 CA4 176 7.392 4.220 4.163 0.3463 0.7509 0.5186 + 715CDL2 H4A 177 7.428 4.156 4.245 0.3069 -1.5070 -1.2044 + 715CDL2 H4B 178 7.342 4.160 4.083 -1.1187 3.3643 -0.5625 + 715CDL2 CA5 179 7.274 4.298 4.222 -0.2234 0.1052 0.2554 + 715CDL2 H5A 180 7.192 4.227 4.245 0.2396 -0.2600 0.7787 + 715CDL2 H5B 181 7.228 4.357 4.139 -2.5469 -0.7296 0.9457 + 715CDL2 CA6 182 7.298 4.372 4.354 -0.3482 -0.0563 0.3672 + 715CDL2 H6A 183 7.302 4.305 4.442 0.6169 0.6789 0.8959 + 715CDL2 H6B 184 7.400 4.417 4.357 0.4095 -1.8140 0.7774 + 715CDL2 CA7 185 7.194 4.482 4.376 -0.2388 0.1234 -0.0108 + 715CDL2 H7A 186 7.091 4.445 4.355 0.1822 -1.1333 0.1256 + 715CDL2 H7B 187 7.211 4.561 4.300 0.6040 0.0570 0.1083 + 715CDL2 CA8 188 7.199 4.546 4.515 -0.4789 0.4546 -0.1526 + 715CDL2 H8A 189 7.150 4.645 4.508 -0.3771 0.2824 -3.1315 + 715CDL2 H8B 190 7.302 4.579 4.541 0.1129 -0.9257 -0.7141 + 715CDL2 CA9 191 7.142 4.480 4.638 0.1154 -0.0418 -0.1449 + 715CDL2 H9A 192 7.189 4.384 4.663 1.2430 1.1496 2.3322 + 715CDL2 CA10 193 7.042 4.516 4.720 -0.0514 -0.4528 -0.1721 + 715CDL2 H10A 194 7.030 4.464 4.816 -0.5106 1.6099 0.8929 + 715CDL2 CA11 195 6.949 4.632 4.701 -0.0727 -0.3887 0.3029 + 715CDL2 H11A 196 6.946 4.670 4.596 1.1529 -0.0105 0.4044 + 715CDL2 H11B 197 6.845 4.597 4.715 -0.5333 -0.1028 -2.2291 + 715CDL2 CA12 198 6.987 4.747 4.795 -0.3263 0.3259 -0.4642 + 715CDL2 H12A 199 6.939 4.837 4.750 -0.5623 1.7534 2.6540 + 715CDL2 H12B 200 7.097 4.763 4.792 -0.4848 1.2568 -1.4652 + 715CDL2 CA13 201 6.931 4.726 4.936 0.2008 -0.0776 -0.3154 + 715CDL2 H13A 202 6.969 4.630 4.976 -1.1605 -0.3937 0.2234 + 715CDL2 H13B 203 6.821 4.714 4.926 0.4323 -1.5942 -1.0695 + 715CDL2 CA14 204 6.961 4.844 5.029 0.0887 0.0315 -0.4208 + 715CDL2 H14A 205 6.908 4.930 4.983 0.5001 0.2771 -0.4346 + 715CDL2 H14B 206 7.070 4.865 5.031 0.4255 -1.7729 0.8453 + 715CDL2 CA15 207 6.925 4.821 5.176 0.2192 0.1163 -0.3734 + 715CDL2 H15A 208 6.969 4.723 5.203 1.7678 1.0672 0.5427 + 715CDL2 H15B 209 6.814 4.817 5.185 0.2909 0.8697 0.8251 + 715CDL2 CA16 210 6.964 4.933 5.272 -0.4988 -0.0961 0.1644 + 715CDL2 H16A 211 7.074 4.930 5.282 -0.5876 -0.0807 1.2651 + 715CDL2 H16B 212 6.941 5.031 5.224 -1.4471 0.2925 1.4009 + 715CDL2 CA17 213 6.911 4.912 5.415 0.1487 -0.5662 0.3359 + 715CDL2 H17A 214 6.938 4.809 5.444 0.7159 -0.8490 -1.1938 + 715CDL2 H17B 215 6.801 4.927 5.406 0.2290 0.2062 0.5979 + 715CDL2 CA18 216 6.967 5.001 5.525 -0.4915 -0.4602 0.5698 + 715CDL2 H18A 217 6.933 5.104 5.503 0.2608 -0.6485 -1.4055 + 715CDL2 H18B 218 7.077 4.988 5.521 -0.5642 -0.8202 -0.2333 + 715CDL2 H18C 219 6.932 4.974 5.627 -2.0572 -0.6148 -0.0045 + 715CDL2 CB3 220 6.992 4.589 3.875 0.1410 0.5747 -0.1453 + 715CDL2 H3D 221 7.077 4.647 3.834 0.0813 0.9635 0.2895 + 715CDL2 H3E 222 7.033 4.515 3.947 -1.9179 -0.1763 0.2611 + 715CDL2 CB4 223 6.896 4.690 3.938 -0.0725 0.3434 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0.0853 0.5218 0.4054 + 715CDL2 H16D 258 6.484 5.127 5.080 4.1775 -0.8913 -0.6296 + 715CDL2 H16E 259 6.352 5.019 5.025 0.8950 -0.6025 -0.8990 + 715CDL2 CB17 260 6.416 4.966 5.221 -0.4349 -0.1643 0.0153 + 715CDL2 H17D 261 6.508 4.985 5.280 0.1865 2.2019 -1.7059 + 715CDL2 H17E 262 6.332 5.027 5.260 -0.7996 0.3478 -1.5425 + 715CDL2 CB18 263 6.386 4.817 5.228 -0.6745 -0.1309 -0.2732 + 715CDL2 H18D 264 6.469 4.754 5.189 0.2741 0.9197 0.0349 + 715CDL2 H18E 265 6.289 4.791 5.180 -1.8494 0.2373 1.9132 + 715CDL2 H18F 266 6.373 4.788 5.334 0.0157 -1.2817 -0.5079 + 715CDL2 CC3 267 7.233 4.902 3.808 0.1500 -0.1080 -0.1258 + 715CDL2 H3R 268 7.141 4.862 3.760 -0.8355 2.2661 -0.2341 + 715CDL2 H3S 269 7.189 4.976 3.878 1.5837 1.2604 -0.6771 + 715CDL2 CC4 270 7.319 4.804 3.888 0.1208 0.2096 0.3022 + 715CDL2 H4R 271 7.221 4.754 3.902 0.1744 0.5155 1.7888 + 715CDL2 H4S 272 7.371 4.900 3.905 -0.3075 0.4877 0.0818 + 715CDL2 CC5 273 7.325 4.784 4.039 -0.4691 0.5709 0.3771 + 715CDL2 H5R 274 7.236 4.826 4.090 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7.291 4.510 5.221 4.7542 0.5898 -0.2147 + 715CDL2 H17S 309 7.369 4.367 5.136 0.1054 0.2565 -0.5851 + 715CDL2 CC18 310 7.156 4.377 5.120 -0.0223 -0.0915 0.2616 + 715CDL2 H18R 311 7.157 4.300 5.040 -2.4135 1.1539 -0.9799 + 715CDL2 H18S 312 7.076 4.452 5.102 -0.3668 -0.4611 0.2893 + 715CDL2 H18T 313 7.138 4.324 5.216 -0.9499 -1.3293 -0.5927 + 715CDL2 CD3 314 7.825 4.616 3.956 -0.4214 0.2045 0.2679 + 715CDL2 H3X 315 7.930 4.648 3.940 -1.0300 2.8216 1.4666 + 715CDL2 H3Y 316 7.807 4.512 3.922 1.0725 -0.3091 1.0390 + 715CDL2 CD4 317 7.815 4.616 4.109 0.2483 0.1793 0.3083 + 715CDL2 H4X 318 7.847 4.519 4.154 -0.9543 -0.3821 -0.0339 + 715CDL2 H4Y 319 7.707 4.615 4.134 0.3189 -0.9460 0.6065 + 715CDL2 CD5 320 7.884 4.731 4.181 -0.2827 0.6342 0.0952 + 715CDL2 H5X 321 7.979 4.742 4.125 -0.1042 -1.0122 0.0578 + 715CDL2 H5Y 322 7.829 4.824 4.156 1.1949 1.8627 1.4251 + 715CDL2 CD6 323 7.900 4.706 4.331 -0.5479 -0.1373 -0.0028 + 715CDL2 H6X 324 7.969 4.620 4.348 -0.1921 0.0379 -0.5743 + 715CDL2 H6Y 325 7.800 4.682 4.372 -1.4351 2.0216 -0.9119 + 715CDL2 CD7 326 7.933 4.832 4.412 -0.0757 -0.1236 -0.2187 + 715CDL2 H7X 327 8.037 4.870 4.399 -0.2260 0.1096 -0.7236 + 715CDL2 H7Y 328 7.865 4.905 4.363 -0.8593 -0.4570 0.3610 + 715CDL2 CD8 329 7.919 4.830 4.564 0.2149 -0.2810 -0.1905 + 715CDL2 H8X 330 7.810 4.838 4.584 -0.0744 -0.2035 -1.7793 + 715CDL2 H8Y 331 7.968 4.924 4.598 -0.2696 -0.1361 0.0889 + 715CDL2 CD9 332 7.979 4.707 4.628 0.2286 -0.1998 -0.0398 + 715CDL2 H9X 333 8.045 4.647 4.563 -0.8627 0.5276 -1.8317 + 715CDL2 CD10 334 7.933 4.651 4.741 0.3459 -0.4136 -0.0985 + 715CDL2 H10X 335 7.995 4.569 4.781 1.3953 1.0468 1.2898 + 715CDL2 CD11 336 7.829 4.695 4.840 0.8226 0.4009 0.0385 + 715CDL2 H11X 337 7.772 4.608 4.879 0.6967 0.0578 -0.9038 + 715CDL2 H11Y 338 7.759 4.769 4.795 -1.8244 -1.5490 0.9809 + 715CDL2 CD12 339 7.894 4.767 4.958 0.2844 0.3846 0.3461 + 715CDL2 H12X 340 7.985 4.710 4.987 -0.3943 -0.9992 -0.2732 + 715CDL2 H12Y 341 7.927 4.868 4.927 -0.6008 1.2808 2.2410 + 715CDL2 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715CDL2 H18Y 359 7.317 4.817 5.476 0.6092 0.1773 2.0168 + 715CDL2 H18Z 360 7.380 4.982 5.470 1.3153 0.7261 -1.5238 + 716CDL2 C3 361 7.545 0.259 3.595 0.7015 0.9113 0.8691 + 716CDL2 HG31 362 7.538 0.270 3.706 0.5980 -1.7674 1.1253 + 716CDL2 HG32 363 7.471 0.187 3.555 1.2886 0.6079 0.3425 + 716CDL2 P3 364 7.543 0.525 3.607 -0.1154 -0.0031 0.1009 + 716CDL2 OP33 365 7.678 0.580 3.584 -0.0544 -0.3312 -0.3240 + 716CDL2 OP34 366 7.428 0.605 3.561 -0.1170 -0.0238 0.0678 + 716CDL2 OP31 367 7.526 0.385 3.530 -0.0623 0.2025 -0.2849 + 716CDL2 OP32 368 7.536 0.493 3.764 0.7548 1.0633 0.3605 + 716CDL2 C31 369 7.433 0.549 3.846 -0.2042 -0.1778 0.0081 + 716CDL2 H31J 370 7.341 0.488 3.846 0.2083 -0.8379 3.8084 + 716CDL2 H31K 371 7.399 0.652 3.823 -0.9289 0.6517 4.6993 + 716CDL2 C2 372 7.685 0.203 3.569 0.2288 0.1076 0.0586 + 716CDL2 HG22 373 7.723 0.224 3.467 -1.1781 0.0264 -0.4883 + 716CDL2 OG12 374 7.699 0.062 3.586 -0.2139 0.0427 -0.1296 + 716CDL2 HO12 375 7.795 0.060 3.591 -0.2854 -1.6333 0.5486 + 716CDL2 C1 376 7.792 0.260 3.664 0.1601 -0.1832 0.3109 + 716CDL2 HG11 377 7.773 0.369 3.656 -2.2356 -0.7101 -1.3460 + 716CDL2 HG12 378 7.770 0.232 3.769 -1.0132 -1.3313 -0.2409 + 716CDL2 P1 379 8.045 0.322 3.603 0.1175 -0.2116 0.0387 + 716CDL2 OP13 380 8.148 0.273 3.508 0.1122 -0.3887 0.1274 + 716CDL2 OP14 381 8.001 0.462 3.584 -0.0055 -0.3044 -0.3785 + 716CDL2 OP11 382 7.923 0.220 3.621 0.1461 -0.2063 0.2917 + 716CDL2 OP12 383 8.117 0.317 3.746 -0.0831 -0.2945 0.1365 + 716CDL2 C11 384 8.060 0.236 3.849 -0.1198 -0.3720 0.0566 + 716CDL2 H11J 385 7.960 0.268 3.884 -1.4043 -0.9563 -3.0568 + 716CDL2 H11K 386 8.062 0.131 3.814 1.1033 -0.2941 -0.1284 + 716CDL2 C12 387 8.159 0.230 3.966 0.1233 0.0118 -0.1329 + 716CDL2 H12J 388 8.148 0.128 4.009 0.4155 -0.5692 -1.4604 + 716CDL2 O12 389 8.153 0.325 4.073 0.1751 0.2484 -0.3368 + 716CDL2 CA1 390 8.104 0.447 4.056 -0.5327 0.0741 0.4779 + 716CDL2 OA1 391 8.032 0.486 3.966 -0.3584 -0.4003 0.1314 + 716CDL2 CA2 392 8.180 0.538 4.152 -0.1171 0.8231 -0.5716 + 716CDL2 H2A 393 8.223 0.617 4.087 -0.2115 0.6223 -0.8783 + 716CDL2 H2B 394 8.264 0.488 4.204 0.8798 2.0535 -0.9782 + 716CDL2 C13 395 8.305 0.222 3.918 0.1245 -0.3035 -0.0976 + 716CDL2 H13J 396 8.342 0.322 3.886 1.9267 -1.4794 -1.7078 + 716CDL2 H13K 397 8.298 0.151 3.833 -1.3030 -1.0638 0.6560 + 716CDL2 O13 398 8.384 0.160 4.021 -0.1912 -0.0547 0.2866 + 716CDL2 CB1 399 8.478 0.238 4.074 0.1090 -0.3661 0.1979 + 716CDL2 OB1 400 8.491 0.357 4.052 -0.0758 -0.3455 0.2010 + 716CDL2 CB2 401 8.550 0.159 4.183 -0.0949 -0.5481 0.2083 + 716CDL2 H2D 402 8.552 0.060 4.134 -0.1919 -0.9474 1.0149 + 716CDL2 H2E 403 8.487 0.145 4.273 -0.6378 -0.9468 -0.2318 + 716CDL2 C32 404 7.468 0.548 3.996 -0.4614 -0.1798 0.0684 + 716CDL2 H32J 405 7.374 0.565 4.052 -1.5081 0.4996 -1.8838 + 716CDL2 O32 406 7.554 0.661 4.015 -0.2540 -0.2751 -0.2697 + 716CDL2 CC1 407 7.531 0.740 4.121 0.3677 -0.2216 -0.1800 + 716CDL2 OC1 408 7.441 0.728 4.202 0.5641 -0.4787 0.0020 + 716CDL2 CC2 409 7.619 0.864 4.107 -0.0345 0.0697 -0.0900 + 716CDL2 H2R 410 7.721 0.826 4.085 1.4914 2.5946 2.5891 + 716CDL2 H2S 411 7.569 0.917 4.023 -1.7261 -1.5560 -0.1405 + 716CDL2 C33 412 7.539 0.421 4.045 0.1186 0.0768 -0.0922 + 716CDL2 H33J 413 7.645 0.428 4.014 -0.1381 0.1344 -0.9578 + 716CDL2 H33K 414 7.488 0.340 3.990 -0.3188 -0.1821 0.6828 + 716CDL2 O33 415 7.532 0.397 4.186 0.1479 -0.0366 -0.1118 + 716CDL2 CD1 416 7.645 0.409 4.256 -0.0781 0.2731 0.1993 + 716CDL2 OD1 417 7.755 0.439 4.212 0.2270 -0.2624 0.6040 + 716CDL2 CD2 418 7.616 0.385 4.403 -0.2325 0.3036 0.1720 + 716CDL2 H2X 419 7.606 0.275 4.419 0.3528 0.1778 -0.3181 + 716CDL2 H2Y 420 7.514 0.426 4.423 0.4443 1.1697 1.9026 + 716CDL2 CA3 421 8.086 0.614 4.246 0.0424 0.5935 -0.2221 + 716CDL2 H3A 422 8.023 0.537 4.295 1.6126 -0.4618 0.1379 + 716CDL2 H3B 423 8.020 0.686 4.192 -2.0042 -1.1219 -0.0125 + 716CDL2 CA4 424 8.163 0.695 4.350 0.1140 0.4593 -0.1692 + 716CDL2 H4A 425 8.227 0.769 4.298 0.2274 0.7200 0.3427 + 716CDL2 H4B 426 8.228 0.627 4.410 -0.1708 0.4361 0.1145 + 716CDL2 CA5 427 8.076 0.763 4.456 0.3582 -0.0053 0.3301 + 716CDL2 H5A 428 8.001 0.692 4.499 -0.3224 0.6407 0.2299 + 716CDL2 H5B 429 8.016 0.839 4.401 0.0099 -0.1871 0.4582 + 716CDL2 CA6 430 8.154 0.834 4.566 0.0071 0.3682 0.3316 + 716CDL2 H6A 431 8.084 0.915 4.596 -0.5259 0.1964 -0.4504 + 716CDL2 H6B 432 8.249 0.883 4.537 0.2969 -0.2169 0.2990 + 716CDL2 CA7 433 8.173 0.744 4.688 0.1736 -0.0038 0.0352 + 716CDL2 H7A 434 8.078 0.711 4.733 -0.1934 1.0216 0.0138 + 716CDL2 H7B 435 8.221 0.652 4.650 -1.1740 0.0194 -1.6867 + 716CDL2 CA8 436 8.261 0.816 4.791 0.3117 -0.0828 -0.0324 + 716CDL2 H8A 437 8.202 0.887 4.854 0.8789 -0.4613 0.9272 + 716CDL2 H8B 438 8.341 0.872 4.739 -0.2979 0.7760 -0.0567 + 716CDL2 CA9 439 8.321 0.714 4.884 -0.0282 -0.3633 -0.1179 + 716CDL2 H9A 440 8.314 0.610 4.851 -0.1314 -0.8356 1.3810 + 716CDL2 CA10 441 8.375 0.734 5.005 -0.2406 0.4899 -0.1546 + 716CDL2 H10A 442 8.425 0.648 5.052 -0.3539 1.2075 1.2678 + 716CDL2 CA11 443 8.398 0.862 5.079 0.0513 0.1105 0.4098 + 716CDL2 H11A 444 8.352 0.949 5.026 0.1192 0.9717 1.7552 + 716CDL2 H11B 445 8.505 0.890 5.089 -0.0818 1.2640 -1.3096 + 716CDL2 CA12 446 8.328 0.887 5.213 0.1103 0.0508 0.4523 + 716CDL2 H12A 447 8.218 0.886 5.200 0.3693 -0.7577 -1.6777 + 716CDL2 H12B 448 8.350 0.797 5.275 3.9166 2.2436 2.3275 + 716CDL2 CA13 449 8.372 1.008 5.296 0.5104 0.2321 -0.0199 + 716CDL2 H13A 450 8.478 1.037 5.280 -0.3063 1.6774 -2.9230 + 716CDL2 H13B 451 8.327 1.104 5.264 -0.6794 -0.0599 0.7668 + 716CDL2 CA14 452 8.364 0.981 5.446 0.4196 0.3523 -0.0049 + 716CDL2 H14A 453 8.408 0.879 5.456 -1.3299 -0.2330 1.7158 + 716CDL2 H14B 454 8.259 0.985 5.483 0.7946 0.1647 1.0946 + 716CDL2 CA15 455 8.455 1.081 5.518 0.3261 -0.1293 0.7791 + 716CDL2 H15A 456 8.562 1.076 5.492 -0.2142 -0.7561 -1.4040 + 716CDL2 H15B 457 8.443 1.055 5.626 0.6742 1.0653 1.0978 + 716CDL2 CA16 458 8.403 1.224 5.503 0.8218 0.0023 0.3344 + 716CDL2 H16A 459 8.298 1.222 5.539 0.3213 -0.4501 -1.1548 + 716CDL2 H16B 460 8.407 1.245 5.394 1.0328 -1.6939 0.0005 + 716CDL2 CA17 461 8.474 1.328 5.589 0.6768 0.3731 0.0054 + 716CDL2 H17A 462 8.489 1.289 5.692 -1.6253 -1.7746 -0.4802 + 716CDL2 H17B 463 8.580 1.330 5.556 0.8225 -0.5481 0.4178 + 716CDL2 CA18 464 8.406 1.464 5.578 0.0258 0.0786 0.3698 + 716CDL2 H18A 465 8.395 1.498 5.473 -0.1796 -0.9992 0.0380 + 716CDL2 H18B 466 8.468 1.539 5.633 -4.9356 3.1004 1.9408 + 716CDL2 H18C 467 8.309 1.475 5.631 0.5591 -0.9977 1.5850 + 716CDL2 CB3 468 8.688 0.214 4.220 -0.0893 -0.4344 0.0413 + 716CDL2 H3D 469 8.754 0.210 4.131 0.4755 -1.2328 0.4924 + 716CDL2 H3E 470 8.687 0.311 4.274 0.2771 -0.6691 0.4757 + 716CDL2 CB4 471 8.754 0.123 4.325 0.3440 0.1765 0.2927 + 716CDL2 H4D 472 8.782 0.026 4.278 -0.9262 1.2686 -2.7614 + 716CDL2 H4E 473 8.671 0.097 4.394 1.5001 -0.4034 1.4500 + 716CDL2 CB5 474 8.871 0.184 4.402 0.9793 -0.2349 -0.3497 + 716CDL2 H5D 475 8.945 0.239 4.340 0.1978 -0.3732 -1.4054 + 716CDL2 H5E 476 8.830 0.253 4.479 0.9822 1.5146 -1.9124 + 716CDL2 CB6 477 8.951 0.081 4.482 0.0565 -1.0130 -0.4300 + 716CDL2 H6D 478 9.029 0.129 4.545 0.5401 -1.0365 -1.0083 + 716CDL2 H6E 479 9.003 0.011 4.414 -1.1932 -0.9623 -1.4332 + 716CDL2 CB7 480 8.874 -0.001 4.586 -0.2729 -0.1452 0.0081 + 716CDL2 H7D 481 8.802 0.069 4.635 0.4487 0.6456 -0.0658 + 716CDL2 H7E 482 8.811 -0.071 4.528 -1.6344 2.0377 -1.1581 + 716CDL2 CB8 483 8.959 -0.066 4.696 0.1326 0.3861 0.0134 + 716CDL2 H8D 484 8.897 -0.138 4.753 -1.6509 1.9770 0.0878 + 716CDL2 H8E 485 8.993 0.020 4.757 1.0116 -0.6906 1.0250 + 716CDL2 CB9 486 9.086 -0.135 4.653 0.1752 0.2313 0.3795 + 716CDL2 H9D 487 9.110 -0.124 4.546 -0.0357 -2.6948 0.0266 + 716CDL2 CB10 488 9.179 -0.187 4.733 0.1250 -0.2330 0.1332 + 716CDL2 H10D 489 9.264 -0.241 4.688 1.3795 2.9469 -1.3040 + 716CDL2 CB11 490 9.169 -0.209 4.882 -0.0083 0.5183 0.2353 + 716CDL2 H11D 491 9.062 -0.200 4.912 -0.0174 -1.0922 0.6955 + 716CDL2 H11E 492 9.221 -0.121 4.925 -0.3773 1.1026 -0.4891 + 716CDL2 CB12 493 9.239 -0.334 4.935 -0.2087 0.1191 -0.4316 + 716CDL2 H12D 494 9.198 -0.424 4.885 1.3628 -0.4321 -0.7250 + 716CDL2 H12E 495 9.343 -0.330 4.897 0.3879 1.9001 1.3432 + 716CDL2 CB13 496 9.222 -0.342 5.087 -0.5829 -0.3344 -0.4948 + 716CDL2 H13D 497 9.265 -0.246 5.122 -1.3883 -0.5511 1.0975 + 716CDL2 H13E 498 9.118 -0.354 5.124 -1.1048 2.2886 -1.1461 + 716CDL2 CB14 499 9.310 -0.448 5.153 -0.7623 -0.1268 0.0604 + 716CDL2 H14D 500 9.266 -0.544 5.116 1.6140 -0.5589 -1.6397 + 716CDL2 H14E 501 9.405 -0.436 5.097 0.2818 -0.9966 1.6151 + 716CDL2 CB15 502 9.320 -0.448 5.306 -0.3830 0.3757 0.0394 + 716CDL2 H15D 503 9.216 -0.451 5.345 0.2687 0.5066 1.7889 + 716CDL2 H15E 504 9.375 -0.537 5.344 0.2952 0.7853 0.0084 + 716CDL2 CB16 505 9.399 -0.331 5.365 0.0777 -0.1378 0.4324 + 716CDL2 H16D 506 9.347 -0.243 5.322 -2.5460 -1.6996 0.3514 + 716CDL2 H16E 507 9.502 -0.333 5.323 -0.1422 -1.6107 -0.0402 + 716CDL2 CB17 508 9.390 -0.294 5.513 -0.4985 0.2928 0.2936 + 716CDL2 H17D 509 9.473 -0.341 5.571 2.3568 2.4166 -2.0782 + 716CDL2 H17E 510 9.297 -0.334 5.558 -0.9722 0.5095 -0.4864 + 716CDL2 CB18 511 9.404 -0.147 5.550 0.6001 0.1256 0.5755 + 716CDL2 H18D 512 9.503 -0.120 5.506 1.2545 -0.2207 1.8191 + 716CDL2 H18E 513 9.319 -0.092 5.503 0.5287 -0.1919 0.3506 + 716CDL2 H18F 514 9.404 -0.131 5.660 -1.7808 0.1880 0.5816 + 716CDL2 CC3 515 7.615 0.951 4.232 -0.1733 0.0924 -0.1152 + 716CDL2 H3R 516 7.702 1.019 4.222 -0.5930 0.7819 0.9459 + 716CDL2 H3S 517 7.626 0.891 4.325 2.3480 1.3787 0.4149 + 716CDL2 CC4 518 7.491 1.040 4.244 -0.6205 -0.5612 0.1937 + 716CDL2 H4R 519 7.482 1.124 4.171 2.3488 -0.0645 0.3796 + 716CDL2 H4S 520 7.403 0.974 4.229 0.0732 -1.5720 0.5888 + 716CDL2 CC5 521 7.474 1.086 4.389 -0.6424 -0.3625 0.1277 + 716CDL2 H5R 522 7.449 0.996 4.450 2.6633 -0.8230 0.8712 + 716CDL2 H5S 523 7.570 1.131 4.423 -0.6900 -2.9164 3.7387 + 716CDL2 CC6 524 7.359 1.185 4.407 -0.0142 0.3781 0.0673 + 716CDL2 H6R 525 7.270 1.132 4.367 -0.3545 1.6983 -0.9431 + 716CDL2 H6S 526 7.380 1.268 4.336 0.6383 -0.2127 -0.4424 + 716CDL2 CC7 527 7.360 1.239 4.550 -0.6135 -0.0995 0.2488 + 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0.1126 0.2937 -0.0440 + 717CDL2 OP33 613 12.773 2.626 4.077 -0.2230 0.1853 -0.3892 + 717CDL2 OP34 614 12.781 2.405 3.965 -0.0003 0.2851 0.0913 + 717CDL2 OP31 615 12.978 2.564 3.944 0.2825 -0.2918 -0.1602 + 717CDL2 OP32 616 12.941 2.447 4.153 -0.4068 0.2902 0.3205 + 717CDL2 C31 617 12.956 2.498 4.286 0.1819 0.4217 0.2047 + 717CDL2 H31J 618 12.883 2.579 4.305 -1.0008 -0.4738 -0.5623 + 717CDL2 H31K 619 13.061 2.533 4.292 0.6230 -0.9131 0.4247 + 717CDL2 C2 620 13.145 2.387 3.890 -0.0042 -0.5885 0.2954 + 717CDL2 HG22 621 13.106 2.319 3.969 0.0005 -1.0769 -0.1259 + 717CDL2 OG12 622 13.195 2.318 3.776 0.0888 -0.2346 0.1188 + 717CDL2 HO12 623 13.124 2.265 3.741 -0.3698 0.9541 -0.7645 + 717CDL2 C1 624 13.257 2.468 3.958 0.1412 -0.4111 -0.1633 + 717CDL2 HG11 625 13.340 2.398 3.978 1.4534 1.2664 0.2751 + 717CDL2 HG12 626 13.217 2.500 4.057 0.4929 2.1752 -0.8438 + 717CDL2 P1 627 13.368 2.699 3.958 -0.2240 0.0613 -0.1185 + 717CDL2 OP13 628 13.450 2.643 4.068 -0.0347 0.0383 -0.2666 + 717CDL2 OP14 629 13.442 2.770 3.851 -0.2132 0.2521 0.0117 + 717CDL2 OP11 630 13.298 2.580 3.879 -0.7077 0.1480 0.1789 + 717CDL2 OP12 631 13.239 2.777 4.012 0.0736 0.2728 0.2805 + 717CDL2 C11 632 13.250 2.875 4.116 -0.3373 0.4763 0.1282 + 717CDL2 H11J 633 13.351 2.896 4.156 0.0111 1.5411 -1.2849 + 717CDL2 H11K 634 13.209 2.975 4.087 -1.2907 -0.0228 -0.2570 + 717CDL2 C12 635 13.172 2.830 4.240 0.1026 -0.4642 0.0653 + 717CDL2 H12J 636 13.091 2.764 4.203 1.0040 -1.8523 0.5772 + 717CDL2 O12 637 13.107 2.945 4.297 0.6107 -0.0479 -0.1853 + 717CDL2 CA1 638 13.014 2.923 4.391 0.7693 -0.0329 -0.0354 + 717CDL2 OA1 639 12.981 2.815 4.436 0.0703 -0.0698 -0.6362 + 717CDL2 CA2 640 12.952 3.055 4.434 0.2376 -0.2041 -0.2743 + 717CDL2 H2A 641 13.029 3.135 4.436 0.7006 -0.6551 -0.3330 + 717CDL2 H2B 642 12.872 3.083 4.362 -0.0589 1.1920 0.5796 + 717CDL2 C13 643 13.256 2.747 4.338 0.1115 -0.6598 -0.1189 + 717CDL2 H13J 644 13.310 2.664 4.289 0.8379 -0.8624 1.0035 + 717CDL2 H13K 645 13.186 2.692 4.404 1.4209 -2.1648 0.0207 + 717CDL2 O13 646 13.352 2.828 4.407 -0.5342 -0.1388 0.1728 + 717CDL2 CB1 647 13.457 2.762 4.456 -0.5457 -0.3096 -0.0263 + 717CDL2 OB1 648 13.482 2.642 4.456 -0.0143 -0.1995 -0.3877 + 717CDL2 CB2 649 13.558 2.867 4.500 -0.4375 -0.2650 -0.3835 + 717CDL2 H2D 650 13.650 2.805 4.510 -0.3992 0.0343 1.2313 + 717CDL2 H2E 651 13.569 2.940 4.417 -1.0366 0.9231 0.5843 + 717CDL2 C32 652 12.935 2.387 4.390 0.1299 0.0700 -0.1763 + 717CDL2 H32J 653 12.832 2.347 4.379 -0.6692 2.1321 -0.2450 + 717CDL2 O32 654 12.954 2.430 4.525 0.1897 0.0476 -0.1774 + 717CDL2 CC1 655 12.872 2.521 4.579 0.0035 -0.2813 0.1042 + 717CDL2 OC1 656 12.763 2.558 4.538 0.1595 -0.4622 -0.4715 + 717CDL2 CC2 657 12.936 2.568 4.709 -0.0420 -0.4954 0.2039 + 717CDL2 H2R 658 13.044 2.580 4.687 -0.6768 2.2375 -1.5582 + 717CDL2 H2S 659 12.911 2.484 4.777 -2.6465 0.1934 0.0970 + 717CDL2 C33 660 13.033 2.272 4.359 0.0907 -0.0676 0.1840 + 717CDL2 H33J 661 12.999 2.185 4.419 -0.4289 0.2655 0.3783 + 717CDL2 H33K 662 13.025 2.246 4.251 0.4914 0.0777 0.1203 + 717CDL2 O33 663 13.166 2.317 4.386 -0.1729 0.7908 0.0595 + 717CDL2 CD1 664 13.262 2.269 4.307 -0.4329 0.0197 0.2023 + 717CDL2 OD1 665 13.249 2.185 4.220 0.4325 -0.2989 0.3807 + 717CDL2 CD2 666 13.397 2.309 4.366 -0.5891 0.3100 0.3690 + 717CDL2 H2X 667 13.478 2.307 4.290 -0.2474 1.0430 0.7150 + 717CDL2 H2Y 668 13.395 2.411 4.411 1.3944 0.1518 0.7888 + 717CDL2 CA3 669 12.899 3.034 4.576 -0.3349 0.2718 -0.4206 + 717CDL2 H3A 670 12.814 2.962 4.579 0.1237 -0.3620 -2.3403 + 717CDL2 H3B 671 12.980 2.997 4.642 -0.1960 0.0720 -0.7057 + 717CDL2 CA4 672 12.850 3.164 4.639 -0.2927 0.3371 -0.5261 + 717CDL2 H4A 673 12.777 3.228 4.584 -0.9879 0.4387 0.5068 + 717CDL2 H4B 674 12.937 3.231 4.656 0.6694 -0.7380 -1.2382 + 717CDL2 CA5 675 12.799 3.129 4.779 0.2419 -0.2764 -0.4811 + 717CDL2 H5A 676 12.870 3.056 4.822 1.1355 1.1687 0.4862 + 717CDL2 H5B 677 12.702 3.074 4.772 -0.2227 0.6471 -1.3793 + 717CDL2 CA6 678 12.779 3.247 4.874 0.5208 -0.2945 -0.3981 + 717CDL2 H6A 679 12.694 3.314 4.848 0.9246 0.3216 -0.1329 + 717CDL2 H6B 680 12.866 3.316 4.876 0.0859 0.3328 -3.3410 + 717CDL2 CA7 681 12.759 3.187 5.014 0.1554 -0.0114 -0.3317 + 717CDL2 H7A 682 12.680 3.109 5.010 1.0334 -0.8721 -0.8092 + 717CDL2 H7B 683 12.852 3.131 5.038 0.4777 1.0052 0.7858 + 717CDL2 CA8 684 12.714 3.294 5.114 -0.2353 -0.1138 -0.3940 + 717CDL2 H8A 685 12.783 3.381 5.112 -0.3697 -0.0102 -0.5962 + 717CDL2 H8B 686 12.615 3.337 5.087 0.1931 0.0941 -1.6502 + 717CDL2 CA9 687 12.707 3.238 5.253 -0.3802 0.7463 -0.0601 + 717CDL2 H9A 688 12.659 3.140 5.271 0.8620 0.4607 1.7177 + 717CDL2 CA10 689 12.763 3.295 5.360 0.2925 0.0993 -0.0692 + 717CDL2 H10A 690 12.757 3.245 5.458 -0.0600 -0.3663 -0.3296 + 717CDL2 CA11 691 12.842 3.422 5.372 0.1266 0.2242 -0.2767 + 717CDL2 H11A 692 12.941 3.394 5.413 -0.2715 0.2213 0.6857 + 717CDL2 H11B 693 12.863 3.470 5.274 -0.6941 -1.3713 -1.2238 + 717CDL2 CA12 694 12.776 3.526 5.463 -0.3219 -0.2192 -0.0983 + 717CDL2 H12A 695 12.843 3.614 5.450 0.0451 -0.5679 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2.999 0.2466 0.6556 -1.5996 + 720CDL2 C1 1368 9.788 13.542 3.064 0.0187 -0.1548 -0.3583 + 720CDL2 HG11 1369 9.690 13.590 3.087 -0.5002 -0.2707 -2.2953 + 720CDL2 HG12 1370 9.817 13.559 2.958 -1.0352 -1.1054 -0.8025 + 720CDL2 P1 1371 10.033 13.579 3.131 -0.0735 -0.0795 -0.2261 + 720CDL2 OP13 1372 10.061 13.652 3.005 0.0006 0.2338 -0.0288 + 720CDL2 OP14 1373 10.065 13.434 3.141 -0.1913 -0.1112 -0.3129 + 720CDL2 OP11 1374 9.877 13.596 3.162 -0.0899 -0.8660 0.1356 + 720CDL2 OP12 1375 10.106 13.664 3.245 -0.2150 0.0385 -0.2198 + 720CDL2 C11 1376 10.032 13.767 3.311 0.7201 0.5752 -0.0123 + 720CDL2 H11J 1377 9.951 13.815 3.253 1.9766 0.5395 -1.7971 + 720CDL2 H11K 1378 10.100 13.852 3.335 -0.2134 0.5304 2.7720 + 720CDL2 C12 1379 9.965 13.720 3.441 0.0095 0.6616 -0.3529 + 720CDL2 H12J 1380 9.928 13.617 3.420 -1.1722 0.8992 0.5354 + 720CDL2 O12 1381 9.844 13.790 3.471 -0.1765 0.2641 -0.1736 + 720CDL2 CA1 1382 9.844 13.923 3.479 -0.4128 0.2654 -0.1734 + 720CDL2 OA1 1383 9.939 13.998 3.466 -0.2962 0.1835 0.1733 + 720CDL2 CA2 1384 9.700 13.961 3.511 -0.2688 0.5459 0.1297 + 720CDL2 H2A 1385 9.645 13.980 3.416 0.5595 -0.3109 -0.5170 + 720CDL2 H2B 1386 9.646 13.876 3.557 0.6489 -0.1205 -0.0373 + 720CDL2 C13 1387 10.063 13.717 3.559 0.2006 0.1625 -0.5254 + 720CDL2 H13J 1388 10.106 13.817 3.581 -1.0869 0.4168 0.7841 + 720CDL2 H13K 1389 10.004 13.682 3.646 0.4379 0.7782 -0.1164 + 720CDL2 O13 1390 10.160 13.614 3.540 0.0469 -0.1036 0.0823 + 720CDL2 CB1 1391 10.267 13.605 3.619 0.0728 -0.0832 0.0440 + 720CDL2 OB1 1392 10.330 13.501 3.629 -0.3916 -0.4086 -0.4042 + 720CDL2 CB2 1393 10.287 13.720 3.717 -0.3450 0.3163 -0.3355 + 720CDL2 H2D 1394 10.198 13.733 3.781 0.2370 1.6458 0.2178 + 720CDL2 H2E 1395 10.301 13.805 3.647 1.6650 0.9301 0.8007 + 720CDL2 C32 1396 9.654 13.220 3.719 -0.4081 0.1369 -0.0704 + 720CDL2 H32J 1397 9.617 13.115 3.716 -0.5149 0.0933 2.0512 + 720CDL2 O32 1398 9.586 13.289 3.825 0.1383 -0.4187 0.6438 + 720CDL2 CC1 1399 9.630 13.412 3.852 -0.1437 -0.1577 -0.0670 + 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5.220 0.0664 2.3220 1.7603 + 720CDL2 CC17 1547 9.360 13.623 5.403 0.5997 0.1349 -0.0961 + 720CDL2 H17R 1548 9.422 13.574 5.481 1.0273 1.8323 0.6287 + 720CDL2 H17S 1549 9.295 13.548 5.351 0.7858 -0.7675 0.9727 + 720CDL2 CC18 1550 9.275 13.724 5.479 0.0045 -0.5157 0.1164 + 720CDL2 H18R 1551 9.340 13.802 5.525 -1.5282 1.4383 -0.9902 + 720CDL2 H18S 1552 9.207 13.671 5.548 1.4475 -3.5844 -0.8107 + 720CDL2 H18T 1553 9.223 13.776 5.395 -1.9197 0.1878 1.7232 + 720CDL2 CD3 1554 10.064 13.188 4.139 -0.3847 -0.0254 0.1278 + 720CDL2 H3X 1555 10.113 13.272 4.085 -1.0447 0.6947 0.6467 + 720CDL2 H3Y 1556 10.002 13.232 4.221 0.2433 -0.0897 0.6252 + 720CDL2 CD4 1557 10.172 13.108 4.212 -0.4359 0.1451 0.4018 + 720CDL2 H4X 1558 10.228 13.050 4.136 0.5488 0.6063 0.7711 + 720CDL2 H4Y 1559 10.239 13.178 4.267 -0.8185 0.8399 -0.0136 + 720CDL2 CD5 1560 10.111 13.008 4.310 -0.0253 -0.5956 -0.0866 + 720CDL2 H5X 1561 10.036 12.942 4.261 0.1814 1.1940 -2.8175 + 720CDL2 H5Y 1562 10.198 12.947 4.341 0.2774 -0.0586 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1595 9.734 12.883 5.569 0.0565 -1.5631 0.2041 + 720CDL2 H17Y 1596 9.867 12.966 5.650 2.0237 -0.0762 -0.4264 + 720CDL2 CD18 1597 9.900 12.759 5.633 -0.2439 -0.3077 0.0291 + 720CDL2 H18X 1598 9.886 12.681 5.555 -0.1835 0.4837 -0.7760 + 720CDL2 H18Y 1599 10.007 12.764 5.661 0.6399 -0.9437 -3.1622 + 720CDL2 H18Z 1600 9.857 12.728 5.731 0.9367 1.1731 1.0152 + 721CDL2 C3 1601 8.722 5.423 3.257 0.2856 0.4744 -0.1324 + 721CDL2 HG31 1602 8.770 5.323 3.258 -0.2493 0.2285 0.6401 + 721CDL2 HG32 1603 8.696 5.450 3.361 1.3349 -0.0822 0.2718 + 721CDL2 P3 1604 8.462 5.383 3.226 -0.0130 0.3981 -0.1014 + 721CDL2 OP33 1605 8.390 5.293 3.133 0.0811 0.0538 0.1707 + 721CDL2 OP34 1606 8.413 5.519 3.258 -0.0910 0.2918 0.2482 + 721CDL2 OP31 1607 8.611 5.405 3.169 0.2171 -0.4761 0.1558 + 721CDL2 OP32 1608 8.489 5.307 3.363 0.5843 0.9266 0.0751 + 721CDL2 C31 1609 8.372 5.278 3.441 1.0869 0.3355 0.6085 + 721CDL2 H31J 1610 8.396 5.189 3.504 1.8961 0.4268 0.4338 + 721CDL2 H31K 1611 8.286 5.242 3.381 1.1467 -1.3440 1.5130 + 721CDL2 C2 1612 8.822 5.527 3.201 0.7234 0.0867 -0.0807 + 721CDL2 HG22 1613 8.810 5.539 3.092 1.7529 0.0048 -0.1933 + 721CDL2 OG12 1614 8.797 5.650 3.268 0.3098 -0.1505 0.2060 + 721CDL2 HO12 1615 8.767 5.717 3.205 0.5281 -0.5050 -0.2752 + 721CDL2 C1 1616 8.970 5.497 3.225 0.7527 0.4346 0.1771 + 721CDL2 HG11 1617 9.030 5.591 3.226 2.9464 -0.9492 0.2168 + 721CDL2 HG12 1618 8.979 5.449 3.325 0.7251 -2.0941 -1.0155 + 721CDL2 P1 1619 9.043 5.259 3.121 -0.1456 -0.0257 -0.0221 + 721CDL2 OP13 1620 8.927 5.198 3.052 0.0591 -0.1356 -0.2780 + 721CDL2 OP14 1621 9.174 5.239 3.054 -0.0597 -0.5095 0.2787 + 721CDL2 OP11 1622 9.021 5.417 3.118 0.2752 0.0357 0.2445 + 721CDL2 OP12 1623 9.063 5.219 3.275 -0.1012 0.4179 0.0845 + 721CDL2 C11 1624 9.184 5.254 3.342 0.3178 -0.0832 -0.3992 + 721CDL2 H11J 1625 9.253 5.313 3.278 -0.0714 -1.7478 -2.3593 + 721CDL2 H11K 1626 9.237 5.163 3.377 0.3273 1.4411 3.6698 + 721CDL2 C12 1627 9.158 5.338 3.469 -0.0198 -0.8808 0.0619 + 721CDL2 H12J 1628 9.162 5.445 3.439 0.5408 -0.7336 0.6605 + 721CDL2 O12 1629 9.253 5.299 3.569 0.1152 0.2063 0.3524 + 721CDL2 CA1 1630 9.377 5.342 3.550 -0.0109 0.3094 -0.3091 + 721CDL2 OA1 1631 9.424 5.403 3.455 0.2838 -0.0517 -0.3941 + 721CDL2 CA2 1632 9.460 5.299 3.671 0.1160 0.7126 -0.2506 + 721CDL2 H2A 1633 9.389 5.240 3.733 -1.5003 1.1607 -1.6507 + 721CDL2 H2B 1634 9.541 5.238 3.625 0.5138 0.0520 1.3348 + 721CDL2 C13 1635 9.021 5.308 3.532 -0.2946 0.2659 0.0206 + 721CDL2 H13J 1636 9.028 5.204 3.569 1.5714 -0.7477 -3.2003 + 721CDL2 H13K 1637 8.935 5.298 3.463 -1.2015 -3.4465 1.6795 + 721CDL2 O13 1638 8.980 5.398 3.636 -0.0637 0.5661 -0.1502 + 721CDL2 CB1 1639 8.870 5.362 3.701 0.4408 0.0008 0.3994 + 721CDL2 OB1 1640 8.814 5.256 3.682 0.4184 0.1083 -0.0868 + 721CDL2 CB2 1641 8.827 5.472 3.798 0.3174 0.4916 -0.2250 + 721CDL2 H2D 1642 8.894 5.560 3.788 0.2671 0.3688 -1.6095 + 721CDL2 H2E 1643 8.723 5.496 3.766 0.1806 0.1163 -0.0642 + 721CDL2 C32 1644 8.328 5.400 3.522 -0.3764 -0.0024 0.3141 + 721CDL2 H32J 1645 8.366 5.492 3.473 -1.3443 0.6124 0.7131 + 721CDL2 O32 1646 8.395 5.406 3.648 -0.7381 0.7368 0.4725 + 721CDL2 CC1 1647 8.363 5.317 3.742 -0.2876 0.2947 0.2063 + 721CDL2 OC1 1648 8.335 5.199 3.726 0.0368 0.2041 0.3427 + 721CDL2 CC2 1649 8.345 5.377 3.880 0.0402 0.2917 0.2529 + 721CDL2 H2R 1650 8.378 5.483 3.871 1.9609 -0.3403 -0.1202 + 721CDL2 H2S 1651 8.238 5.394 3.907 0.0021 1.9927 -1.0240 + 721CDL2 C33 1652 8.175 5.415 3.535 -0.4510 -0.1590 -0.3421 + 721CDL2 H33J 1653 8.152 5.510 3.588 -1.4008 -0.1046 -0.8498 + 721CDL2 H33K 1654 8.134 5.431 3.433 1.4509 -2.4532 -1.4874 + 721CDL2 O33 1655 8.115 5.299 3.592 0.2723 -0.1480 0.4406 + 721CDL2 CD1 1656 8.041 5.303 3.703 -0.5154 0.3072 -0.1074 + 721CDL2 OD1 1657 8.011 5.405 3.763 -0.1749 0.0686 0.4598 + 721CDL2 CD2 1658 7.992 5.166 3.747 0.4313 -0.0652 -0.2097 + 721CDL2 H2X 1659 8.056 5.098 3.685 -2.0065 0.8197 -3.7431 + 721CDL2 H2Y 1660 7.887 5.157 3.712 0.7001 0.4950 -1.1733 + 721CDL2 CA3 1661 9.541 5.408 3.741 0.4501 0.2969 -0.0047 + 721CDL2 H3A 1662 9.636 5.423 3.685 -0.0570 -2.2065 -1.5429 + 721CDL2 H3B 1663 9.481 5.501 3.744 0.5674 0.3482 0.9981 + 721CDL2 CA4 1664 9.567 5.369 3.886 0.7734 0.2820 -0.0676 + 721CDL2 H4A 1665 9.624 5.274 3.897 -1.3101 -1.0179 -0.6272 + 721CDL2 H4B 1666 9.478 5.368 3.952 0.6609 -1.5861 -0.2656 + 721CDL2 CA5 1667 9.648 5.479 3.956 0.4726 0.1748 0.4631 + 721CDL2 H5A 1668 9.739 5.510 3.900 0.9292 -2.6845 -0.3951 + 721CDL2 H5B 1669 9.587 5.571 3.949 -0.3437 -0.6023 -3.0866 + 721CDL2 CA6 1670 9.678 5.453 4.103 -0.1095 -0.1326 0.5262 + 721CDL2 H6A 1671 9.579 5.417 4.140 -0.7861 1.0589 -0.1017 + 721CDL2 H6B 1672 9.751 5.370 4.112 -0.0022 -0.0591 0.2851 + 721CDL2 CA7 1673 9.724 5.584 4.168 -0.0009 0.0458 0.0775 + 721CDL2 H7A 1674 9.646 5.662 4.164 0.7881 0.8272 0.0790 + 721CDL2 H7B 1675 9.808 5.623 4.107 0.0410 0.2197 0.2501 + 721CDL2 CA8 1676 9.753 5.569 4.318 -0.0098 0.1218 0.0856 + 721CDL2 H8A 1677 9.661 5.550 4.376 -1.6187 2.9151 -1.5391 + 721CDL2 H8B 1678 9.811 5.475 4.327 -2.9142 -1.6748 0.1313 + 721CDL2 CA9 1679 9.840 5.680 4.370 -0.2062 0.0629 0.5621 + 721CDL2 H9A 1680 9.904 5.727 4.293 1.1331 -2.6114 0.0531 + 721CDL2 CA10 1681 9.839 5.734 4.493 0.3415 0.4031 0.4155 + 721CDL2 H10A 1682 9.906 5.818 4.516 0.1505 0.3908 1.0298 + 721CDL2 CA11 1683 9.750 5.696 4.608 -0.2313 -0.3006 -0.2591 + 721CDL2 H11A 1684 9.661 5.762 4.605 0.2520 0.3096 -1.0056 + 721CDL2 H11B 1685 9.718 5.590 4.596 -2.0423 -0.1320 3.1516 + 721CDL2 CA12 1686 9.810 5.711 4.748 -0.5094 0.2050 -0.1977 + 721CDL2 H12A 1687 9.841 5.817 4.762 -0.7614 0.3696 -0.8354 + 721CDL2 H12B 1688 9.900 5.648 4.762 -1.0284 -0.0008 2.1410 + 721CDL2 CA13 1689 9.710 5.682 4.860 -0.3076 0.5336 0.0794 + 721CDL2 H13A 1690 9.651 5.591 4.835 0.8741 -0.2766 0.2024 + 721CDL2 H13B 1691 9.627 5.756 4.860 0.2700 1.1691 -0.9233 + 721CDL2 CA14 1692 9.785 5.664 4.992 0.2899 0.5994 -0.2512 + 721CDL2 H14A 1693 9.839 5.568 4.981 2.0762 1.5657 0.0755 + 721CDL2 H14B 1694 9.871 5.731 5.013 0.6122 -0.7551 2.8861 + 721CDL2 CA15 1695 9.700 5.668 5.120 -0.1667 0.0571 -0.5365 + 721CDL2 H15A 1696 9.653 5.767 5.140 -1.4032 -0.5553 -0.4372 + 721CDL2 H15B 1697 9.617 5.595 5.116 -1.2806 1.3355 -0.7831 + 721CDL2 CA16 1698 9.787 5.630 5.240 -0.6182 0.5753 -0.0528 + 721CDL2 H16A 1699 9.875 5.698 5.238 -0.4724 0.3822 -0.0765 + 721CDL2 H16B 1700 9.825 5.527 5.227 -1.8596 0.1021 0.0192 + 721CDL2 CA17 1701 9.722 5.632 5.379 -0.3399 0.4056 0.0831 + 721CDL2 H17A 1702 9.801 5.563 5.417 -1.3492 -0.8418 -0.0909 + 721CDL2 H17B 1703 9.723 5.736 5.339 0.3875 -0.0155 -0.9902 + 721CDL2 CA18 1704 9.744 5.706 5.511 0.5101 0.4806 -0.0970 + 721CDL2 H18A 1705 9.729 5.642 5.600 2.5810 0.2169 0.0702 + 721CDL2 H18B 1706 9.846 5.751 5.517 0.9810 -0.7676 1.4286 + 721CDL2 H18C 1707 9.670 5.789 5.521 0.9369 0.8462 0.0739 + 721CDL2 CB3 1708 8.830 5.429 3.944 0.3828 0.0773 -0.3485 + 721CDL2 H3D 1709 8.760 5.498 3.996 -0.1149 -0.9718 0.3988 + 721CDL2 H3E 1710 8.810 5.320 3.954 0.2820 0.1073 -0.2320 + 721CDL2 CB4 1711 8.972 5.451 3.997 0.1871 -0.0068 0.2166 + 721CDL2 H4D 1712 9.045 5.400 3.931 -0.3721 0.6312 -0.8854 + 721CDL2 H4E 1713 9.005 5.557 3.994 -1.4492 0.4178 -2.8452 + 721CDL2 CB5 1714 8.993 5.402 4.141 0.4240 0.2887 0.2807 + 721CDL2 H5D 1715 8.990 5.291 4.141 -2.1367 0.3694 2.2686 + 721CDL2 H5E 1716 9.096 5.436 4.164 0.4369 1.2318 -1.1177 + 721CDL2 CB6 1717 8.898 5.458 4.247 0.0292 0.2888 -0.0809 + 721CDL2 H6D 1718 8.790 5.432 4.237 0.3795 -1.7944 1.4491 + 721CDL2 H6E 1719 8.894 5.568 4.229 -2.2215 0.1689 -0.4033 + 721CDL2 CB7 1720 8.951 5.441 4.389 -1.0551 0.0844 0.2990 + 721CDL2 H7D 1721 9.058 5.470 4.389 -1.2374 0.7604 0.4701 + 721CDL2 H7E 1722 8.897 5.515 4.452 -0.7695 -1.2697 2.1559 + 721CDL2 CB8 1723 8.928 5.300 4.443 -0.3424 0.0424 0.5019 + 721CDL2 H8D 1724 8.882 5.246 4.357 -2.7736 1.6555 0.7796 + 721CDL2 H8E 1725 9.027 5.252 4.458 -0.4273 -0.0554 0.7456 + 721CDL2 CB9 1726 8.852 5.280 4.571 0.7862 0.0770 1.1727 + 721CDL2 H9D 1727 8.871 5.184 4.622 -0.7746 -0.9853 -0.2098 + 721CDL2 CB10 1728 8.762 5.367 4.616 0.4859 0.0926 0.5471 + 721CDL2 H10D 1729 8.739 5.460 4.561 0.1110 0.3727 1.1654 + 721CDL2 CB11 1730 8.694 5.366 4.750 -0.2563 -0.0010 0.1677 + 721CDL2 H11D 1731 8.597 5.420 4.746 0.0923 0.6327 0.2953 + 721CDL2 H11E 1732 8.757 5.423 4.822 0.4569 -0.4783 -0.0846 + 721CDL2 CB12 1733 8.679 5.221 4.797 -0.0800 -0.0459 0.0962 + 721CDL2 H12D 1734 8.627 5.163 4.717 -0.8881 2.1313 -0.9749 + 721CDL2 H12E 1735 8.781 5.178 4.806 -0.6434 -1.4874 -0.3416 + 721CDL2 CB13 1736 8.610 5.202 4.932 0.1241 0.2416 0.2381 + 721CDL2 H13D 1737 8.512 5.254 4.934 0.7974 1.5247 0.1507 + 721CDL2 H13E 1738 8.672 5.242 5.016 0.7519 -1.5830 0.6650 + 721CDL2 CB14 1739 8.588 5.051 4.951 -0.4332 0.2767 -0.0948 + 721CDL2 H14D 1740 8.689 5.006 4.963 -0.3651 0.4277 -0.0638 + 721CDL2 H14E 1741 8.543 5.013 4.858 0.7231 -0.7326 -0.2411 + 721CDL2 CB15 1742 8.499 5.020 5.071 -0.0031 -0.0352 0.1425 + 721CDL2 H15D 1743 8.507 4.912 5.095 -0.1704 -0.7227 -2.8719 + 721CDL2 H15E 1744 8.537 5.076 5.159 1.5984 0.0357 -0.6002 + 721CDL2 CB16 1745 8.350 5.050 5.052 -0.0612 -0.2588 0.2782 + 721CDL2 H16D 1746 8.344 5.159 5.030 -0.8365 -0.6036 -1.1499 + 721CDL2 H16E 1747 8.311 4.998 4.962 1.1833 -1.7525 0.5940 + 721CDL2 CB17 1748 8.275 5.005 5.178 0.0537 -0.0727 0.4173 + 721CDL2 H17D 1749 8.178 5.060 5.174 0.4938 0.8443 1.9579 + 721CDL2 H17E 1750 8.336 5.041 5.263 1.0772 -1.1462 0.1388 + 721CDL2 CB18 1751 8.244 4.856 5.190 0.4245 -0.1645 0.2550 + 721CDL2 H18D 1752 8.332 4.791 5.211 0.3860 -0.1264 0.5701 + 721CDL2 H18E 1753 8.197 4.814 5.098 1.1878 -1.3768 0.4185 + 721CDL2 H18F 1754 8.175 4.833 5.274 2.2796 0.9822 2.0911 + 721CDL2 CC3 1755 8.428 5.315 3.993 -0.5398 -0.2075 0.4134 + 721CDL2 H3R 1756 8.530 5.292 3.955 0.1017 0.3051 1.8332 + 721CDL2 H3S 1757 8.384 5.218 4.024 -1.7361 -0.4725 -2.1486 + 721CDL2 CC4 1758 8.434 5.421 4.104 -0.5255 -0.1129 0.3202 + 721CDL2 H4R 1759 8.500 5.503 4.069 0.2819 -0.3885 1.2040 + 721CDL2 H4S 1760 8.481 5.369 4.190 -0.7180 -0.8485 -0.0146 + 721CDL2 CC5 1761 8.302 5.482 4.151 -0.4611 -0.2542 0.6849 + 721CDL2 H5R 1762 8.254 5.537 4.067 0.9375 -0.4721 -0.2538 + 721CDL2 H5S 1763 8.223 5.413 4.187 -1.0545 1.2197 2.2551 + 721CDL2 CC6 1764 8.323 5.605 4.241 0.1624 0.1016 0.0543 + 721CDL2 H6R 1765 8.235 5.671 4.224 -0.1952 -0.5346 -0.5975 + 721CDL2 H6S 1766 8.410 5.663 4.203 1.6995 -2.2880 -0.0975 + 721CDL2 CC7 1767 8.332 5.564 4.388 -0.0856 0.0608 0.0599 + 721CDL2 H7R 1768 8.230 5.543 4.427 -0.0591 1.5726 0.9491 + 721CDL2 H7S 1769 8.402 5.481 4.409 -1.3702 -1.2675 -0.9121 + 721CDL2 CC8 1770 8.391 5.674 4.477 -0.0745 -0.2790 0.4736 + 721CDL2 H8R 1771 8.391 5.638 4.582 -0.7112 -2.4406 -0.2490 + 721CDL2 H8S 1772 8.324 5.763 4.472 0.4390 0.0948 0.3771 + 721CDL2 CC9 1773 8.535 5.703 4.447 -0.0386 -0.3838 0.5312 + 721CDL2 H9R 1774 8.561 5.697 4.340 0.1954 -0.8817 0.6173 + 721CDL2 CC10 1775 8.634 5.723 4.534 0.7100 -0.1900 -0.3533 + 721CDL2 H10R 1776 8.733 5.755 4.497 -0.3466 -0.8755 -3.7189 + 721CDL2 CC11 1777 8.636 5.718 4.684 0.4129 0.1989 -0.3356 + 721CDL2 H11R 1778 8.536 5.720 4.732 1.0969 -0.2000 1.1320 + 721CDL2 H11S 1779 8.690 5.636 4.737 0.4458 -0.2539 -1.0782 + 721CDL2 CC12 1780 8.706 5.847 4.727 0.7933 0.0406 -0.4680 + 721CDL2 H12R 1781 8.657 5.938 4.686 2.0385 0.9013 -0.0611 + 721CDL2 H12S 1782 8.817 5.845 4.717 1.0756 0.8906 2.2172 + 721CDL2 CC13 1783 8.682 5.883 4.874 0.0436 -0.8561 -0.3752 + 721CDL2 H13R 1784 8.573 5.895 4.891 0.2892 1.1889 -0.2173 + 721CDL2 H13S 1785 8.727 5.981 4.900 0.2921 -0.7293 -1.2833 + 721CDL2 CC14 1786 8.722 5.780 4.980 0.6605 -0.2037 0.0178 + 721CDL2 H14R 1787 8.833 5.776 4.975 0.7866 1.6860 1.0425 + 721CDL2 H14S 1788 8.689 5.677 4.956 -2.6034 0.2407 2.5603 + 721CDL2 CC15 1789 8.686 5.805 5.126 -0.0202 -0.0862 -0.1719 + 721CDL2 H15R 1790 8.768 5.757 5.184 -0.3314 0.7988 1.0128 + 721CDL2 H15S 1791 8.678 5.914 5.145 -0.4370 -0.0691 -0.4444 + 721CDL2 CC16 1792 8.556 5.737 5.169 0.1084 -0.0644 0.2855 + 721CDL2 H16R 1793 8.560 5.627 5.153 -3.1367 -0.1404 -0.1204 + 721CDL2 H16S 1794 8.475 5.783 5.109 1.3345 0.2424 -1.1006 + 721CDL2 CC17 1795 8.529 5.758 5.319 0.2801 0.2055 0.2779 + 721CDL2 H17R 1796 8.423 5.734 5.339 0.2946 0.8959 1.1949 + 721CDL2 H17S 1797 8.596 5.688 5.373 -0.4787 0.7305 1.8871 + 721CDL2 CC18 1798 8.544 5.898 5.376 -0.5523 0.1558 0.6000 + 721CDL2 H18R 1799 8.649 5.916 5.406 -1.0042 -1.0270 2.8880 + 721CDL2 H18S 1800 8.520 5.984 5.310 -0.4747 -0.2759 0.0150 + 721CDL2 H18T 1801 8.491 5.916 5.472 -1.0516 2.5956 -0.1073 + 721CDL2 CD3 1802 8.012 5.136 3.895 0.0846 0.5773 -0.0402 + 721CDL2 H3X 1803 8.116 5.162 3.923 -0.2435 1.2906 0.5774 + 721CDL2 H3Y 1804 7.980 5.032 3.919 0.4413 -0.1409 -2.6461 + 721CDL2 CD4 1805 7.926 5.219 3.990 -0.6676 -0.3165 0.0611 + 721CDL2 H4X 1806 7.820 5.194 3.968 -0.3342 -0.7288 -1.0514 + 721CDL2 H4Y 1807 7.944 5.327 3.972 1.3252 -0.8931 -1.3836 + 721CDL2 CD5 1808 7.947 5.190 4.139 -0.3458 -0.6911 -0.0569 + 721CDL2 H5X 1809 8.041 5.242 4.166 -0.0476 -1.1751 -0.1658 + 721CDL2 H5Y 1810 7.968 5.083 4.162 -0.3523 -0.8332 -0.7005 + 721CDL2 CD6 1811 7.835 5.236 4.232 -0.1036 -0.3646 0.0663 + 721CDL2 H6X 1812 7.748 5.169 4.220 -1.2147 1.0567 0.0765 + 721CDL2 H6Y 1813 7.800 5.336 4.197 0.8564 -0.3632 -0.9092 + 721CDL2 CD7 1814 7.876 5.246 4.379 -0.0146 0.1099 0.0140 + 721CDL2 H7X 1815 7.934 5.159 4.417 -2.2543 -1.1544 0.5328 + 721CDL2 H7Y 1816 7.952 5.325 4.398 0.6940 -0.0449 -2.1493 + 721CDL2 CD8 1817 7.759 5.268 4.474 -0.1722 -0.0692 -0.1421 + 721CDL2 H8X 1818 7.700 5.174 4.461 -0.6142 0.1106 0.5432 + 721CDL2 H8Y 1819 7.806 5.274 4.575 -0.4155 2.8404 -0.2007 + 721CDL2 CD9 1820 7.675 5.387 4.437 -0.5679 -0.3266 -0.0813 + 721CDL2 H9X 1821 7.622 5.381 4.341 -1.3670 2.5916 0.1621 + 721CDL2 CD10 1822 7.646 5.493 4.514 -0.1116 -0.2620 -0.0015 + 721CDL2 H10X 1823 7.570 5.563 4.477 0.3106 1.0201 1.5611 + 721CDL2 CD11 1824 7.701 5.540 4.646 -0.8527 0.4015 0.0772 + 721CDL2 H11X 1825 7.752 5.460 4.705 -0.7377 0.4965 0.1024 + 721CDL2 H11Y 1826 7.615 5.568 4.710 -0.5850 1.2228 0.0717 + 721CDL2 CD12 1827 7.808 5.647 4.628 -0.3405 -0.0627 0.3556 + 721CDL2 H12X 1828 7.885 5.615 4.554 -0.2024 -0.8722 0.8520 + 721CDL2 H12Y 1829 7.756 5.735 4.584 1.8208 0.3252 -1.4189 + 721CDL2 CD13 1830 7.873 5.695 4.759 -0.2860 0.0404 0.3022 + 721CDL2 H13X 1831 7.918 5.608 4.812 -0.5701 -0.3600 -0.1090 + 721CDL2 H13Y 1832 7.788 5.729 4.822 -0.1106 1.7373 -0.3834 + 721CDL2 CD14 1833 7.981 5.802 4.744 -0.4354 0.0768 -0.4939 + 721CDL2 H14X 1834 7.929 5.888 4.696 -0.5852 0.8148 1.0082 + 721CDL2 H14Y 1835 8.064 5.779 4.674 -0.4711 0.0582 -0.5304 + 721CDL2 CD15 1836 8.041 5.840 4.879 0.2148 -0.9211 -0.4954 + 721CDL2 H15X 1837 7.973 5.913 4.929 -0.9348 -1.9616 -0.5626 + 721CDL2 H15Y 1838 8.045 5.749 4.942 -2.2328 -0.8775 -0.2429 + 721CDL2 CD16 1839 8.180 5.904 4.879 -0.4555 0.5697 -0.0154 + 721CDL2 H16X 1840 8.257 5.831 4.847 -0.3639 0.5997 0.1439 + 721CDL2 H16Y 1841 8.181 5.990 4.808 3.7864 0.0113 -0.6511 + 721CDL2 CD17 1842 8.218 5.965 5.014 -0.6388 0.0569 0.2647 + 721CDL2 H17X 1843 8.133 6.024 5.054 -0.0666 0.3712 1.0164 + 721CDL2 H17Y 1844 8.238 5.877 5.080 -1.6429 1.6012 2.6212 + 721CDL2 CD18 1845 8.340 6.057 5.001 -0.4489 -0.1635 0.4184 + 721CDL2 H18X 1846 8.424 5.985 4.996 -2.4939 -2.5368 -0.4516 + 721CDL2 H18Y 1847 8.355 6.128 5.085 0.9594 -1.9268 1.6542 + 721CDL2 H18Z 1848 8.330 6.120 4.911 -0.2346 0.6774 0.9821 + 722CDL2 C3 1849 8.208 13.401 3.741 -0.5767 -0.0780 -0.2524 + 722CDL2 HG31 1850 8.149 13.326 3.684 -0.5715 -0.9680 0.9279 + 722CDL2 HG32 1851 8.135 13.481 3.767 0.5017 0.2267 1.8327 + 722CDL2 P3 1852 8.392 13.585 3.670 -0.1259 -0.2988 0.2277 + 722CDL2 OP33 1853 8.330 13.689 3.584 0.3645 -0.1419 0.0591 + 722CDL2 OP34 1854 8.537 13.559 3.657 -0.1320 -0.0471 -0.3527 + 722CDL2 OP31 1855 8.312 13.448 3.654 -0.4832 -0.0424 -0.1249 + 722CDL2 OP32 1856 8.379 13.615 3.827 -0.0878 -0.0236 0.1817 + 722CDL2 C31 1857 8.454 13.728 3.870 -0.0102 -0.2359 0.6031 + 722CDL2 H31J 1858 8.555 13.741 3.825 -0.5134 -0.7495 -0.6696 + 722CDL2 H31K 1859 8.397 13.823 3.862 0.2973 -0.0789 0.3207 + 722CDL2 C2 1860 8.267 13.329 3.863 0.5590 0.2442 -0.6077 + 722CDL2 HG22 1861 8.378 13.329 3.857 0.4699 -0.1530 -2.0698 + 722CDL2 OG12 1862 8.240 13.414 3.974 0.7564 0.2892 -0.5968 + 722CDL2 HO12 1863 8.255 13.501 3.936 1.0752 0.7913 0.6720 + 722CDL2 C1 1864 8.205 13.192 3.897 0.4238 0.3877 -0.2622 + 722CDL2 HG11 1865 8.095 13.207 3.894 0.3495 -0.1696 -0.4264 + 722CDL2 HG12 1866 8.228 13.164 4.001 -1.9906 1.0789 0.4712 + 722CDL2 P1 1867 8.381 13.010 3.816 -0.1020 -0.0528 0.3623 + 722CDL2 OP13 1868 8.344 12.869 3.839 0.2438 -0.1734 0.1701 + 722CDL2 OP14 1869 8.472 13.038 3.703 0.1514 0.0973 0.6059 + 722CDL2 OP11 1870 8.251 13.101 3.797 0.2552 0.3312 -0.2880 + 722CDL2 OP12 1871 8.457 13.066 3.945 -0.1903 0.3766 0.2318 + 722CDL2 C11 1872 8.439 13.022 4.080 0.2656 0.2535 0.2538 + 722CDL2 H11J 1873 8.337 12.978 4.090 -0.7410 2.2848 -1.0715 + 722CDL2 H11K 1874 8.434 13.105 4.155 -2.1494 1.5096 -1.2865 + 722CDL2 C12 1875 8.548 12.921 4.118 -0.1384 -0.2799 0.0393 + 722CDL2 H12J 1876 8.551 12.851 4.032 1.9973 1.5744 -1.4087 + 722CDL2 O12 1877 8.494 12.843 4.225 0.2243 -0.2800 0.2117 + 722CDL2 CA1 1878 8.485 12.897 4.347 0.1105 -0.2173 0.1743 + 722CDL2 OA1 1879 8.515 13.011 4.379 0.1598 -0.1621 -0.0561 + 722CDL2 CA2 1880 8.418 12.793 4.436 -0.1967 -0.1618 0.0018 + 722CDL2 H2A 1881 8.311 12.816 4.449 0.1942 1.7974 -0.2432 + 722CDL2 H2B 1882 8.434 12.695 4.385 -0.7032 -0.3145 0.1530 + 722CDL2 C13 1883 8.691 12.972 4.142 -0.0475 -0.2911 -0.4467 + 722CDL2 H13J 1884 8.682 13.078 4.173 0.2041 0.3762 -2.5824 + 722CDL2 H13K 1885 8.747 12.961 4.046 0.9465 -0.5082 0.1571 + 722CDL2 O13 1886 8.767 12.898 4.237 -0.0113 0.3151 -0.0127 + 722CDL2 CB1 1887 8.866 12.963 4.299 0.2245 -0.1842 0.1338 + 722CDL2 OB1 1888 8.915 13.068 4.262 0.4361 -0.1940 0.3898 + 722CDL2 CB2 1889 8.915 12.879 4.416 -0.0170 0.1759 0.4829 + 722CDL2 H2D 1890 9.026 12.872 4.426 -0.0109 0.1695 0.4803 + 722CDL2 H2E 1891 8.895 12.770 4.410 -0.9313 0.2958 1.3940 + 722CDL2 C32 1892 8.477 13.702 4.020 -0.1029 -0.4273 0.5852 + 722CDL2 H32J 1893 8.387 13.645 4.052 -0.4936 -0.1729 -0.0553 + 722CDL2 O32 1894 8.467 13.822 4.097 -0.4589 0.3790 -0.7132 + 722CDL2 CC1 1895 8.575 13.899 4.112 -0.0592 -0.3063 -0.0753 + 722CDL2 OC1 1896 8.677 13.893 4.046 -0.3724 0.0296 -0.6029 + 722CDL2 CC2 1897 8.541 13.996 4.224 0.1793 0.1040 -0.3563 + 722CDL2 H2R 1898 8.590 14.092 4.194 0.5074 0.1510 0.3146 + 722CDL2 H2S 1899 8.430 14.004 4.224 0.1471 -0.3222 0.3476 + 722CDL2 C33 1900 8.600 13.617 4.055 0.4772 -0.0389 -0.5307 + 722CDL2 H33J 1901 8.659 13.619 3.960 -0.1943 -0.5134 -0.9515 + 722CDL2 H33K 1902 8.658 13.664 4.137 1.1395 0.0792 -1.0675 + 722CDL2 O33 1903 8.572 13.479 4.081 0.7129 0.0005 -0.0065 + 722CDL2 CD1 1904 8.547 13.429 4.202 -0.0823 0.6664 0.1034 + 722CDL2 OD1 1905 8.535 13.310 4.224 -0.5766 0.7451 0.2622 + 722CDL2 CD2 1906 8.540 13.533 4.314 0.6329 0.9992 -0.1643 + 722CDL2 H2X 1907 8.641 13.568 4.346 0.2303 2.4351 -0.4800 + 722CDL2 H2Y 1908 8.475 13.618 4.285 2.0350 1.8502 -0.8366 + 722CDL2 CA3 1909 8.486 12.793 4.573 -0.4976 0.7718 0.1431 + 722CDL2 H3A 1910 8.492 12.896 4.615 -0.6277 0.2241 1.5118 + 722CDL2 H3B 1911 8.588 12.754 4.553 -0.6747 0.3528 0.0523 + 722CDL2 CA4 1912 8.419 12.701 4.675 -0.3640 0.4590 -0.0532 + 722CDL2 H4A 1913 8.308 12.708 4.686 -0.3125 -0.5867 1.1260 + 722CDL2 H4B 1914 8.442 12.603 4.629 -1.7748 0.2151 -0.2760 + 722CDL2 CA5 1915 8.488 12.695 4.811 0.0929 -0.0019 -0.3033 + 722CDL2 H5A 1916 8.595 12.670 4.795 -0.3338 -1.9863 -0.0702 + 722CDL2 H5B 1917 8.489 12.794 4.861 0.5997 -0.3121 0.3096 + 722CDL2 CA6 1918 8.423 12.591 4.903 -0.1985 0.4013 -0.0542 + 722CDL2 H6A 1919 8.313 12.611 4.903 -0.0987 0.9202 0.9598 + 722CDL2 H6B 1920 8.425 12.487 4.865 -0.5407 0.2947 0.2085 + 722CDL2 CA7 1921 8.480 12.601 5.045 0.0499 -0.4958 -0.0894 + 722CDL2 H7A 1922 8.544 12.691 5.054 -0.7103 0.0490 -0.1966 + 722CDL2 H7B 1923 8.547 12.515 5.068 1.1457 0.6288 0.9042 + 722CDL2 CA8 1924 8.370 12.603 5.151 0.1858 -0.3880 0.0504 + 722CDL2 H8A 1925 8.425 12.575 5.244 0.0852 -3.5586 -0.8344 + 722CDL2 H8B 1926 8.307 12.514 5.131 1.2383 -0.8532 -1.1920 + 722CDL2 CA9 1927 8.284 12.726 5.156 -0.0622 -0.5714 0.4562 + 722CDL2 H9A 1928 8.241 12.760 5.061 -0.4366 -1.6696 0.2248 + 722CDL2 CA10 1929 8.268 12.792 5.271 0.1143 0.2030 0.0249 + 722CDL2 H10A 1930 8.197 12.877 5.272 -0.9405 -0.6847 0.7424 + 722CDL2 CA11 1931 8.319 12.762 5.409 -0.5290 -0.4491 0.1226 + 722CDL2 H11A 1932 8.332 12.856 5.466 0.2219 0.5674 -1.6963 + 722CDL2 H11B 1933 8.423 12.724 5.398 -0.1564 1.0664 -1.6788 + 722CDL2 CA12 1934 8.233 12.663 5.487 -0.2274 -0.9148 -0.1353 + 722CDL2 H12A 1935 8.125 12.685 5.472 -0.1892 0.1400 1.0832 + 722CDL2 H12B 1936 8.250 12.558 5.458 2.3399 -0.4658 -0.2414 + 722CDL2 CA13 1937 8.263 12.678 5.637 0.1560 -0.4084 -0.2634 + 722CDL2 H13A 1938 8.231 12.781 5.665 1.2313 -0.2127 0.2437 + 722CDL2 H13B 1939 8.372 12.678 5.659 -0.1629 0.8566 1.3237 + 722CDL2 CA14 1940 8.205 12.567 5.724 0.3887 -0.3568 -0.0546 + 722CDL2 H14A 1941 8.096 12.586 5.714 0.4029 -0.4871 -0.3792 + 722CDL2 H14B 1942 8.245 12.471 5.686 1.0473 -0.4462 0.8207 + 722CDL2 CA15 1943 8.247 12.573 5.872 -0.3578 -0.1875 0.1508 + 722CDL2 H15A 1944 8.357 12.558 5.868 0.1013 3.8011 -3.3275 + 722CDL2 H15B 1945 8.201 12.484 5.920 0.7312 -0.2313 1.1007 + 722CDL2 CA16 1946 8.205 12.694 5.955 -0.9032 -0.3744 0.1522 + 722CDL2 H16A 1947 8.245 12.779 5.896 -0.4005 0.8298 2.2472 + 722CDL2 H16B 1948 8.094 12.699 5.955 -0.9320 -0.6456 -2.4878 + 722CDL2 CA17 1949 8.266 12.690 6.095 -0.4551 -0.0851 -0.0303 + 722CDL2 H17A 1950 8.237 12.786 6.142 -0.6476 0.8750 -2.0544 + 722CDL2 H17B 1951 8.375 12.684 6.074 -0.3062 -1.5822 1.1460 + 722CDL2 CA18 1952 8.219 12.589 6.199 -0.1017 0.0672 0.2712 + 722CDL2 H18A 1953 8.244 12.484 6.169 1.1105 0.4014 0.0933 + 722CDL2 H18B 1954 8.270 12.609 6.296 0.0509 2.0617 -0.2238 + 722CDL2 H18C 1955 8.112 12.602 6.227 -1.1683 -0.7710 -3.4500 + 722CDL2 CB3 1956 8.873 12.936 4.552 -0.4249 0.2167 0.3413 + 722CDL2 H3D 1957 8.763 12.949 4.545 -0.4953 0.0062 0.9723 + 722CDL2 H3E 1958 8.923 13.034 4.569 1.2311 -0.1869 -2.1695 + 722CDL2 CB4 1959 8.906 12.853 4.677 0.1762 0.2588 0.2163 + 722CDL2 H4D 1960 9.016 12.840 4.687 -0.0066 -2.4476 -1.1277 + 722CDL2 H4E 1961 8.869 12.751 4.652 -0.1013 0.3533 0.2477 + 722CDL2 CB5 1962 8.844 12.904 4.807 0.3198 0.4909 0.1947 + 722CDL2 H5D 1963 8.734 12.902 4.794 0.4261 0.0150 -0.6358 + 722CDL2 H5E 1964 8.879 13.008 4.825 0.6651 0.2933 0.6405 + 722CDL2 CB6 1965 8.892 12.822 4.927 -0.1296 -0.6615 -0.4164 + 722CDL2 H6D 1966 9.001 12.837 4.939 -0.6533 1.5907 1.5780 + 722CDL2 H6E 1967 8.869 12.714 4.910 -1.8124 0.0134 -2.4206 + 722CDL2 CB7 1968 8.834 12.876 5.058 -0.2983 -0.4835 -0.5656 + 722CDL2 H7D 1969 8.861 12.983 5.068 0.6761 -0.9478 1.6280 + 722CDL2 H7E 1970 8.723 12.870 5.055 -0.4489 2.8032 -2.0539 + 722CDL2 CB8 1971 8.875 12.795 5.181 0.1003 -0.2278 -0.5362 + 722CDL2 H8D 1972 8.945 12.713 5.153 1.4223 0.9079 -0.5893 + 722CDL2 H8E 1973 8.916 12.867 5.254 -0.0077 -2.0749 1.3718 + 722CDL2 CB9 1974 8.761 12.711 5.232 -0.1254 0.5245 0.1783 + 722CDL2 H9D 1975 8.719 12.630 5.172 -1.9945 0.9024 0.9461 + 722CDL2 CB10 1976 8.705 12.717 5.354 -0.1884 0.2841 0.1598 + 722CDL2 H10D 1977 8.611 12.663 5.372 -0.2382 0.0471 -0.7728 + 722CDL2 CB11 1978 8.740 12.826 5.451 0.3773 0.0024 0.2743 + 722CDL2 H11D 1979 8.792 12.906 5.394 0.3712 0.5475 1.0237 + 722CDL2 H11E 1980 8.652 12.857 5.511 0.1017 1.4432 -0.8721 + 722CDL2 CB12 1981 8.845 12.775 5.551 0.3221 -0.4982 0.0711 + 722CDL2 H12D 1982 8.818 12.674 5.589 -1.2816 0.4341 1.4426 + 722CDL2 H12E 1983 8.942 12.775 5.497 1.3189 -0.2028 1.8924 + 722CDL2 CB13 1984 8.872 12.876 5.662 -0.4839 -0.3267 0.1098 + 722CDL2 H13D 1985 8.778 12.878 5.722 -0.2985 -0.8854 0.4177 + 722CDL2 H13E 1986 8.955 12.842 5.727 0.8327 -1.2190 -2.0422 + 722CDL2 CB14 1987 8.886 13.021 5.615 -0.2477 -0.1960 0.5568 + 722CDL2 H14D 1988 8.790 13.061 5.577 -0.6604 -2.2016 -0.5072 + 722CDL2 H14E 1989 8.966 13.036 5.539 -1.9828 -0.5794 -1.3583 + 722CDL2 CB15 1990 8.912 13.110 5.736 0.2064 0.1126 0.2271 + 722CDL2 H15D 1991 8.900 13.056 5.832 -1.9557 -0.5847 -0.4281 + 722CDL2 H15E 1992 8.835 13.190 5.742 -0.5819 -0.5491 -0.9343 + 722CDL2 CB16 1993 9.045 13.185 5.725 0.3757 -0.2245 -0.0473 + 722CDL2 H16D 1994 9.129 13.114 5.707 -0.1388 -1.4159 2.2255 + 722CDL2 H16E 1995 9.040 13.244 5.631 1.4575 -1.1644 -0.7097 + 722CDL2 CB17 1996 9.085 13.277 5.840 0.0859 -0.7479 0.4687 + 722CDL2 H17D 1997 9.095 13.214 5.931 -0.1861 -0.2759 0.8317 + 722CDL2 H17E 1998 9.011 13.355 5.869 -0.7316 -1.5124 0.4371 + 722CDL2 CB18 1999 9.222 13.345 5.827 -0.3689 0.1085 0.2641 + 722CDL2 H18D 2000 9.236 13.424 5.904 -0.2514 -1.3745 1.7645 + 722CDL2 H18E 2001 9.221 13.393 5.727 0.1598 0.1546 0.2904 + 722CDL2 H18F 2002 9.312 13.281 5.823 -1.0541 -0.8089 -1.0008 + 722CDL2 CC3 2003 8.586 13.957 4.365 -0.1915 -0.2018 -0.3217 + 722CDL2 H3R 2004 8.558 13.853 4.393 0.8298 -0.6589 -0.9782 + 722CDL2 H3S 2005 8.530 14.018 4.438 -0.7926 -0.8588 -0.2230 + 722CDL2 CC4 2006 8.738 13.966 4.380 -0.1629 -0.1919 -0.6199 + 722CDL2 H4R 2007 8.770 14.073 4.372 -1.4374 0.4141 2.2931 + 722CDL2 H4S 2008 8.787 13.911 4.297 2.1599 -0.8515 1.1852 + 722CDL2 CC5 2009 8.797 13.902 4.505 -0.2273 0.9195 -0.0210 + 722CDL2 H5R 2010 8.770 13.795 4.517 0.8381 0.5044 -1.3532 + 722CDL2 H5S 2011 8.908 13.909 4.501 -0.0712 -1.2992 0.4636 + 722CDL2 CC6 2012 8.750 13.964 4.637 -0.0496 -0.3313 0.6404 + 722CDL2 H6R 2013 8.639 13.967 4.638 -0.1081 -1.8143 -2.2500 + 722CDL2 H6S 2014 8.782 13.909 4.728 0.6147 0.0801 0.6566 + 722CDL2 CC7 2015 8.799 14.109 4.652 0.1558 -0.3970 0.6384 + 722CDL2 H7R 2016 8.792 14.157 4.552 -2.1562 0.7238 1.3441 + 722CDL2 H7S 2017 8.908 14.109 4.674 0.2308 -2.2103 0.3013 + 722CDL2 CC8 2018 8.731 14.206 4.749 -0.3235 0.1306 -0.2327 + 722CDL2 H8R 2019 8.716 14.165 4.851 1.8669 -0.0478 0.0193 + 722CDL2 H8S 2020 8.629 14.215 4.704 -0.3098 1.7648 0.0677 + 722CDL2 CC9 2021 8.796 14.341 4.741 0.1051 -0.0942 -0.4717 + 722CDL2 H9R 2022 8.765 14.392 4.648 1.1339 -0.1025 -0.8162 + 722CDL2 CC10 2023 8.886 14.398 4.822 0.1093 -0.7242 -0.0279 + 722CDL2 H10R 2024 8.928 14.497 4.799 -1.0459 -0.3246 -0.4382 + 722CDL2 CC11 2025 8.941 14.335 4.946 -0.3400 0.0375 0.5549 + 722CDL2 H11R 2026 8.868 14.341 5.030 -2.0681 -0.0873 -0.9637 + 722CDL2 H11S 2027 9.030 14.394 4.979 0.6878 -1.6036 0.6837 + 722CDL2 CC12 2028 8.978 14.187 4.938 -0.2093 0.1243 -0.5320 + 722CDL2 H12R 2029 9.041 14.171 4.848 0.0900 0.5596 -0.4063 + 722CDL2 H12S 2030 8.889 14.124 4.918 0.6667 -1.9267 1.9424 + 722CDL2 CC13 2031 9.049 14.132 5.062 -0.2461 -0.3741 -0.7312 + 722CDL2 H13R 2032 9.055 14.024 5.034 -1.3755 -0.7420 0.4455 + 722CDL2 H13S 2033 8.977 14.154 5.144 -0.2256 1.3816 -1.1912 + 722CDL2 CC14 2034 9.191 14.183 5.088 -0.3562 -0.5731 0.2677 + 722CDL2 H14R 2035 9.221 14.152 5.190 -1.8917 -0.5158 0.7480 + 722CDL2 H14S 2036 9.193 14.294 5.090 0.3287 -0.6072 1.2825 + 722CDL2 CC15 2037 9.290 14.131 4.983 0.2591 0.0075 0.5705 + 722CDL2 H15R 2038 9.275 14.186 4.887 -0.2639 -2.9164 -1.0193 + 722CDL2 H15S 2039 9.282 14.022 4.968 -0.7618 0.7637 -4.4768 + 722CDL2 CC16 2040 9.432 14.160 5.032 0.3042 0.0709 0.4194 + 722CDL2 H16R 2041 9.440 14.114 5.133 0.1303 -1.9710 -0.4841 + 722CDL2 H16S 2042 9.451 14.269 5.043 -0.4282 0.1762 0.6439 + 722CDL2 CC17 2043 9.552 14.108 4.952 -0.0352 0.4268 -0.3187 + 722CDL2 H17R 2044 9.529 14.001 4.931 -0.5725 0.3344 0.7212 + 722CDL2 H17S 2045 9.568 14.160 4.855 0.6348 0.4132 -0.2155 + 722CDL2 CC18 2046 9.680 14.119 5.035 0.1164 -0.0469 -0.4793 + 722CDL2 H18R 2047 9.771 14.085 4.982 -1.0498 -2.2741 -1.0956 + 722CDL2 H18S 2048 9.696 14.226 5.059 0.0969 0.0856 -1.0588 + 722CDL2 H18T 2049 9.671 14.069 5.134 -0.7036 0.4765 -0.2933 + 722CDL2 CD3 2050 8.479 13.480 4.444 0.4372 -0.0664 -0.6813 + 722CDL2 H3X 2051 8.543 13.403 4.492 -0.2176 -0.2399 -0.1036 + 722CDL2 H3Y 2052 8.382 13.431 4.422 0.0644 0.7180 -0.8050 + 722CDL2 CD4 2053 8.458 13.595 4.542 0.1492 -0.6800 -0.0158 + 722CDL2 H4X 2054 8.548 13.660 4.547 -0.6589 0.4909 -0.4940 + 722CDL2 H4Y 2055 8.380 13.653 4.488 0.5233 -1.5763 -1.5249 + 722CDL2 CD5 2056 8.409 13.549 4.680 -0.1779 0.3834 0.2230 + 722CDL2 H5X 2057 8.309 13.506 4.658 -0.9604 2.1097 0.4213 + 722CDL2 H5Y 2058 8.478 13.471 4.718 0.0526 0.2207 -0.5224 + 722CDL2 CD6 2059 8.412 13.659 4.786 -0.1467 0.3746 0.2332 + 722CDL2 H6X 2060 8.373 13.755 4.747 1.1696 1.4580 1.5526 + 722CDL2 H6Y 2061 8.343 13.622 4.865 -0.6378 1.3018 0.2296 + 722CDL2 CD7 2062 8.549 13.678 4.852 0.1500 -0.4187 -0.1414 + 722CDL2 H7X 2063 8.549 13.782 4.891 0.8141 0.0420 -1.3580 + 722CDL2 H7Y 2064 8.631 13.677 4.777 1.5424 0.3755 1.3507 + 722CDL2 CD8 2065 8.564 13.579 4.967 -0.3893 -0.4366 -0.0911 + 722CDL2 H8X 2066 8.467 13.551 5.012 -1.2302 -1.0792 -2.3253 + 722CDL2 H8Y 2067 8.604 13.631 5.057 -2.3946 0.2289 0.4202 + 722CDL2 CD9 2068 8.634 13.451 4.931 -0.0159 -0.2873 0.0408 + 722CDL2 H9X 2069 8.574 13.380 4.871 0.4943 -1.3150 0.7363 + 722CDL2 CD10 2070 8.759 13.423 4.972 -0.1106 -0.2311 0.3324 + 722CDL2 H10X 2071 8.801 13.325 4.947 -0.1690 -0.0751 -0.4088 + 722CDL2 CD11 2072 8.857 13.501 5.055 -0.1190 -0.0035 0.1308 + 722CDL2 H11X 2073 8.819 13.605 5.061 0.2106 0.1144 0.3022 + 722CDL2 H11Y 2074 8.956 13.507 5.006 0.0002 -0.5287 0.3125 + 722CDL2 CD12 2075 8.872 13.440 5.195 -0.0374 0.1035 0.1684 + 722CDL2 H12X 2076 8.774 13.435 5.246 -0.8994 -0.3650 -1.5269 + 722CDL2 H12Y 2077 8.913 13.337 5.192 -1.6861 -0.5371 -0.2219 + 722CDL2 CD13 2078 8.971 13.524 5.276 0.0558 -0.4921 0.6729 + 722CDL2 H13X 2079 9.072 13.523 5.230 -0.5819 -1.6232 -0.7074 + 722CDL2 H13Y 2080 8.938 13.630 5.264 -1.0294 -0.9081 -0.0441 + 722CDL2 CD14 2081 8.974 13.503 5.428 0.4152 -0.2290 0.7036 + 722CDL2 H14X 2082 8.965 13.394 5.448 2.0645 -0.4765 0.1519 + 722CDL2 H14Y 2083 9.069 13.544 5.467 -0.4713 2.4862 0.0304 + 722CDL2 CD15 2084 8.866 13.582 5.502 -0.0565 -0.2888 0.0682 + 722CDL2 H15X 2085 8.882 13.686 5.467 0.7087 -0.2309 0.5881 + 722CDL2 H15Y 2086 8.762 13.557 5.474 -0.2496 -0.0948 0.5957 + 722CDL2 CD16 2087 8.897 13.578 5.652 0.3432 0.0113 -0.0000 + 722CDL2 H16X 2088 9.007 13.580 5.662 0.3748 -0.1895 -0.3454 + 722CDL2 H16Y 2089 8.863 13.478 5.688 1.3920 0.1972 1.4697 + 722CDL2 CD17 2090 8.839 13.695 5.730 -0.0973 -0.1286 -0.1009 + 722CDL2 H17X 2091 8.731 13.712 5.711 0.1942 2.2878 0.3424 + 722CDL2 H17Y 2092 8.892 13.788 5.699 -0.5786 0.7685 1.7184 + 722CDL2 CD18 2093 8.856 13.669 5.880 0.1877 0.2728 -0.0623 + 722CDL2 H18X 2094 8.963 13.652 5.903 0.2158 0.7013 0.1203 + 722CDL2 H18Y 2095 8.822 13.761 5.932 -1.5493 -0.3083 -0.1705 + 722CDL2 H18Z 2096 8.789 13.590 5.921 -0.7686 -0.1178 -2.3376 + 723CDL2 C3 2097 11.307 7.193 3.553 -0.8178 0.0072 -0.0832 + 723CDL2 HG31 2098 11.365 7.215 3.646 -2.0722 -0.9200 0.9233 + 723CDL2 HG32 2099 11.206 7.159 3.584 -1.1864 0.7262 -0.4851 + 723CDL2 P3 2100 11.368 6.943 3.518 -0.1971 0.2285 -0.1723 + 723CDL2 OP33 2101 11.508 6.896 3.528 -0.5614 -0.8278 -0.0813 + 723CDL2 OP34 2102 11.277 6.871 3.426 -0.6758 0.1351 0.3815 + 723CDL2 OP31 2103 11.371 7.096 3.470 -0.2809 0.2880 0.0107 + 723CDL2 OP32 2104 11.313 6.947 3.668 0.7331 -0.0638 0.1769 + 723CDL2 C31 2105 11.276 6.836 3.750 -0.7960 -0.2894 -0.8226 + 723CDL2 H31J 2106 11.217 6.765 3.688 0.6086 -3.6848 1.7587 + 723CDL2 H31K 2107 11.361 6.773 3.784 -0.6395 1.2409 1.6514 + 723CDL2 C2 2108 11.280 7.320 3.472 -0.1768 -0.1778 -0.5855 + 723CDL2 HG22 2109 11.232 7.285 3.378 -0.2222 -0.3189 -0.5075 + 723CDL2 OG12 2110 11.396 7.393 3.435 -0.0427 -0.1653 -0.1327 + 723CDL2 HO12 2111 11.458 7.324 3.412 0.9365 0.0307 1.9190 + 723CDL2 C1 2112 11.180 7.420 3.532 0.0640 -0.1012 -0.3004 + 723CDL2 HG11 2113 11.213 7.439 3.636 0.8970 -0.3616 -0.5219 + 723CDL2 HG12 2114 11.195 7.518 3.482 -0.3804 0.2720 0.2867 + 723CDL2 P1 2115 10.938 7.439 3.621 -0.3306 0.1242 0.2139 + 723CDL2 OP13 2116 10.904 7.580 3.592 -0.2057 0.0009 -0.4962 + 723CDL2 OP14 2117 10.825 7.342 3.614 -0.3829 0.2050 -0.0402 + 723CDL2 OP11 2118 11.043 7.379 3.517 -0.0876 0.0941 0.4772 + 723CDL2 OP12 2119 11.025 7.426 3.755 0.0742 0.1299 -0.0480 + 723CDL2 C11 2120 10.966 7.402 3.883 0.6584 -0.1828 0.1646 + 723CDL2 H11J 2121 11.035 7.335 3.939 -0.6532 -0.7663 1.0895 + 723CDL2 H11K 2122 10.865 7.358 3.874 0.7570 -0.2138 -0.8010 + 723CDL2 C12 2123 10.965 7.536 3.960 0.3554 0.0778 -0.2968 + 723CDL2 H12J 2124 11.070 7.571 3.950 0.9215 -1.5270 -0.0759 + 723CDL2 O12 2125 10.932 7.502 4.095 0.6538 -0.0648 -0.2591 + 723CDL2 CA1 2126 10.982 7.574 4.196 0.0670 0.1393 -0.1148 + 723CDL2 OA1 2127 11.046 7.678 4.185 0.1212 0.1275 0.1120 + 723CDL2 CA2 2128 10.947 7.513 4.330 -0.0984 0.1325 -0.1594 + 723CDL2 H2A 2129 10.993 7.412 4.337 1.2053 0.6243 -1.5525 + 723CDL2 H2B 2130 10.839 7.491 4.338 0.0434 -0.6199 -0.2142 + 723CDL2 C13 2131 10.864 7.639 3.907 -0.0688 -0.2042 -0.0503 + 723CDL2 H13J 2132 10.768 7.585 3.898 -0.1690 0.0883 -0.7538 + 723CDL2 H13K 2133 10.901 7.670 3.807 0.0348 0.2155 0.1152 + 723CDL2 O13 2134 10.837 7.752 3.989 0.0320 -0.0201 -0.2709 + 723CDL2 CB1 2135 10.916 7.857 3.970 -0.0794 0.1146 -0.0136 + 723CDL2 OB1 2136 11.014 7.868 3.897 -0.1479 -0.1293 -0.1359 + 723CDL2 CB2 2137 10.867 7.969 4.060 -0.0932 -0.1267 0.2771 + 723CDL2 H2D 2138 10.854 7.930 4.163 2.2351 -0.4147 0.4625 + 723CDL2 H2E 2139 10.764 7.996 4.026 -0.0979 -0.6265 -0.1153 + 723CDL2 C32 2140 11.202 6.887 3.875 0.0518 -0.2058 -0.3671 + 723CDL2 H32J 2141 11.263 6.966 3.924 0.5867 1.2015 -3.2844 + 723CDL2 O32 2142 11.195 6.784 3.974 -0.1150 0.3733 0.2281 + 723CDL2 CC1 2143 11.111 6.684 3.945 0.2329 0.2088 -0.2274 + 723CDL2 OC1 2144 11.044 6.664 3.845 0.1208 -0.0502 -0.0990 + 723CDL2 CC2 2145 11.139 6.583 4.056 -0.5780 -0.0821 -0.2920 + 723CDL2 H2R 2146 11.096 6.486 4.022 -0.3916 0.6052 -2.4958 + 723CDL2 H2S 2147 11.248 6.564 4.065 -0.7620 0.0698 2.3479 + 723CDL2 C33 2148 11.066 6.954 3.854 -0.1399 -0.5105 -0.0812 + 723CDL2 H33J 2149 11.100 7.052 3.815 0.1225 -0.2244 0.8654 + 723CDL2 H33K 2150 11.008 6.910 3.769 1.5830 1.3241 -2.2202 + 723CDL2 O33 2151 10.986 6.960 3.972 -0.2969 -0.0812 -0.2030 + 723CDL2 CD1 2152 10.871 7.028 3.961 -0.3075 -0.1038 -0.1684 + 723CDL2 OD1 2153 10.832 7.086 3.861 -0.1619 -0.0175 -0.1763 + 723CDL2 CD2 2154 10.791 7.021 4.090 -0.2064 0.1706 -0.0903 + 723CDL2 H2X 2155 10.762 6.915 4.105 1.2678 -0.0389 1.2623 + 723CDL2 H2Y 2156 10.697 7.077 4.075 -0.2588 0.8154 2.5674 + 723CDL2 CA3 2157 10.980 7.593 4.456 -0.3282 -0.0617 0.0191 + 723CDL2 H3A 2158 10.931 7.693 4.456 -2.1911 -0.9830 0.0724 + 723CDL2 H3B 2159 11.088 7.620 4.453 -0.1940 -0.6094 0.1273 + 723CDL2 CA4 2160 10.951 7.530 4.593 -0.1639 0.0695 0.1128 + 723CDL2 H4A 2161 11.000 7.431 4.598 -0.1574 0.1821 2.0791 + 723CDL2 H4B 2162 10.840 7.524 4.595 -0.2243 -0.3402 -2.9143 + 723CDL2 CA5 2163 10.993 7.616 4.712 0.1215 -0.0206 0.0769 + 723CDL2 H5A 2164 10.954 7.718 4.694 1.1559 0.2865 -0.4681 + 723CDL2 H5B 2165 11.103 7.629 4.727 0.1627 -0.7457 0.4256 + 723CDL2 CA6 2166 10.937 7.564 4.845 -0.1570 0.0505 -0.0173 + 723CDL2 H6A 2167 10.971 7.460 4.862 -2.1694 -0.5923 0.0284 + 723CDL2 H6B 2168 10.826 7.559 4.843 -0.0873 -1.1371 -0.8059 + 723CDL2 CA7 2169 10.989 7.653 4.959 -0.4015 0.1502 0.0140 + 723CDL2 H7A 2170 10.928 7.746 4.960 1.4576 1.3949 -0.5485 + 723CDL2 H7B 2171 11.097 7.677 4.951 -0.4010 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-0.9847 0.4973 0.8749 + 760CDL2 H18S11472 16.598 3.729 5.552 -0.5157 -1.8547 -0.8554 + 760CDL2 H18T11473 16.696 3.664 5.685 -1.6380 -0.5264 0.0202 + 760CDL2 CD311474 16.472 3.844 4.286 -0.0224 -0.4530 0.5882 + 760CDL2 H3X11475 16.375 3.845 4.341 -0.1257 1.3235 0.3671 + 760CDL2 H3Y11476 16.477 3.941 4.232 0.8786 -1.0448 -0.3764 + 760CDL2 CD411477 16.590 3.841 4.384 0.0248 -0.7815 0.5190 + 760CDL2 H4X11478 16.682 3.857 4.325 -0.5653 1.5687 0.2028 + 760CDL2 H4Y11479 16.604 3.742 4.431 -0.6063 0.2276 2.8598 + 760CDL2 CD511480 16.576 3.933 4.505 0.7664 -0.0292 0.0344 + 760CDL2 H5X11481 16.591 4.038 4.471 1.8767 -0.5645 -1.1508 + 760CDL2 H5Y11482 16.477 3.915 4.553 1.0423 -0.9074 0.2616 + 760CDL2 CD611483 16.688 3.908 4.606 0.3407 -0.8106 0.3073 + 760CDL2 H6X11484 16.696 3.799 4.627 2.2645 -1.0457 -1.6810 + 760CDL2 H6Y11485 16.784 3.944 4.565 0.0596 -1.2071 -0.7035 + 760CDL2 CD711486 16.668 3.974 4.743 -0.4492 -0.3406 -0.0387 + 760CDL2 H7X11487 16.661 4.085 4.740 -1.4269 -0.3326 2.1997 + 760CDL2 H7Y11488 16.569 3.939 4.780 -0.7244 -0.8594 -1.2505 + 760CDL2 CD811489 16.778 3.936 4.841 -0.1881 0.3942 -0.0427 + 760CDL2 H8X11490 16.789 3.825 4.847 -0.8054 0.3360 0.0271 + 760CDL2 H8Y11491 16.876 3.973 4.803 -1.2882 0.3775 -2.9362 + 760CDL2 CD911492 16.754 4.007 4.971 -1.2127 0.6078 -0.3533 + 760CDL2 H9X11493 16.677 3.964 5.036 0.2059 -1.2991 0.0640 + 760CDL2 CD1011494 16.816 4.116 5.017 -0.5985 0.2379 -0.3224 + 760CDL2 H10X11495 16.806 4.148 5.122 2.0813 1.8247 -0.5334 + 760CDL2 CD1111496 16.933 4.182 4.949 0.1128 -0.8555 -0.1631 + 760CDL2 H11X11497 16.922 4.176 4.839 0.7386 -0.9394 -0.2215 + 760CDL2 H11Y11498 16.941 4.289 4.978 0.1209 -0.3843 -1.8609 + 760CDL2 CD1211499 17.067 4.115 4.979 0.5369 -0.1518 -0.4920 + 760CDL2 H12X11500 17.066 4.007 4.953 0.4322 -0.3164 0.1942 + 760CDL2 H12Y11501 17.147 4.171 4.927 0.4689 1.2589 0.9147 + 760CDL2 CD1311502 17.111 4.123 5.126 0.0454 0.4953 -0.3795 + 760CDL2 H13X11503 17.029 4.069 5.179 -0.3120 1.6969 0.2880 + 760CDL2 H13Y11504 17.117 4.225 5.169 2.1195 0.4569 -0.5752 + 760CDL2 CD1411505 17.243 4.052 5.156 -0.1622 0.3014 0.0901 + 760CDL2 H14X11506 17.234 3.954 5.104 0.1985 -0.4256 1.4010 + 760CDL2 H14Y11507 17.251 4.036 5.266 -1.4349 -1.1553 -0.0201 + 760CDL2 CD1511508 17.373 4.103 5.093 -0.2682 -0.0127 -0.3795 + 760CDL2 H15X11509 17.390 4.205 5.133 1.0545 -0.3131 -0.1657 + 760CDL2 H15Y11510 17.353 4.110 4.984 2.0767 1.0386 -0.7424 + 760CDL2 CD1611511 17.498 4.021 5.122 -0.0001 0.6299 0.2676 + 760CDL2 H16X11512 17.485 3.925 5.068 1.7076 -0.5813 1.9920 + 760CDL2 H16Y11513 17.500 3.984 5.227 1.3462 0.4239 0.1698 + 760CDL2 CD1711514 17.627 4.100 5.100 0.1459 0.4103 0.3222 + 760CDL2 H17X11515 17.610 4.203 5.138 -0.1850 0.6073 -0.3495 + 760CDL2 H17Y11516 17.635 4.117 4.990 0.1645 1.3749 0.4705 + 760CDL2 CD1811517 17.761 4.043 5.145 0.0526 0.1951 0.3366 + 760CDL2 H18X11518 17.771 3.944 5.096 0.7136 0.2445 0.3757 + 760CDL2 H18Y11519 17.765 4.031 5.256 -1.5811 0.4668 0.4259 + 760CDL2 H18Z11520 17.850 4.097 5.106 0.8542 -0.9248 0.5991 + 16.18101 16.18101 11.11383 diff --git a/tests/data/membrane/membrane.map b/tests/data/membrane/membrane.map new file mode 100644 index 0000000..3d4c58b --- /dev/null +++ b/tests/data/membrane/membrane.map @@ -0,0 +1,6 @@ +; TEST MAPPING - DO NOT USE FOR MODEL GENERATION +[ POPE ] +PO4 Qa P O13 O14 O11 O12 + +[ POPG ] +GL0 P4 C13 H13A H13B OC3 HO3 C12 H12A OC2 HO2 diff --git a/tests/data/membrane/membrane.top b/tests/data/membrane/membrane.top new file mode 100755 index 0000000..0d743d8 --- /dev/null +++ b/tests/data/membrane/membrane.top @@ -0,0 +1,18 @@ +#include "TOCL2.itp" +#include "AT_AA_POPE.itp" +#include "AT_AA_POPG.itp" +#include "PII_charmm36.itp" + +[ system ] +; name +Martini system + +[ molecules ] +; name number +PII 10 +POPE 270 +POPG 45 +CDL2 60 +POPE 270 +POPG 45 +CDL2 60 diff --git a/tests/data/membrane/twice.itp b/tests/data/membrane/twice.itp new file mode 100755 index 0000000..21193c5 --- /dev/null +++ b/tests/data/membrane/twice.itp @@ -0,0 +1,2354 @@ +;; +;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 +;; +;; psf2itp.py +;; +;; Correspondance: +;; jul316@lehigh.edu or wonpil@lehigh.edu +;; +;; GROMACS topology file for POPE +;; + + +[ moleculetype ] +; name nrexcl +POPE 3 + +[ atoms ] +; nr type resnr residu atom cgnr charge mass + 1 NH3L 1 POPE N 1 -0.300 14.0070 ; qtot -0.300 + 2 HCL 1 POPE HN1 2 0.330 1.0080 ; qtot 0.030 + 3 HCL 1 POPE HN2 3 0.330 1.0080 ; qtot 0.360 + 4 HCL 1 POPE HN3 4 0.330 1.0080 ; qtot 0.690 + 5 CTL2 1 POPE C12 5 0.130 12.0110 ; qtot 0.820 + 6 HAL2 1 POPE H12A 6 0.090 1.0080 ; qtot 0.910 + 7 HAL2 1 POPE H12B 7 0.090 1.0080 ; qtot 1.000 + 8 CTL2 1 POPE C11 8 -0.080 12.0110 ; qtot 0.920 + 9 HAL2 1 POPE H11A 9 0.090 1.0080 ; qtot 1.010 + 10 HAL2 1 POPE H11B 10 0.090 1.0080 ; qtot 1.100 + 11 PL 1 POPE P 11 1.500 30.9740 ; qtot 2.600 + 12 O2L 1 POPE O13 12 -0.780 15.9994 ; qtot 1.820 + 13 O2L 1 POPE O14 13 -0.780 15.9994 ; qtot 1.040 + 14 OSLP 1 POPE O11 14 -0.570 15.9994 ; qtot 0.470 + 15 OSLP 1 POPE O12 15 -0.570 15.9994 ; qtot -0.100 + 16 CTL2 1 POPE C1 16 -0.080 12.0110 ; qtot -0.180 + 17 HAL2 1 POPE HA 17 0.090 1.0080 ; qtot -0.090 + 18 HAL2 1 POPE HB 18 0.090 1.0080 ; qtot 0.000 + 19 CTL1 1 POPE C2 19 0.170 12.0110 ; qtot 0.170 + 20 HAL1 1 POPE HS 20 0.090 1.0080 ; qtot 0.260 + 21 OSL 1 POPE O21 21 -0.490 15.9994 ; qtot -0.230 + 22 CL 1 POPE C21 22 0.900 12.0110 ; qtot 0.670 + 23 OBL 1 POPE O22 23 -0.630 15.9994 ; qtot 0.040 + 24 CTL2 1 POPE C22 24 -0.220 12.0110 ; qtot -0.180 + 25 HAL2 1 POPE H2R 25 0.090 1.0080 ; qtot -0.090 + 26 HAL2 1 POPE H2S 26 0.090 1.0080 ; qtot 0.000 + 27 CTL2 1 POPE C3 27 0.080 12.0110 ; qtot 0.080 + 28 HAL2 1 POPE HX 28 0.090 1.0080 ; qtot 0.170 + 29 HAL2 1 POPE HY 29 0.090 1.0080 ; qtot 0.260 + 30 OSL 1 POPE O31 30 -0.490 15.9994 ; qtot -0.230 + 31 CL 1 POPE C31 31 0.900 12.0110 ; qtot 0.670 + 32 OBL 1 POPE O32 32 -0.630 15.9994 ; qtot 0.040 + 33 CTL2 1 POPE C32 33 -0.220 12.0110 ; qtot -0.180 + 34 HAL2 1 POPE H2X 34 0.090 1.0080 ; qtot -0.090 + 35 HAL2 1 POPE H2Y 35 0.090 1.0080 ; qtot 0.000 + 36 CTL2 1 POPE C23 36 -0.180 12.0110 ; qtot -0.180 + 37 HAL2 1 POPE H3R 37 0.090 1.0080 ; qtot -0.090 + 38 HAL2 1 POPE H3S 38 0.090 1.0080 ; qtot 0.000 + 39 CTL2 1 POPE C24 39 -0.180 12.0110 ; qtot -0.180 + 40 HAL2 1 POPE H4R 40 0.090 1.0080 ; qtot -0.090 + 41 HAL2 1 POPE H4S 41 0.090 1.0080 ; qtot 0.000 + 42 CTL2 1 POPE C25 42 -0.180 12.0110 ; qtot -0.180 + 43 HAL2 1 POPE H5R 43 0.090 1.0080 ; qtot -0.090 + 44 HAL2 1 POPE H5S 44 0.090 1.0080 ; qtot 0.000 + 45 CTL2 1 POPE C26 45 -0.180 12.0110 ; qtot -0.180 + 46 HAL2 1 POPE H6R 46 0.090 1.0080 ; qtot -0.090 + 47 HAL2 1 POPE H6S 47 0.090 1.0080 ; qtot 0.000 + 48 CTL2 1 POPE C27 48 -0.180 12.0110 ; qtot -0.180 + 49 HAL2 1 POPE H7R 49 0.090 1.0080 ; qtot -0.090 + 50 HAL2 1 POPE H7S 50 0.090 1.0080 ; qtot 0.000 + 51 CTL2 1 POPE C28 51 -0.180 12.0110 ; qtot -0.180 + 52 HAL2 1 POPE H8R 52 0.090 1.0080 ; qtot -0.090 + 53 HAL2 1 POPE H8S 53 0.090 1.0080 ; qtot 0.000 + 54 CEL1 1 POPE C29 54 -0.150 12.0110 ; qtot -0.150 + 55 HEL1 1 POPE H91 55 0.150 1.0080 ; qtot 0.000 + 56 CEL1 1 POPE C210 56 -0.150 12.0110 ; qtot -0.150 + 57 HEL1 1 POPE H101 57 0.150 1.0080 ; qtot 0.000 + 58 CTL2 1 POPE C211 58 -0.180 12.0110 ; qtot -0.180 + 59 HAL2 1 POPE H11R 59 0.090 1.0080 ; qtot -0.090 + 60 HAL2 1 POPE H11S 60 0.090 1.0080 ; qtot 0.000 + 61 CTL2 1 POPE C212 61 -0.180 12.0110 ; qtot -0.180 + 62 HAL2 1 POPE H12R 62 0.090 1.0080 ; qtot -0.090 + 63 HAL2 1 POPE H12S 63 0.090 1.0080 ; qtot 0.000 + 64 CTL2 1 POPE C213 64 -0.180 12.0110 ; qtot -0.180 + 65 HAL2 1 POPE H13R 65 0.090 1.0080 ; qtot -0.090 + 66 HAL2 1 POPE H13S 66 0.090 1.0080 ; qtot 0.000 + 67 CTL2 1 POPE C214 67 -0.180 12.0110 ; qtot -0.180 + 68 HAL2 1 POPE H14R 68 0.090 1.0080 ; qtot -0.090 + 69 HAL2 1 POPE H14S 69 0.090 1.0080 ; qtot 0.000 + 70 CTL2 1 POPE C215 70 -0.180 12.0110 ; qtot -0.180 + 71 HAL2 1 POPE H15R 71 0.090 1.0080 ; qtot -0.090 + 72 HAL2 1 POPE H15S 72 0.090 1.0080 ; qtot 0.000 + 73 CTL2 1 POPE C216 73 -0.180 12.0110 ; qtot -0.180 + 74 HAL2 1 POPE H16R 74 0.090 1.0080 ; qtot -0.090 + 75 HAL2 1 POPE H16S 75 0.090 1.0080 ; qtot 0.000 + 76 CTL2 1 POPE C217 76 -0.180 12.0110 ; qtot -0.180 + 77 HAL2 1 POPE H17R 77 0.090 1.0080 ; qtot -0.090 + 78 HAL2 1 POPE H17S 78 0.090 1.0080 ; qtot 0.000 + 79 CTL3 1 POPE C218 79 -0.270 12.0110 ; qtot -0.270 + 80 HAL3 1 POPE H18R 80 0.090 1.0080 ; qtot -0.180 + 81 HAL3 1 POPE H18S 81 0.090 1.0080 ; qtot -0.090 + 82 HAL3 1 POPE H18T 82 0.090 1.0080 ; qtot 0.000 + 83 CTL2 1 POPE C33 83 -0.180 12.0110 ; qtot -0.180 + 84 HAL2 1 POPE H3X 84 0.090 1.0080 ; qtot -0.090 + 85 HAL2 1 POPE H3Y 85 0.090 1.0080 ; qtot 0.000 + 86 CTL2 1 POPE C34 86 -0.180 12.0110 ; qtot -0.180 + 87 HAL2 1 POPE H4X 87 0.090 1.0080 ; qtot -0.090 + 88 HAL2 1 POPE H4Y 88 0.090 1.0080 ; qtot 0.000 + 89 CTL2 1 POPE C35 89 -0.180 12.0110 ; qtot -0.180 + 90 HAL2 1 POPE H5X 90 0.090 1.0080 ; qtot -0.090 + 91 HAL2 1 POPE H5Y 91 0.090 1.0080 ; qtot 0.000 + 92 CTL2 1 POPE C36 92 -0.180 12.0110 ; qtot -0.180 + 93 HAL2 1 POPE H6X 93 0.090 1.0080 ; qtot -0.090 + 94 HAL2 1 POPE H6Y 94 0.090 1.0080 ; qtot 0.000 + 95 CTL2 1 POPE C37 95 -0.180 12.0110 ; qtot -0.180 + 96 HAL2 1 POPE H7X 96 0.090 1.0080 ; qtot -0.090 + 97 HAL2 1 POPE H7Y 97 0.090 1.0080 ; qtot 0.000 + 98 CTL2 1 POPE C38 98 -0.180 12.0110 ; qtot -0.180 + 99 HAL2 1 POPE H8X 99 0.090 1.0080 ; qtot -0.090 + 100 HAL2 1 POPE H8Y 100 0.090 1.0080 ; qtot 0.000 + 101 CTL2 1 POPE C39 101 -0.180 12.0110 ; qtot -0.180 + 102 HAL2 1 POPE H9X 102 0.090 1.0080 ; qtot -0.090 + 103 HAL2 1 POPE H9Y 103 0.090 1.0080 ; qtot 0.000 + 104 CTL2 1 POPE C310 104 -0.180 12.0110 ; qtot -0.180 + 105 HAL2 1 POPE H10X 105 0.090 1.0080 ; qtot -0.090 + 106 HAL2 1 POPE H10Y 106 0.090 1.0080 ; qtot 0.000 + 107 CTL2 1 POPE C311 107 -0.180 12.0110 ; qtot -0.180 + 108 HAL2 1 POPE H11X 108 0.090 1.0080 ; qtot -0.090 + 109 HAL2 1 POPE H11Y 109 0.090 1.0080 ; qtot 0.000 + 110 CTL2 1 POPE C312 110 -0.180 12.0110 ; qtot -0.180 + 111 HAL2 1 POPE H12X 111 0.090 1.0080 ; qtot -0.090 + 112 HAL2 1 POPE H12Y 112 0.090 1.0080 ; qtot 0.000 + 113 CTL2 1 POPE C313 113 -0.180 12.0110 ; qtot -0.180 + 114 HAL2 1 POPE H13X 114 0.090 1.0080 ; qtot -0.090 + 115 HAL2 1 POPE H13Y 115 0.090 1.0080 ; qtot 0.000 + 116 CTL2 1 POPE C314 116 -0.180 12.0110 ; qtot -0.180 + 117 HAL2 1 POPE H14X 117 0.090 1.0080 ; qtot -0.090 + 118 HAL2 1 POPE H14Y 118 0.090 1.0080 ; qtot 0.000 + 119 CTL2 1 POPE C315 119 -0.180 12.0110 ; qtot -0.180 + 120 HAL2 1 POPE H15X 120 0.090 1.0080 ; qtot -0.090 + 121 HAL2 1 POPE H15Y 121 0.090 1.0080 ; qtot 0.000 + 122 CTL3 1 POPE C316 122 -0.270 12.0110 ; qtot -0.270 + 123 HAL3 1 POPE H16X 123 0.090 1.0080 ; qtot -0.180 + 124 HAL3 1 POPE H16Y 124 0.090 1.0080 ; qtot -0.090 + 125 HAL3 1 POPE H16Z 125 0.090 1.0080 ; qtot 0.000 + +[ bonds ] +; ai aj funct b0 Kb + 1 2 1 + 1 3 1 + 1 4 1 + 1 5 1 + 5 6 1 + 5 7 1 + 5 8 1 + 8 9 1 + 8 10 1 + 8 15 1 + 11 12 1 + 11 13 1 + 11 14 1 + 11 15 1 + 14 16 1 + 16 17 1 + 16 18 1 + 16 19 1 + 19 20 1 + 19 21 1 + 19 27 1 + 21 22 1 + 22 23 1 + 22 24 1 + 24 25 1 + 24 26 1 + 24 36 1 + 27 28 1 + 27 29 1 + 27 30 1 + 30 31 1 + 31 32 1 + 31 33 1 + 33 34 1 + 33 35 1 + 33 83 1 + 36 37 1 + 36 38 1 + 36 39 1 + 39 40 1 + 39 41 1 + 39 42 1 + 42 43 1 + 42 44 1 + 42 45 1 + 45 46 1 + 45 47 1 + 45 48 1 + 48 49 1 + 48 50 1 + 48 51 1 + 51 52 1 + 51 53 1 + 51 54 1 + 54 55 1 + 54 56 1 + 56 57 1 + 56 58 1 + 58 59 1 + 58 60 1 + 58 61 1 + 61 62 1 + 61 63 1 + 61 64 1 + 64 65 1 + 64 66 1 + 64 67 1 + 67 68 1 + 67 69 1 + 67 70 1 + 70 71 1 + 70 72 1 + 70 73 1 + 73 74 1 + 73 75 1 + 73 76 1 + 76 77 1 + 76 78 1 + 76 79 1 + 79 80 1 + 79 81 1 + 79 82 1 + 83 84 1 + 83 85 1 + 83 86 1 + 86 87 1 + 86 88 1 + 86 89 1 + 89 90 1 + 89 91 1 + 89 92 1 + 92 93 1 + 92 94 1 + 92 95 1 + 95 96 1 + 95 97 1 + 95 98 1 + 98 99 1 + 98 100 1 + 98 101 1 + 101 102 1 + 101 103 1 + 101 104 1 + 104 105 1 + 104 106 1 + 104 107 1 + 107 108 1 + 107 109 1 + 107 110 1 + 110 111 1 + 110 112 1 + 110 113 1 + 113 114 1 + 113 115 1 + 113 116 1 + 116 117 1 + 116 118 1 + 116 119 1 + 119 120 1 + 119 121 1 + 119 122 1 + 122 123 1 + 122 124 1 + 122 125 1 + +[ pairs ] +; ai aj funct c6 c12 + 1 9 1 + 1 10 1 + 1 15 1 + 2 6 1 + 2 7 1 + 2 8 1 + 3 6 1 + 3 7 1 + 3 8 1 + 4 6 1 + 4 7 1 + 4 8 1 + 5 11 1 + 6 9 1 + 6 10 1 + 6 15 1 + 7 9 1 + 7 10 1 + 7 15 1 + 8 12 1 + 8 13 1 + 8 14 1 + 9 11 1 + 10 11 1 + 11 17 1 + 11 18 1 + 11 19 1 + 12 16 1 + 13 16 1 + 14 20 1 + 14 21 1 + 14 27 1 + 15 16 1 + 16 22 1 + 16 28 1 + 16 29 1 + 16 30 1 + 17 20 1 + 17 21 1 + 17 27 1 + 18 20 1 + 18 21 1 + 18 27 1 + 19 23 1 + 19 24 1 + 19 31 1 + 20 22 1 + 20 28 1 + 20 29 1 + 20 30 1 + 21 25 1 + 21 26 1 + 21 28 1 + 21 29 1 + 21 30 1 + 21 36 1 + 22 27 1 + 22 37 1 + 22 38 1 + 22 39 1 + 23 25 1 + 23 26 1 + 23 36 1 + 24 40 1 + 24 41 1 + 24 42 1 + 25 37 1 + 25 38 1 + 25 39 1 + 26 37 1 + 26 38 1 + 26 39 1 + 27 32 1 + 27 33 1 + 28 31 1 + 29 31 1 + 30 34 1 + 30 35 1 + 30 83 1 + 31 84 1 + 31 85 1 + 31 86 1 + 32 34 1 + 32 35 1 + 32 83 1 + 33 87 1 + 33 88 1 + 33 89 1 + 34 84 1 + 34 85 1 + 34 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80 9 + 73 76 79 81 9 + 73 76 79 82 9 + 77 76 79 80 9 + 77 76 79 81 9 + 77 76 79 82 9 + 78 76 79 80 9 + 78 76 79 81 9 + 78 76 79 82 9 + 33 83 86 87 9 + 33 83 86 88 9 + 33 83 86 89 9 + 84 83 86 87 9 + 84 83 86 88 9 + 84 83 86 89 9 + 85 83 86 87 9 + 85 83 86 88 9 + 85 83 86 89 9 + 83 86 89 90 9 + 83 86 89 91 9 + 83 86 89 92 9 + 87 86 89 90 9 + 87 86 89 91 9 + 87 86 89 92 9 + 88 86 89 90 9 + 88 86 89 91 9 + 88 86 89 92 9 + 86 89 92 93 9 + 86 89 92 94 9 + 86 89 92 95 9 + 90 89 92 93 9 + 90 89 92 94 9 + 90 89 92 95 9 + 91 89 92 93 9 + 91 89 92 94 9 + 91 89 92 95 9 + 89 92 95 96 9 + 89 92 95 97 9 + 89 92 95 98 9 + 93 92 95 96 9 + 93 92 95 97 9 + 93 92 95 98 9 + 94 92 95 96 9 + 94 92 95 97 9 + 94 92 95 98 9 + 92 95 98 99 9 + 92 95 98 100 9 + 92 95 98 101 9 + 96 95 98 99 9 + 96 95 98 100 9 + 96 95 98 101 9 + 97 95 98 99 9 + 97 95 98 100 9 + 97 95 98 101 9 + 95 98 101 102 9 + 95 98 101 103 9 + 95 98 101 104 9 + 99 98 101 102 9 + 99 98 101 103 9 + 99 98 101 104 9 + 100 98 101 102 9 + 100 98 101 103 9 + 100 98 101 104 9 + 98 101 104 105 9 + 98 101 104 106 9 + 98 101 104 107 9 + 102 101 104 105 9 + 102 101 104 106 9 + 102 101 104 107 9 + 103 101 104 105 9 + 103 101 104 106 9 + 103 101 104 107 9 + 101 104 107 108 9 + 101 104 107 109 9 + 101 104 107 110 9 + 105 104 107 108 9 + 105 104 107 109 9 + 105 104 107 110 9 + 106 104 107 108 9 + 106 104 107 109 9 + 106 104 107 110 9 + 104 107 110 111 9 + 104 107 110 112 9 + 104 107 110 113 9 + 108 107 110 111 9 + 108 107 110 112 9 + 108 107 110 113 9 + 109 107 110 111 9 + 109 107 110 112 9 + 109 107 110 113 9 + 107 110 113 114 9 + 107 110 113 115 9 + 107 110 113 116 9 + 111 110 113 114 9 + 111 110 113 115 9 + 111 110 113 116 9 + 112 110 113 114 9 + 112 110 113 115 9 + 112 110 113 116 9 + 110 113 116 117 9 + 110 113 116 118 9 + 110 113 116 119 9 + 114 113 116 117 9 + 114 113 116 118 9 + 114 113 116 119 9 + 115 113 116 117 9 + 115 113 116 118 9 + 115 113 116 119 9 + 113 116 119 120 9 + 113 116 119 121 9 + 113 116 119 122 9 + 117 116 119 120 9 + 117 116 119 121 9 + 117 116 119 122 9 + 118 116 119 120 9 + 118 116 119 121 9 + 118 116 119 122 9 + 116 119 122 123 9 + 116 119 122 124 9 + 116 119 122 125 9 + 120 119 122 123 9 + 120 119 122 124 9 + 120 119 122 125 9 + 121 119 122 123 9 + 121 119 122 124 9 + 121 119 122 125 9 + +[ dihedrals ] +; ai aj ak al funct q0 cq + 22 21 24 23 2 + 31 30 33 32 2 + + +[ moleculetype ] +; name nrexcl +POPE 3 + +[ atoms ] +; nr type resnr residu atom cgnr charge mass + 1 NH3L 1 POPE N 1 -0.300 14.0070 ; qtot -0.300 + 2 HCL 1 POPE HN1 2 0.330 1.0080 ; qtot 0.030 + 3 HCL 1 POPE HN2 3 0.330 1.0080 ; qtot 0.360 + 4 HCL 1 POPE HN3 4 0.330 1.0080 ; qtot 0.690 + 5 CTL2 1 POPE C12 5 0.130 12.0110 ; qtot 0.820 + 6 HAL2 1 POPE H12A 6 0.090 1.0080 ; qtot 0.910 + 7 HAL2 1 POPE H12B 7 0.090 1.0080 ; qtot 1.000 + 8 CTL2 1 POPE C11 8 -0.080 12.0110 ; qtot 0.920 + 9 HAL2 1 POPE H11A 9 0.090 1.0080 ; qtot 1.010 + 10 HAL2 1 POPE H11B 10 0.090 1.0080 ; qtot 1.100 + 11 PL 1 POPE P 11 1.500 30.9740 ; qtot 2.600 + 12 O2L 1 POPE O13 12 -0.780 15.9994 ; qtot 1.820 + 13 O2L 1 POPE O14 13 -0.780 15.9994 ; qtot 1.040 + 14 OSLP 1 POPE O11 14 -0.570 15.9994 ; qtot 0.470 + 15 OSLP 1 POPE O12 15 -0.570 15.9994 ; qtot -0.100 + 16 CTL2 1 POPE C1 16 -0.080 12.0110 ; qtot -0.180 + 17 HAL2 1 POPE HA 17 0.090 1.0080 ; qtot -0.090 + 18 HAL2 1 POPE HB 18 0.090 1.0080 ; qtot 0.000 + 19 CTL1 1 POPE C2 19 0.170 12.0110 ; qtot 0.170 + 20 HAL1 1 POPE HS 20 0.090 1.0080 ; qtot 0.260 + 21 OSL 1 POPE O21 21 -0.490 15.9994 ; qtot -0.230 + 22 CL 1 POPE C21 22 0.900 12.0110 ; qtot 0.670 + 23 OBL 1 POPE O22 23 -0.630 15.9994 ; qtot 0.040 + 24 CTL2 1 POPE C22 24 -0.220 12.0110 ; qtot -0.180 + 25 HAL2 1 POPE H2R 25 0.090 1.0080 ; qtot -0.090 + 26 HAL2 1 POPE H2S 26 0.090 1.0080 ; qtot 0.000 + 27 CTL2 1 POPE C3 27 0.080 12.0110 ; qtot 0.080 + 28 HAL2 1 POPE HX 28 0.090 1.0080 ; qtot 0.170 + 29 HAL2 1 POPE HY 29 0.090 1.0080 ; qtot 0.260 + 30 OSL 1 POPE O31 30 -0.490 15.9994 ; qtot -0.230 + 31 CL 1 POPE C31 31 0.900 12.0110 ; qtot 0.670 + 32 OBL 1 POPE O32 32 -0.630 15.9994 ; qtot 0.040 + 33 CTL2 1 POPE C32 33 -0.220 12.0110 ; qtot -0.180 + 34 HAL2 1 POPE H2X 34 0.090 1.0080 ; qtot -0.090 + 35 HAL2 1 POPE H2Y 35 0.090 1.0080 ; qtot 0.000 + 36 CTL2 1 POPE C23 36 -0.180 12.0110 ; qtot -0.180 + 37 HAL2 1 POPE H3R 37 0.090 1.0080 ; qtot -0.090 + 38 HAL2 1 POPE H3S 38 0.090 1.0080 ; qtot 0.000 + 39 CTL2 1 POPE C24 39 -0.180 12.0110 ; qtot -0.180 + 40 HAL2 1 POPE H4R 40 0.090 1.0080 ; qtot -0.090 + 41 HAL2 1 POPE H4S 41 0.090 1.0080 ; qtot 0.000 + 42 CTL2 1 POPE C25 42 -0.180 12.0110 ; qtot -0.180 + 43 HAL2 1 POPE H5R 43 0.090 1.0080 ; qtot -0.090 + 44 HAL2 1 POPE H5S 44 0.090 1.0080 ; qtot 0.000 + 45 CTL2 1 POPE C26 45 -0.180 12.0110 ; qtot -0.180 + 46 HAL2 1 POPE H6R 46 0.090 1.0080 ; qtot -0.090 + 47 HAL2 1 POPE H6S 47 0.090 1.0080 ; qtot 0.000 + 48 CTL2 1 POPE C27 48 -0.180 12.0110 ; qtot -0.180 + 49 HAL2 1 POPE H7R 49 0.090 1.0080 ; qtot -0.090 + 50 HAL2 1 POPE H7S 50 0.090 1.0080 ; qtot 0.000 + 51 CTL2 1 POPE C28 51 -0.180 12.0110 ; qtot -0.180 + 52 HAL2 1 POPE H8R 52 0.090 1.0080 ; qtot -0.090 + 53 HAL2 1 POPE H8S 53 0.090 1.0080 ; qtot 0.000 + 54 CEL1 1 POPE C29 54 -0.150 12.0110 ; qtot -0.150 + 55 HEL1 1 POPE H91 55 0.150 1.0080 ; qtot 0.000 + 56 CEL1 1 POPE C210 56 -0.150 12.0110 ; qtot -0.150 + 57 HEL1 1 POPE H101 57 0.150 1.0080 ; qtot 0.000 + 58 CTL2 1 POPE C211 58 -0.180 12.0110 ; qtot -0.180 + 59 HAL2 1 POPE H11R 59 0.090 1.0080 ; qtot -0.090 + 60 HAL2 1 POPE H11S 60 0.090 1.0080 ; qtot 0.000 + 61 CTL2 1 POPE C212 61 -0.180 12.0110 ; qtot -0.180 + 62 HAL2 1 POPE H12R 62 0.090 1.0080 ; qtot -0.090 + 63 HAL2 1 POPE H12S 63 0.090 1.0080 ; qtot 0.000 + 64 CTL2 1 POPE C213 64 -0.180 12.0110 ; qtot -0.180 + 65 HAL2 1 POPE H13R 65 0.090 1.0080 ; qtot -0.090 + 66 HAL2 1 POPE H13S 66 0.090 1.0080 ; qtot 0.000 + 67 CTL2 1 POPE C214 67 -0.180 12.0110 ; qtot -0.180 + 68 HAL2 1 POPE H14R 68 0.090 1.0080 ; qtot -0.090 + 69 HAL2 1 POPE H14S 69 0.090 1.0080 ; qtot 0.000 + 70 CTL2 1 POPE C215 70 -0.180 12.0110 ; qtot -0.180 + 71 HAL2 1 POPE H15R 71 0.090 1.0080 ; qtot -0.090 + 72 HAL2 1 POPE H15S 72 0.090 1.0080 ; qtot 0.000 + 73 CTL2 1 POPE C216 73 -0.180 12.0110 ; qtot -0.180 + 74 HAL2 1 POPE H16R 74 0.090 1.0080 ; qtot -0.090 + 75 HAL2 1 POPE H16S 75 0.090 1.0080 ; qtot 0.000 + 76 CTL2 1 POPE C217 76 -0.180 12.0110 ; qtot -0.180 + 77 HAL2 1 POPE H17R 77 0.090 1.0080 ; qtot -0.090 + 78 HAL2 1 POPE H17S 78 0.090 1.0080 ; qtot 0.000 + 79 CTL3 1 POPE C218 79 -0.270 12.0110 ; qtot -0.270 + 80 HAL3 1 POPE H18R 80 0.090 1.0080 ; qtot -0.180 + 81 HAL3 1 POPE H18S 81 0.090 1.0080 ; qtot -0.090 + 82 HAL3 1 POPE H18T 82 0.090 1.0080 ; qtot 0.000 + 83 CTL2 1 POPE C33 83 -0.180 12.0110 ; qtot -0.180 + 84 HAL2 1 POPE H3X 84 0.090 1.0080 ; qtot -0.090 + 85 HAL2 1 POPE H3Y 85 0.090 1.0080 ; qtot 0.000 + 86 CTL2 1 POPE C34 86 -0.180 12.0110 ; qtot -0.180 + 87 HAL2 1 POPE H4X 87 0.090 1.0080 ; qtot -0.090 + 88 HAL2 1 POPE H4Y 88 0.090 1.0080 ; qtot 0.000 + 89 CTL2 1 POPE C35 89 -0.180 12.0110 ; qtot -0.180 + 90 HAL2 1 POPE H5X 90 0.090 1.0080 ; qtot -0.090 + 91 HAL2 1 POPE H5Y 91 0.090 1.0080 ; qtot 0.000 + 92 CTL2 1 POPE C36 92 -0.180 12.0110 ; qtot -0.180 + 93 HAL2 1 POPE H6X 93 0.090 1.0080 ; qtot -0.090 + 94 HAL2 1 POPE H6Y 94 0.090 1.0080 ; qtot 0.000 + 95 CTL2 1 POPE C37 95 -0.180 12.0110 ; qtot -0.180 + 96 HAL2 1 POPE H7X 96 0.090 1.0080 ; qtot -0.090 + 97 HAL2 1 POPE H7Y 97 0.090 1.0080 ; qtot 0.000 + 98 CTL2 1 POPE C38 98 -0.180 12.0110 ; qtot -0.180 + 99 HAL2 1 POPE H8X 99 0.090 1.0080 ; qtot -0.090 + 100 HAL2 1 POPE H8Y 100 0.090 1.0080 ; qtot 0.000 + 101 CTL2 1 POPE C39 101 -0.180 12.0110 ; qtot -0.180 + 102 HAL2 1 POPE H9X 102 0.090 1.0080 ; qtot -0.090 + 103 HAL2 1 POPE H9Y 103 0.090 1.0080 ; qtot 0.000 + 104 CTL2 1 POPE C310 104 -0.180 12.0110 ; qtot -0.180 + 105 HAL2 1 POPE H10X 105 0.090 1.0080 ; qtot -0.090 + 106 HAL2 1 POPE H10Y 106 0.090 1.0080 ; qtot 0.000 + 107 CTL2 1 POPE C311 107 -0.180 12.0110 ; qtot -0.180 + 108 HAL2 1 POPE H11X 108 0.090 1.0080 ; qtot -0.090 + 109 HAL2 1 POPE H11Y 109 0.090 1.0080 ; qtot 0.000 + 110 CTL2 1 POPE C312 110 -0.180 12.0110 ; qtot -0.180 + 111 HAL2 1 POPE H12X 111 0.090 1.0080 ; qtot -0.090 + 112 HAL2 1 POPE H12Y 112 0.090 1.0080 ; qtot 0.000 + 113 CTL2 1 POPE C313 113 -0.180 12.0110 ; qtot -0.180 + 114 HAL2 1 POPE H13X 114 0.090 1.0080 ; qtot -0.090 + 115 HAL2 1 POPE H13Y 115 0.090 1.0080 ; qtot 0.000 + 116 CTL2 1 POPE C314 116 -0.180 12.0110 ; qtot -0.180 + 117 HAL2 1 POPE H14X 117 0.090 1.0080 ; qtot -0.090 + 118 HAL2 1 POPE H14Y 118 0.090 1.0080 ; qtot 0.000 + 119 CTL2 1 POPE C315 119 -0.180 12.0110 ; qtot -0.180 + 120 HAL2 1 POPE H15X 120 0.090 1.0080 ; qtot -0.090 + 121 HAL2 1 POPE H15Y 121 0.090 1.0080 ; qtot 0.000 + 122 CTL3 1 POPE C316 122 -0.270 12.0110 ; qtot -0.270 + 123 HAL3 1 POPE H16X 123 0.090 1.0080 ; qtot -0.180 + 124 HAL3 1 POPE H16Y 124 0.090 1.0080 ; qtot -0.090 + 125 HAL3 1 POPE H16Z 125 0.090 1.0080 ; qtot 0.000 + +[ bonds ] +; ai aj funct b0 Kb + 1 2 1 + 1 3 1 + 1 4 1 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5 8 9 + 3 1 5 6 9 + 3 1 5 7 9 + 3 1 5 8 9 + 4 1 5 6 9 + 4 1 5 7 9 + 4 1 5 8 9 + 1 5 8 9 9 + 1 5 8 10 9 + 1 5 8 15 9 + 6 5 8 9 9 + 6 5 8 10 9 + 6 5 8 15 9 + 7 5 8 9 9 + 7 5 8 10 9 + 7 5 8 15 9 + 5 8 15 11 9 + 9 8 15 11 9 + 10 8 15 11 9 + 12 11 14 16 9 + 13 11 14 16 9 + 15 11 14 16 9 + 11 14 16 17 9 + 11 14 16 18 9 + 11 14 16 19 9 + 8 15 11 12 9 + 8 15 11 13 9 + 8 15 11 14 9 + 14 16 19 20 9 + 14 16 19 21 9 + 14 16 19 27 9 + 17 16 19 20 9 + 17 16 19 21 9 + 17 16 19 27 9 + 18 16 19 20 9 + 18 16 19 21 9 + 18 16 19 27 9 + 16 19 21 22 9 + 20 19 21 22 9 + 16 19 27 28 9 + 16 19 27 29 9 + 16 19 27 30 9 + 20 19 27 28 9 + 20 19 27 29 9 + 20 19 27 30 9 + 21 19 27 28 9 + 21 19 27 29 9 + 21 19 27 30 9 + 22 21 19 27 9 + 19 21 22 23 9 + 19 21 22 24 9 + 21 22 24 25 9 + 21 22 24 26 9 + 21 22 24 36 9 + 23 22 24 25 9 + 23 22 24 26 9 + 23 22 24 36 9 + 22 24 36 37 9 + 22 24 36 38 9 + 22 24 36 39 9 + 25 24 36 37 9 + 25 24 36 38 9 + 25 24 36 39 9 + 26 24 36 37 9 + 26 24 36 38 9 + 26 24 36 39 9 + 19 27 30 31 9 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51 53 9 + 50 48 51 54 9 + 48 51 54 55 9 + 48 51 54 56 9 + 52 51 54 55 9 + 52 51 54 56 9 + 53 51 54 55 9 + 53 51 54 56 9 + 51 54 56 57 9 + 51 54 56 58 9 + 55 54 56 57 9 + 55 54 56 58 9 + 54 56 58 59 9 + 54 56 58 60 9 + 54 56 58 61 9 + 57 56 58 59 9 + 57 56 58 60 9 + 57 56 58 61 9 + 56 58 61 62 9 + 56 58 61 63 9 + 56 58 61 64 9 + 59 58 61 62 9 + 59 58 61 63 9 + 59 58 61 64 9 + 60 58 61 62 9 + 60 58 61 63 9 + 60 58 61 64 9 + 58 61 64 65 9 + 58 61 64 66 9 + 58 61 64 67 9 + 62 61 64 65 9 + 62 61 64 66 9 + 62 61 64 67 9 + 63 61 64 65 9 + 63 61 64 66 9 + 63 61 64 67 9 + 61 64 67 68 9 + 61 64 67 69 9 + 61 64 67 70 9 + 65 64 67 68 9 + 65 64 67 69 9 + 65 64 67 70 9 + 66 64 67 68 9 + 66 64 67 69 9 + 66 64 67 70 9 + 64 67 70 71 9 + 64 67 70 72 9 + 64 67 70 73 9 + 68 67 70 71 9 + 68 67 70 72 9 + 68 67 70 73 9 + 69 67 70 71 9 + 69 67 70 72 9 + 69 67 70 73 9 + 67 70 73 74 9 + 67 70 73 75 9 + 67 70 73 76 9 + 71 70 73 74 9 + 71 70 73 75 9 + 71 70 73 76 9 + 72 70 73 74 9 + 72 70 73 75 9 + 72 70 73 76 9 + 70 73 76 77 9 + 70 73 76 78 9 + 70 73 76 79 9 + 74 73 76 77 9 + 74 73 76 78 9 + 74 73 76 79 9 + 75 73 76 77 9 + 75 73 76 78 9 + 75 73 76 79 9 + 73 76 79 80 9 + 73 76 79 81 9 + 73 76 79 82 9 + 77 76 79 80 9 + 77 76 79 81 9 + 77 76 79 82 9 + 78 76 79 80 9 + 78 76 79 81 9 + 78 76 79 82 9 + 33 83 86 87 9 + 33 83 86 88 9 + 33 83 86 89 9 + 84 83 86 87 9 + 84 83 86 88 9 + 84 83 86 89 9 + 85 83 86 87 9 + 85 83 86 88 9 + 85 83 86 89 9 + 83 86 89 90 9 + 83 86 89 91 9 + 83 86 89 92 9 + 87 86 89 90 9 + 87 86 89 91 9 + 87 86 89 92 9 + 88 86 89 90 9 + 88 86 89 91 9 + 88 86 89 92 9 + 86 89 92 93 9 + 86 89 92 94 9 + 86 89 92 95 9 + 90 89 92 93 9 + 90 89 92 94 9 + 90 89 92 95 9 + 91 89 92 93 9 + 91 89 92 94 9 + 91 89 92 95 9 + 89 92 95 96 9 + 89 92 95 97 9 + 89 92 95 98 9 + 93 92 95 96 9 + 93 92 95 97 9 + 93 92 95 98 9 + 94 92 95 96 9 + 94 92 95 97 9 + 94 92 95 98 9 + 92 95 98 99 9 + 92 95 98 100 9 + 92 95 98 101 9 + 96 95 98 99 9 + 96 95 98 100 9 + 96 95 98 101 9 + 97 95 98 99 9 + 97 95 98 100 9 + 97 95 98 101 9 + 95 98 101 102 9 + 95 98 101 103 9 + 95 98 101 104 9 + 99 98 101 102 9 + 99 98 101 103 9 + 99 98 101 104 9 + 100 98 101 102 9 + 100 98 101 103 9 + 100 98 101 104 9 + 98 101 104 105 9 + 98 101 104 106 9 + 98 101 104 107 9 + 102 101 104 105 9 + 102 101 104 106 9 + 102 101 104 107 9 + 103 101 104 105 9 + 103 101 104 106 9 + 103 101 104 107 9 + 101 104 107 108 9 + 101 104 107 109 9 + 101 104 107 110 9 + 105 104 107 108 9 + 105 104 107 109 9 + 105 104 107 110 9 + 106 104 107 108 9 + 106 104 107 109 9 + 106 104 107 110 9 + 104 107 110 111 9 + 104 107 110 112 9 + 104 107 110 113 9 + 108 107 110 111 9 + 108 107 110 112 9 + 108 107 110 113 9 + 109 107 110 111 9 + 109 107 110 112 9 + 109 107 110 113 9 + 107 110 113 114 9 + 107 110 113 115 9 + 107 110 113 116 9 + 111 110 113 114 9 + 111 110 113 115 9 + 111 110 113 116 9 + 112 110 113 114 9 + 112 110 113 115 9 + 112 110 113 116 9 + 110 113 116 117 9 + 110 113 116 118 9 + 110 113 116 119 9 + 114 113 116 117 9 + 114 113 116 118 9 + 114 113 116 119 9 + 115 113 116 117 9 + 115 113 116 118 9 + 115 113 116 119 9 + 113 116 119 120 9 + 113 116 119 121 9 + 113 116 119 122 9 + 117 116 119 120 9 + 117 116 119 121 9 + 117 116 119 122 9 + 118 116 119 120 9 + 118 116 119 121 9 + 118 116 119 122 9 + 116 119 122 123 9 + 116 119 122 124 9 + 116 119 122 125 9 + 120 119 122 123 9 + 120 119 122 124 9 + 120 119 122 125 9 + 121 119 122 123 9 + 121 119 122 124 9 + 121 119 122 125 9 + +[ dihedrals ] +; ai aj ak al funct q0 cq + 22 21 24 23 2 + 31 30 33 32 2 + +;#ifdef REST_ON +;#include "../restraints/POPE_rest.itp" +;#endif diff --git a/test/data/nosections.cfg b/tests/data/nosections.cfg similarity index 100% rename from test/data/nosections.cfg rename to tests/data/nosections.cfg diff --git a/test/data/pbcpolyethene.gro b/tests/data/pbcpolyethene.gro similarity index 100% rename from test/data/pbcpolyethene.gro rename to tests/data/pbcpolyethene.gro diff --git a/test/data/pbcwater.gro b/tests/data/pbcwater.gro similarity index 100% rename from test/data/pbcwater.gro rename to tests/data/pbcwater.gro diff --git a/test/data/polyethene.bnd b/tests/data/polyethene.bnd similarity index 100% rename from test/data/polyethene.bnd rename to tests/data/polyethene.bnd diff --git a/test/data/polyethene.gro b/tests/data/polyethene.gro similarity index 100% rename from test/data/polyethene.gro rename to tests/data/polyethene.gro diff --git a/test/data/polyethene.map b/tests/data/polyethene.map similarity index 100% rename from test/data/polyethene.map rename to tests/data/polyethene.map diff --git a/test/data/sugar-cg.gro b/tests/data/sugar-cg.gro similarity index 100% rename from test/data/sugar-cg.gro rename to tests/data/sugar-cg.gro diff --git a/test/data/sugar.bnd b/tests/data/sugar.bnd similarity index 100% rename from test/data/sugar.bnd rename to tests/data/sugar.bnd diff --git a/test/data/sugar.gro b/tests/data/sugar.gro similarity index 89% rename from test/data/sugar.gro rename to tests/data/sugar.gro index b6b7395..26f00e7 100644 --- a/test/data/sugar.gro +++ b/tests/data/sugar.gro @@ -17,4 +17,4 @@ Alpha-allose in water 1ALLA C1 15 2.895 2.970 1.310 1ALLA O1 16 3.023 2.937 1.367 1ALLA HO1 17 3.040 2.996 1.445 - 3.74699 3.74699 2.67438 + 3.74699 3.74699 2.67438 0.00000 0.00000 0.00000 0.00000 1.87349 1.87349 diff --git a/test/data/sugar.map b/tests/data/sugar.map similarity index 100% rename from test/data/sugar.map rename to tests/data/sugar.map diff --git a/test/data/sugar.xtc b/tests/data/sugar.xtc similarity index 100% rename from test/data/sugar.xtc rename to tests/data/sugar.xtc diff --git a/test/data/sugar_only.map b/tests/data/sugar_only.map similarity index 100% rename from test/data/sugar_only.map rename to tests/data/sugar_only.map diff --git a/test/data/sugar_out.gro b/tests/data/sugar_out.gro similarity index 76% rename from test/data/sugar_out.gro rename to tests/data/sugar_out.gro index 9115b5e..f5c3e7a 100644 --- a/test/data/sugar_out.gro +++ b/tests/data/sugar_out.gro @@ -6,4 +6,4 @@ Alpha-allose in water 1ALLA C4 4 2.682 2.674 1.280 1ALLA C5 5 2.793 2.732 1.076 1ALLA O5 6 2.876 2.895 1.190 - 3.74699 3.74699 2.67438 + 3.74699 3.74699 2.67438 0.00000 0.00000 0.00000 0.00000 1.87349 1.87349 diff --git a/test/data/sugar_out.itp b/tests/data/sugar_out.itp similarity index 74% rename from test/data/sugar_out.itp rename to tests/data/sugar_out.itp index 60a9f10..b6b6617 100644 --- a/test/data/sugar_out.itp +++ b/tests/data/sugar_out.itp @@ -32,12 +32,12 @@ ALLA 1 6 1 2 2 99.29372 800.62783 [ dihedrals ] - 1 2 3 4 1 -82.85912 253.69305 1 - 2 3 4 5 1 61.16832 125.03049 1 - 3 4 5 6 1 -21.40128 135.64451 1 - 4 5 6 1 1 53.15602 51.18275 1 - 5 6 1 2 1 -96.53807 59.39165 1 - 6 1 2 3 1 75.36509 279.84591 1 + 1 2 3 4 1 97.14088 253.69305 1 + 2 3 4 5 1 -118.83168 125.03049 1 + 3 4 5 6 1 158.59872 135.64451 1 + 4 5 6 1 1 -126.84398 51.18275 1 + 5 6 1 2 1 83.46193 59.39165 1 + 6 1 2 3 1 -104.63491 279.84591 1 [ constraints ] 6 1 1 0.18055 diff --git a/tests/data/sugar_out.xtc b/tests/data/sugar_out.xtc new file mode 100644 index 0000000..57faef9 Binary files /dev/null and b/tests/data/sugar_out.xtc differ diff --git a/test/data/triangle.bnd b/tests/data/triangle.bnd similarity index 100% rename from test/data/triangle.bnd rename to tests/data/triangle.bnd diff --git a/test/data/twice.cfg b/tests/data/twice.cfg similarity index 100% rename from test/data/twice.cfg rename to tests/data/twice.cfg diff --git a/test/data/two.gro b/tests/data/two.gro similarity index 100% rename from test/data/two.gro rename to tests/data/two.gro diff --git a/test/data/two.itp b/tests/data/two.itp similarity index 100% rename from test/data/two.itp rename to tests/data/two.itp diff --git a/test/data/two.map b/tests/data/two.map similarity index 100% rename from test/data/two.map rename to tests/data/two.map diff --git a/tests/data/two_double_section.itp b/tests/data/two_double_section.itp new file mode 100644 index 0000000..515cb8d --- /dev/null +++ b/tests/data/two_double_section.itp @@ -0,0 +1,7 @@ +[ moleculetype ] +TWO 1 + +[ atoms ] + 1 H 1 TWO H1 1 0.000 0.000 +[ atoms ] + 2 C 1 TWO C2 1 0.000 1.000 diff --git a/tests/data/two_unknown_section.itp b/tests/data/two_unknown_section.itp new file mode 100644 index 0000000..1fec2a6 --- /dev/null +++ b/tests/data/two_unknown_section.itp @@ -0,0 +1,9 @@ +[ moleculetype ] +TWO 1 + +[ atoms ] + 1 H 1 TWO H1 1 0.000 0.000 + 2 C 1 TWO C2 1 0.000 1.000 + +[ UNKNOWN ] +UNKNOWN SECTION diff --git a/tests/data/water-cg.gro b/tests/data/water-cg.gro new file mode 100644 index 0000000..ab53431 --- /dev/null +++ b/tests/data/water-cg.gro @@ -0,0 +1,224 @@ +Generated with MDTraj, t= 0.0 + 221 + 0HOH W 0 0.716 1.300 1.198 + 1HOH W 1 0.681 0.283 0.408 + 2HOH W 2 1.464 0.059 0.501 + 3HOH W 3 0.161 1.353 -0.019 + 4HOH W 4 0.959 0.155 0.241 + 5HOH W 5 0.501 1.870 0.471 + 6HOH W 6 1.806 0.612 1.024 + 7HOH W 7 0.892 1.694 0.882 + 8HOH W 8 0.419 1.496 0.596 + 9HOH W 9 0.913 -0.009 1.529 + 10HOH W 10 0.566 0.182 1.814 + 11HOH W 11 0.848 1.600 1.166 + 12HOH W 12 1.123 0.457 1.656 + 13HOH W 13 0.545 1.870 1.140 + 14HOH W 14 1.330 0.225 1.235 + 15HOH W 15 1.835 1.272 0.155 + 16HOH W 16 0.105 0.083 0.838 + 17HOH W 17 1.315 0.491 1.215 + 18HOH W 18 1.482 0.667 1.814 + 19HOH W 19 1.421 0.912 1.145 + 20HOH W 20 0.886 1.171 0.917 + 21HOH W 21 1.685 1.764 1.014 + 22HOH W 22 0.320 0.852 0.866 + 23HOH W 23 1.733 0.679 1.604 + 24HOH W 24 1.635 1.804 1.709 + 25HOH W 25 1.565 0.569 0.313 + 26HOH W 26 0.883 1.052 1.827 + 27HOH W 27 1.905 1.261 1.662 + 28HOH W 28 1.280 1.131 1.038 + 29HOH W 29 0.884 0.402 1.537 + 30HOH W 30 0.294 1.043 0.331 + 31HOH W 31 0.328 0.626 0.607 + 32HOH W 32 0.235 0.128 1.614 + 33HOH W 33 1.155 1.147 1.763 + 34HOH W 34 0.866 0.922 0.821 + 35HOH W 35 0.717 1.179 0.154 + 36HOH W 36 0.332 1.715 1.220 + 37HOH W 37 1.676 0.936 1.844 + 38HOH W 38 0.918 0.149 1.301 + 39HOH W 39 0.828 0.706 1.540 + 40HOH W 40 0.151 1.094 1.086 + 41HOH W 41 0.808 0.827 0.076 + 42HOH W 42 0.936 0.428 0.359 + 43HOH W 43 1.066 1.510 1.745 + 44HOH W 44 0.763 1.257 1.642 + 45HOH W 45 0.176 0.662 1.012 + 46HOH W 46 1.772 0.861 0.434 + 47HOH W 47 1.086 0.588 0.699 + 48HOH W 48 1.111 1.777 1.262 + 49HOH W 49 0.740 1.853 0.300 + 50HOH W 50 0.982 1.472 0.250 + 51HOH W 51 0.464 0.611 0.172 + 52HOH W 52 1.013 0.073 0.794 + 53HOH W 53 0.001 1.715 1.521 + 54HOH W 54 1.525 1.611 1.530 + 55HOH W 55 1.398 1.765 1.285 + 56HOH W 56 1.142 1.005 1.454 + 57HOH W 57 1.446 0.597 0.964 + 58HOH W 58 1.709 0.157 0.413 + 59HOH W 59 0.521 1.348 1.756 + 60HOH W 60 1.440 0.370 0.417 + 61HOH W 61 0.535 1.742 0.747 + 62HOH W 62 1.137 1.255 0.161 + 63HOH W 63 1.023 0.747 0.975 + 64HOH W 64 1.481 0.069 1.033 + 65HOH W 65 1.363 1.335 1.685 + 66HOH W 66 0.089 0.315 0.246 + 67HOH W 67 1.477 0.430 1.458 + 68HOH W 68 0.354 1.525 0.155 + 69HOH W 69 1.542 0.010 0.743 + 70HOH W 70 1.191 0.688 1.819 + 71HOH W 71 1.851 1.010 0.812 + 72HOH W 72 1.268 0.236 0.261 + 73HOH W 73 0.158 0.402 1.399 + 74HOH W 74 1.266 0.801 0.763 + 75HOH W 75 0.084 1.624 0.233 + 76HOH W 76 0.191 0.224 1.067 + 77HOH W 77 1.434 1.478 0.463 + 78HOH W 78 0.478 1.271 0.296 + 79HOH W 79 0.131 1.586 1.736 + 80HOH W 80 0.372 0.456 0.911 + 81HOH W 81 1.413 1.249 0.301 + 82HOH W 82 0.982 0.529 0.084 + 83HOH W 83 1.595 0.526 1.186 + 84HOH W 84 0.651 0.094 1.530 + 85HOH W 85 1.779 0.369 0.509 + 86HOH W 86 0.424 0.702 1.740 + 87HOH W 87 1.429 1.008 1.527 + 88HOH W 88 0.330 0.136 0.080 + 89HOH W 89 0.530 0.564 1.424 + 90HOH W 90 1.565 0.873 0.891 + 91HOH W 91 1.845 1.444 0.670 + 92HOH W 92 1.542 1.030 0.373 + 93HOH W 93 0.970 0.958 0.563 + 94HOH W 94 1.457 1.273 1.438 + 95HOH W 95 1.502 0.728 0.528 + 96HOH W 96 1.510 0.185 1.647 + 97HOH W 97 0.554 0.872 1.595 + 98HOH W 98 1.670 1.710 0.286 + 99HOH W 99 0.354 1.244 0.675 + 100HOH W 100 0.360 0.251 0.367 + 101HOH W 101 0.904 0.170 0.525 + 102HOH W 102 0.647 0.203 1.273 + 103HOH W 103 0.517 1.795 0.133 + 104HOH W 104 0.142 1.704 0.845 + 105HOH W 105 1.504 0.806 0.163 + 106HOH W 106 1.843 0.041 0.183 + 107HOH W 107 1.317 1.637 1.067 + 108HOH W 108 0.052 1.654 1.109 + 109HOH W 109 1.794 1.448 0.353 + 110HOH W 110 0.094 0.999 1.533 + 111HOH W 111 1.665 1.494 1.076 + 112HOH W 112 1.788 0.320 1.819 + 113HOH W 113 1.172 0.130 0.581 + 114HOH W 114 1.221 1.857 0.377 + 115HOH W 115 0.074 1.419 0.905 + 116HOH W 116 0.630 1.213 0.790 + 117HOH W 117 0.288 0.410 1.622 + 118HOH W 118 1.823 0.542 0.247 + 119HOH W 119 1.076 0.957 1.193 + 120HOH W 120 1.824 1.219 1.013 + 121HOH W 121 -0.020 1.111 0.354 + 122HOH W 122 0.054 0.127 0.565 + 123HOH W 123 1.172 1.430 0.483 + 124HOH W 124 0.039 0.814 1.741 + 125HOH W 125 1.836 0.583 1.369 + 126HOH W 126 0.694 0.578 0.009 + 127HOH W 127 1.924 1.214 1.299 + 128HOH W 128 1.810 0.329 1.092 + 129HOH W 129 0.384 1.182 0.045 + 130HOH W 130 1.773 0.251 0.835 + 131HOH W 131 0.331 1.278 0.965 + 132HOH W 132 1.163 1.141 0.419 + 133HOH W 133 1.314 1.679 1.714 + 134HOH W 134 0.920 1.578 0.504 + 135HOH W 135 1.478 0.707 1.501 + 136HOH W 136 1.658 1.313 0.544 + 137HOH W 137 0.286 0.605 1.284 + 138HOH W 138 0.088 0.147 1.859 + 139HOH W 139 0.596 0.443 1.710 + 140HOH W 140 1.149 1.574 0.811 + 141HOH W 141 1.301 0.195 0.833 + 142HOH W 142 0.607 1.473 0.416 + 143HOH W 143 1.741 0.563 1.898 + 144HOH W 144 0.630 0.583 0.848 + 145HOH W 145 0.289 1.782 1.548 + 146HOH W 146 0.784 1.443 0.727 + 147HOH W 147 0.815 0.317 1.089 + 148HOH W 148 0.035 0.567 0.504 + 149HOH W 149 0.473 1.452 1.171 + 150HOH W 150 0.728 0.880 0.518 + 151HOH W 151 1.564 1.283 0.088 + 152HOH W 152 1.063 1.313 1.538 + 153HOH W 153 0.110 1.127 0.614 + 154HOH W 154 0.469 0.986 0.617 + 155HOH W 155 1.234 1.260 1.258 + 156HOH W 156 1.551 1.175 1.163 + 157HOH W 157 1.141 0.301 0.038 + 158HOH W 158 1.829 1.517 1.316 + 159HOH W 159 0.599 0.814 1.278 + 160HOH W 160 1.536 1.832 0.071 + 161HOH W 161 0.809 1.614 1.755 + 162HOH W 162 1.311 1.755 0.656 + 163HOH W 163 0.580 1.701 1.576 + 164HOH W 164 1.782 1.712 0.684 + 165HOH W 165 1.863 1.712 -0.024 + 166HOH W 166 0.618 0.972 0.932 + 167HOH W 167 1.591 0.232 1.222 + 168HOH W 168 0.903 1.598 1.442 + 169HOH W 169 1.162 1.276 0.803 + 170HOH W 170 1.221 0.938 0.046 + 171HOH W 171 0.692 1.520 0.134 + 172HOH W 172 1.694 1.407 1.531 + 173HOH W 173 0.450 1.470 1.524 + 174HOH W 174 0.323 0.998 1.704 + 175HOH W 175 0.977 1.327 1.141 + 176HOH W 176 0.946 0.705 0.411 + 177HOH W 177 1.314 1.061 0.624 + 178HOH W 178 1.202 0.017 1.651 + 179HOH W 179 1.775 0.941 1.170 + 180HOH W 180 0.320 0.923 1.245 + 181HOH W 181 1.083 -0.004 0.101 + 182HOH W 182 1.616 0.258 0.131 + 183HOH W 183 1.397 0.422 0.049 + 184HOH W 184 1.162 0.405 0.515 + 185HOH W 185 1.451 1.555 0.034 + 186HOH W 186 0.178 1.404 1.460 + 187HOH W 187 0.025 0.759 0.123 + 188HOH W 188 0.743 0.310 0.103 + 189HOH W 189 0.414 1.629 1.826 + 190HOH W 190 0.818 0.524 0.600 + 191HOH W 191 0.520 0.833 0.344 + 192HOH W 192 0.509 0.434 1.167 + 193HOH W 193 0.885 0.339 0.814 + 194HOH W 194 0.599 1.631 0.989 + 195HOH W 195 1.500 0.397 0.755 + 196HOH W 196 0.771 1.879 0.000 + 197HOH W 197 0.800 0.607 1.055 + 198HOH W 198 1.577 0.042 1.409 + 199HOH W 199 1.581 1.067 0.686 + 200HOH W 200 0.498 0.502 0.411 + 201HOH W 201 1.694 0.567 0.712 + 202HOH W 202 0.285 0.863 0.097 + 203HOH W 203 1.692 1.029 1.420 + 204HOH W 204 0.946 0.176 1.726 + 205HOH W 205 1.841 0.121 1.583 + 206HOH W 206 1.162 0.478 0.972 + 207HOH W 207 1.258 0.750 1.327 + 208HOH W 208 1.116 0.121 1.099 + 209HOH W 209 1.426 1.085 1.818 + 210HOH W 210 0.828 1.810 0.594 + 211HOH W 211 0.162 1.546 0.519 + 212HOH W 212 0.129 0.139 1.366 + 213HOH W 213 1.307 1.634 0.241 + 214HOH W 214 1.254 0.260 1.536 + 215HOH W 215 0.203 1.841 0.417 + 216HOH W 216 1.807 1.906 1.243 + 217HOH W 217 1.017 0.969 0.269 + 218HOH W 218 0.536 0.096 0.893 + 219HOH W 219 0.806 0.975 1.222 + 220HOH W 220 0.924 1.192 0.366 + 1.89868 1.89868 1.89868 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/tests/data/water-nobox.pdb b/tests/data/water-nobox.pdb new file mode 100644 index 0000000..3e5c2da --- /dev/null +++ b/tests/data/water-nobox.pdb @@ -0,0 +1,669 @@ +TITLE Water +REMARK THIS IS A SIMULATION BOX +CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 OW SOL 1 6.960 13.300 12.110 1.00 0.00 +ATOM 2 HW1 SOL 1 6.620 12.360 12.030 1.00 0.00 +ATOM 3 HW2 SOL 1 7.900 13.340 11.790 1.00 0.00 +ATOM 4 OW SOL 2 7.000 2.890 3.760 1.00 0.00 +ATOM 5 HW1 SOL 2 7.140 2.110 4.360 1.00 0.00 +ATOM 6 HW2 SOL 2 6.290 3.480 4.130 1.00 0.00 +ATOM 7 OW SOL 3 14.800 0.880 4.820 1.00 0.00 +ATOM 8 HW1 SOL 3 14.170 0.220 4.420 1.00 0.00 +ATOM 9 HW2 SOL 3 14.940 0.660 5.790 1.00 0.00 +ATOM 10 OW SOL 4 1.310 13.390 0.010 1.00 0.00 +ATOM 11 HW1 SOL 4 2.220 12.990 0.000 1.00 0.00 +ATOM 12 HW2 SOL 4 1.290 14.200 -0.580 1.00 0.00 +ATOM 13 OW SOL 5 9.620 1.630 2.790 1.00 0.00 +ATOM 14 HW1 SOL 5 10.260 1.060 2.280 1.00 0.00 +ATOM 15 HW2 SOL 5 8.900 1.970 2.170 1.00 0.00 +ATOM 16 OW SOL 6 4.670 18.840 4.610 1.00 0.00 +ATOM 17 HW1 SOL 6 4.810 18.030 5.180 1.00 0.00 +ATOM 18 HW2 SOL 6 5.550 19.220 4.350 1.00 0.00 +ATOM 19 OW SOL 7 18.230 6.250 9.910 1.00 0.00 +ATOM 20 HW1 SOL 7 17.820 6.830 10.620 1.00 0.00 +ATOM 21 HW2 SOL 7 18.140 5.290 10.180 1.00 0.00 +ATOM 22 OW SOL 8 8.970 16.720 8.510 1.00 0.00 +ATOM 23 HW1 SOL 8 9.240 17.680 8.590 1.00 0.00 +ATOM 24 HW2 SOL 8 8.550 16.420 9.360 1.00 0.00 +ATOM 25 OW SOL 9 3.940 14.700 6.080 1.00 0.00 +ATOM 26 HW1 SOL 9 4.050 15.620 6.460 1.00 0.00 +ATOM 27 HW2 SOL 9 4.590 14.570 5.330 1.00 0.00 +ATOM 28 OW SOL 10 8.850 0.120 15.120 1.00 0.00 +ATOM 29 HW1 SOL 10 9.510 0.450 15.800 1.00 0.00 +ATOM 30 HW2 SOL 10 9.020 -0.850 14.940 1.00 0.00 +ATOM 31 OW SOL 11 5.930 2.070 18.230 1.00 0.00 +ATOM 32 HW1 SOL 11 5.830 1.610 17.350 1.00 0.00 +ATOM 33 HW2 SOL 11 5.210 1.770 18.850 1.00 0.00 +ATOM 34 OW SOL 12 8.730 16.180 11.890 1.00 0.00 +ATOM 35 HW1 SOL 12 7.900 16.580 11.500 1.00 0.00 +ATOM 36 HW2 SOL 12 8.820 15.230 11.590 1.00 0.00 +ATOM 37 OW SOL 13 11.480 4.800 16.400 1.00 0.00 +ATOM 38 HW1 SOL 13 10.520 4.720 16.130 1.00 0.00 +ATOM 39 HW2 SOL 13 11.680 4.180 17.150 1.00 0.00 +ATOM 40 OW SOL 14 5.640 18.660 11.070 1.00 0.00 +ATOM 41 HW1 SOL 14 5.760 19.420 11.710 1.00 0.00 +ATOM 42 HW2 SOL 14 4.950 18.030 11.420 1.00 0.00 +ATOM 43 OW SOL 15 13.050 2.500 12.190 1.00 0.00 +ATOM 44 HW1 SOL 15 13.560 1.780 11.700 1.00 0.00 +ATOM 45 HW2 SOL 15 13.300 2.480 13.160 1.00 0.00 +ATOM 46 OW SOL 16 18.170 12.380 1.530 1.00 0.00 +ATOM 47 HW1 SOL 16 17.990 13.090 2.210 1.00 0.00 +ATOM 48 HW2 SOL 16 18.890 12.690 0.910 1.00 0.00 +ATOM 49 OW SOL 17 0.820 1.020 8.130 1.00 0.00 +ATOM 50 HW1 SOL 17 1.270 1.430 8.920 1.00 0.00 +ATOM 51 HW2 SOL 17 1.070 0.050 8.080 1.00 0.00 +ATOM 52 OW SOL 18 12.920 5.220 12.170 1.00 0.00 +ATOM 53 HW1 SOL 18 13.900 5.240 11.960 1.00 0.00 +ATOM 54 HW2 SOL 18 12.630 4.280 12.320 1.00 0.00 +ATOM 55 OW SOL 19 14.950 6.310 18.100 1.00 0.00 +ATOM 56 HW1 SOL 19 14.860 6.790 18.970 1.00 0.00 +ATOM 57 HW2 SOL 19 14.660 6.910 17.360 1.00 0.00 +ATOM 58 OW SOL 20 14.160 9.510 11.450 1.00 0.00 +ATOM 59 HW1 SOL 20 14.790 9.000 10.860 1.00 0.00 +ATOM 60 HW2 SOL 20 13.670 8.860 12.030 1.00 0.00 +ATOM 61 OW SOL 21 9.150 11.850 9.380 1.00 0.00 +ATOM 62 HW1 SOL 21 9.090 10.910 9.050 1.00 0.00 +ATOM 63 HW2 SOL 21 8.340 12.360 9.080 1.00 0.00 +ATOM 64 OW SOL 22 16.540 17.870 10.110 1.00 0.00 +ATOM 65 HW1 SOL 22 17.200 17.890 10.850 1.00 0.00 +ATOM 66 HW2 SOL 22 16.800 17.160 9.450 1.00 0.00 +ATOM 67 OW SOL 23 3.450 8.710 8.450 1.00 0.00 +ATOM 68 HW1 SOL 23 3.680 8.000 9.110 1.00 0.00 +ATOM 69 HW2 SOL 23 2.460 8.840 8.430 1.00 0.00 +ATOM 70 OW SOL 24 17.690 6.920 15.990 1.00 0.00 +ATOM 71 HW1 SOL 24 17.450 6.010 16.320 1.00 0.00 +ATOM 72 HW2 SOL 24 16.860 7.440 15.800 1.00 0.00 +ATOM 73 OW SOL 25 16.490 17.990 17.440 1.00 0.00 +ATOM 74 HW1 SOL 25 15.990 17.300 16.920 1.00 0.00 +ATOM 75 HW2 SOL 25 16.570 18.820 16.900 1.00 0.00 +ATOM 76 OW SOL 26 15.920 5.430 3.240 1.00 0.00 +ATOM 77 HW1 SOL 26 15.620 6.210 3.790 1.00 0.00 +ATOM 78 HW2 SOL 26 15.420 5.430 2.370 1.00 0.00 +ATOM 79 OW SOL 27 8.570 10.790 18.190 1.00 0.00 +ATOM 80 HW1 SOL 27 8.380 9.940 18.670 1.00 0.00 +ATOM 81 HW2 SOL 27 9.540 10.840 17.960 1.00 0.00 +ATOM 82 OW SOL 28 18.890 12.880 16.390 1.00 0.00 +ATOM 83 HW1 SOL 28 19.000 11.920 16.140 1.00 0.00 +ATOM 84 HW2 SOL 28 19.250 13.020 17.320 1.00 0.00 +ATOM 85 OW SOL 29 12.490 11.360 10.610 1.00 0.00 +ATOM 86 HW1 SOL 29 12.650 11.820 9.730 1.00 0.00 +ATOM 87 HW2 SOL 29 13.270 10.760 10.810 1.00 0.00 +ATOM 88 OW SOL 30 9.110 3.890 15.620 1.00 0.00 +ATOM 89 HW1 SOL 30 8.960 3.560 14.680 1.00 0.00 +ATOM 90 HW2 SOL 30 8.440 4.610 15.820 1.00 0.00 +ATOM 91 OW SOL 31 3.050 10.090 3.160 1.00 0.00 +ATOM 92 HW1 SOL 31 2.160 10.300 3.580 1.00 0.00 +ATOM 93 HW2 SOL 31 3.620 10.910 3.180 1.00 0.00 +ATOM 94 OW SOL 32 3.570 6.110 5.860 1.00 0.00 +ATOM 95 HW1 SOL 32 2.600 6.050 5.630 1.00 0.00 +ATOM 96 HW2 SOL 32 3.680 6.610 6.720 1.00 0.00 +ATOM 97 OW SOL 33 2.350 1.590 15.920 1.00 0.00 +ATOM 98 HW1 SOL 33 2.530 0.660 15.600 1.00 0.00 +ATOM 99 HW2 SOL 33 2.170 1.580 16.900 1.00 0.00 +ATOM 100 OW SOL 34 11.200 11.560 17.500 1.00 0.00 +ATOM 101 HW1 SOL 34 11.410 10.780 18.080 1.00 0.00 +ATOM 102 HW2 SOL 34 12.030 12.080 17.300 1.00 0.00 +ATOM 103 OW SOL 35 8.840 9.480 8.000 1.00 0.00 +ATOM 104 HW1 SOL 35 7.860 9.460 8.190 1.00 0.00 +ATOM 105 HW2 SOL 35 9.290 8.710 8.450 1.00 0.00 +ATOM 106 OW SOL 36 6.970 12.070 1.720 1.00 0.00 +ATOM 107 HW1 SOL 36 6.830 11.770 0.770 1.00 0.00 +ATOM 108 HW2 SOL 36 7.710 11.540 2.130 1.00 0.00 +ATOM 109 OW SOL 37 3.660 17.020 12.070 1.00 0.00 +ATOM 110 HW1 SOL 37 2.770 16.820 11.660 1.00 0.00 +ATOM 111 HW2 SOL 37 3.540 17.600 12.870 1.00 0.00 +ATOM 112 OW SOL 38 16.750 9.230 18.800 1.00 0.00 +ATOM 113 HW1 SOL 38 17.490 9.060 18.160 1.00 0.00 +ATOM 114 HW2 SOL 38 16.050 9.800 18.360 1.00 0.00 +ATOM 115 OW SOL 39 8.890 1.730 12.930 1.00 0.00 +ATOM 116 HW1 SOL 39 8.980 1.180 13.760 1.00 0.00 +ATOM 117 HW2 SOL 39 9.670 1.560 12.330 1.00 0.00 +ATOM 118 OW SOL 40 8.260 6.700 15.270 1.00 0.00 +ATOM 119 HW1 SOL 40 7.550 7.180 15.800 1.00 0.00 +ATOM 120 HW2 SOL 40 9.040 7.310 15.140 1.00 0.00 +ATOM 121 OW SOL 41 1.640 10.770 11.180 1.00 0.00 +ATOM 122 HW1 SOL 41 0.710 10.670 10.820 1.00 0.00 +ATOM 123 HW2 SOL 41 2.170 11.380 10.590 1.00 0.00 +ATOM 124 OW SOL 42 7.940 8.600 0.620 1.00 0.00 +ATOM 125 HW1 SOL 42 8.630 8.530 1.340 1.00 0.00 +ATOM 126 HW2 SOL 42 7.680 7.680 0.320 1.00 0.00 +ATOM 127 OW SOL 43 9.350 4.660 3.510 1.00 0.00 +ATOM 128 HW1 SOL 43 10.100 4.180 3.980 1.00 0.00 +ATOM 129 HW2 SOL 43 8.630 4.000 3.280 1.00 0.00 +ATOM 130 OW SOL 44 10.420 15.150 17.740 1.00 0.00 +ATOM 131 HW1 SOL 44 10.510 14.310 17.210 1.00 0.00 +ATOM 132 HW2 SOL 44 11.060 15.840 17.390 1.00 0.00 +ATOM 133 OW SOL 45 7.320 12.790 16.470 1.00 0.00 +ATOM 134 HW1 SOL 45 7.620 12.060 17.080 1.00 0.00 +ATOM 135 HW2 SOL 45 7.960 12.860 15.700 1.00 0.00 +ATOM 136 OW SOL 46 2.020 6.540 9.850 1.00 0.00 +ATOM 137 HW1 SOL 46 2.180 6.450 10.830 1.00 0.00 +ATOM 138 HW2 SOL 46 1.090 6.880 9.690 1.00 0.00 +ATOM 139 OW SOL 47 17.780 8.980 4.240 1.00 0.00 +ATOM 140 HW1 SOL 47 17.230 8.680 5.020 1.00 0.00 +ATOM 141 HW2 SOL 47 18.140 8.180 3.760 1.00 0.00 +ATOM 142 OW SOL 48 10.770 5.760 6.640 1.00 0.00 +ATOM 143 HW1 SOL 48 11.140 6.660 6.850 1.00 0.00 +ATOM 144 HW2 SOL 48 10.680 5.230 7.480 1.00 0.00 +ATOM 145 OW SOL 49 11.480 17.660 12.680 1.00 0.00 +ATOM 146 HW1 SOL 49 11.190 18.430 12.100 1.00 0.00 +ATOM 147 HW2 SOL 49 10.670 17.220 13.070 1.00 0.00 +ATOM 148 OW SOL 50 7.030 18.440 2.940 1.00 0.00 +ATOM 149 HW1 SOL 50 7.510 18.300 3.800 1.00 0.00 +ATOM 150 HW2 SOL 50 7.660 18.840 2.270 1.00 0.00 +ATOM 151 OW SOL 51 10.110 14.510 2.360 1.00 0.00 +ATOM 152 HW1 SOL 51 9.290 14.780 1.850 1.00 0.00 +ATOM 153 HW2 SOL 51 10.060 14.880 3.290 1.00 0.00 +ATOM 154 OW SOL 52 4.940 5.880 1.660 1.00 0.00 +ATOM 155 HW1 SOL 52 4.860 6.550 2.400 1.00 0.00 +ATOM 156 HW2 SOL 52 4.110 5.910 1.100 1.00 0.00 +ATOM 157 OW SOL 53 10.090 0.490 8.240 1.00 0.00 +ATOM 158 HW1 SOL 53 9.520 1.290 8.050 1.00 0.00 +ATOM 159 HW2 SOL 53 10.790 0.400 7.530 1.00 0.00 +ATOM 160 OW SOL 54 0.240 17.030 15.500 1.00 0.00 +ATOM 161 HW1 SOL 54 -0.020 17.980 15.340 1.00 0.00 +ATOM 162 HW2 SOL 54 -0.190 16.450 14.800 1.00 0.00 +ATOM 163 OW SOL 55 15.130 16.240 15.640 1.00 0.00 +ATOM 164 HW1 SOL 55 15.070 16.740 14.780 1.00 0.00 +ATOM 165 HW2 SOL 55 15.540 15.340 15.470 1.00 0.00 +ATOM 166 OW SOL 56 14.140 17.760 13.180 1.00 0.00 +ATOM 167 HW1 SOL 56 13.160 17.810 12.950 1.00 0.00 +ATOM 168 HW2 SOL 56 14.650 17.390 12.410 1.00 0.00 +ATOM 169 OW SOL 57 11.240 9.790 14.320 1.00 0.00 +ATOM 170 HW1 SOL 57 12.220 9.780 14.520 1.00 0.00 +ATOM 171 HW2 SOL 57 10.810 10.570 14.780 1.00 0.00 +ATOM 172 OW SOL 58 14.300 6.300 9.500 1.00 0.00 +ATOM 173 HW1 SOL 58 14.280 5.410 9.040 1.00 0.00 +ATOM 174 HW2 SOL 58 14.790 6.210 10.370 1.00 0.00 +ATOM 175 OW SOL 59 17.100 1.760 3.800 1.00 0.00 +ATOM 176 HW1 SOL 59 17.860 1.680 4.430 1.00 0.00 +ATOM 177 HW2 SOL 59 16.300 1.270 4.170 1.00 0.00 +ATOM 178 OW SOL 60 5.080 13.840 17.510 1.00 0.00 +ATOM 179 HW1 SOL 60 4.590 13.120 18.000 1.00 0.00 +ATOM 180 HW2 SOL 60 5.950 13.490 17.180 1.00 0.00 +ATOM 181 OW SOL 61 14.020 3.760 4.120 1.00 0.00 +ATOM 182 HW1 SOL 61 14.740 4.390 3.840 1.00 0.00 +ATOM 183 HW2 SOL 61 14.430 2.950 4.540 1.00 0.00 +ATOM 184 OW SOL 62 5.300 17.330 7.100 1.00 0.00 +ATOM 185 HW1 SOL 62 5.020 18.190 7.540 1.00 0.00 +ATOM 186 HW2 SOL 62 5.720 16.740 7.780 1.00 0.00 +ATOM 187 OW SOL 63 11.690 12.470 1.810 1.00 0.00 +ATOM 188 HW1 SOL 63 11.240 13.360 1.790 1.00 0.00 +ATOM 189 HW2 SOL 63 11.190 11.830 1.230 1.00 0.00 +ATOM 190 OW SOL 64 9.870 7.550 9.630 1.00 0.00 +ATOM 191 HW1 SOL 64 10.330 6.670 9.520 1.00 0.00 +ATOM 192 HW2 SOL 64 10.480 8.180 10.110 1.00 0.00 +ATOM 193 OW SOL 65 14.730 0.900 10.650 1.00 0.00 +ATOM 194 HW1 SOL 65 14.270 0.980 9.760 1.00 0.00 +ATOM 195 HW2 SOL 65 15.440 0.200 10.590 1.00 0.00 +ATOM 196 OW SOL 66 13.400 13.110 17.030 1.00 0.00 +ATOM 197 HW1 SOL 66 13.940 13.840 17.460 1.00 0.00 +ATOM 198 HW2 SOL 66 13.550 13.110 16.050 1.00 0.00 +ATOM 199 OW SOL 67 0.710 3.490 2.440 1.00 0.00 +ATOM 200 HW1 SOL 67 1.560 3.310 2.940 1.00 0.00 +ATOM 201 HW2 SOL 67 0.400 2.650 2.000 1.00 0.00 +ATOM 202 OW SOL 68 14.910 4.580 14.810 1.00 0.00 +ATOM 203 HW1 SOL 68 15.300 4.290 13.930 1.00 0.00 +ATOM 204 HW2 SOL 68 14.100 4.040 15.010 1.00 0.00 +ATOM 205 OW SOL 69 3.260 15.250 1.820 1.00 0.00 +ATOM 206 HW1 SOL 69 3.830 16.040 1.580 1.00 0.00 +ATOM 207 HW2 SOL 69 3.530 14.470 1.260 1.00 0.00 +ATOM 208 OW SOL 70 15.110 0.080 7.200 1.00 0.00 +ATOM 209 HW1 SOL 70 15.310 0.830 7.840 1.00 0.00 +ATOM 210 HW2 SOL 70 15.830 -0.600 7.250 1.00 0.00 +ATOM 211 OW SOL 71 12.070 7.210 18.300 1.00 0.00 +ATOM 212 HW1 SOL 71 11.470 6.650 18.870 1.00 0.00 +ATOM 213 HW2 SOL 71 12.180 6.770 17.400 1.00 0.00 +ATOM 214 OW SOL 72 18.830 9.950 7.950 1.00 0.00 +ATOM 215 HW1 SOL 72 18.820 10.550 8.750 1.00 0.00 +ATOM 216 HW2 SOL 72 17.890 9.790 7.650 1.00 0.00 +ATOM 217 OW SOL 73 12.610 2.020 2.780 1.00 0.00 +ATOM 218 HW1 SOL 73 12.340 2.260 1.850 1.00 0.00 +ATOM 219 HW2 SOL 73 13.090 2.790 3.200 1.00 0.00 +ATOM 220 OW SOL 74 1.380 4.310 13.840 1.00 0.00 +ATOM 221 HW1 SOL 74 2.020 4.390 14.600 1.00 0.00 +ATOM 222 HW2 SOL 74 1.350 3.370 13.520 1.00 0.00 +ATOM 223 OW SOL 75 12.310 7.910 7.520 1.00 0.00 +ATOM 224 HW1 SOL 75 12.750 8.780 7.320 1.00 0.00 +ATOM 225 HW2 SOL 75 12.930 7.340 8.060 1.00 0.00 +ATOM 226 OW SOL 76 0.710 16.310 2.690 1.00 0.00 +ATOM 227 HW1 SOL 76 0.330 16.700 1.850 1.00 0.00 +ATOM 228 HW2 SOL 76 1.470 15.700 2.460 1.00 0.00 +ATOM 229 OW SOL 77 1.600 2.360 10.470 1.00 0.00 +ATOM 230 HW1 SOL 77 2.550 2.520 10.210 1.00 0.00 +ATOM 231 HW2 SOL 77 1.570 1.850 11.330 1.00 0.00 +ATOM 232 OW SOL 78 14.580 14.480 4.640 1.00 0.00 +ATOM 233 HW1 SOL 78 14.840 15.430 4.440 1.00 0.00 +ATOM 234 HW2 SOL 78 13.600 14.440 4.810 1.00 0.00 +ATOM 235 OW SOL 79 4.490 12.500 2.830 1.00 0.00 +ATOM 236 HW1 SOL 79 5.460 12.280 2.720 1.00 0.00 +ATOM 237 HW2 SOL 79 4.390 13.360 3.320 1.00 0.00 +ATOM 238 OW SOL 80 1.130 15.580 17.550 1.00 0.00 +ATOM 239 HW1 SOL 80 0.720 16.130 16.820 1.00 0.00 +ATOM 240 HW2 SOL 80 2.080 15.870 17.700 1.00 0.00 +ATOM 241 OW SOL 81 3.650 4.210 9.270 1.00 0.00 +ATOM 242 HW1 SOL 81 4.510 4.490 8.820 1.00 0.00 +ATOM 243 HW2 SOL 81 3.010 4.980 9.250 1.00 0.00 +ATOM 244 OW SOL 82 14.390 12.320 2.770 1.00 0.00 +ATOM 245 HW1 SOL 82 14.620 12.880 3.570 1.00 0.00 +ATOM 246 HW2 SOL 82 13.390 12.270 2.680 1.00 0.00 +ATOM 247 OW SOL 83 10.190 5.240 0.760 1.00 0.00 +ATOM 248 HW1 SOL 83 9.510 5.630 0.130 1.00 0.00 +ATOM 249 HW2 SOL 83 9.750 5.010 1.630 1.00 0.00 +ATOM 250 OW SOL 84 15.640 5.460 11.740 1.00 0.00 +ATOM 251 HW1 SOL 84 15.840 4.510 11.500 1.00 0.00 +ATOM 252 HW2 SOL 84 16.360 5.810 12.340 1.00 0.00 +ATOM 253 OW SOL 85 6.170 0.870 15.480 1.00 0.00 +ATOM 254 HW1 SOL 85 7.060 0.510 15.770 1.00 0.00 +ATOM 255 HW2 SOL 85 6.300 1.430 14.650 1.00 0.00 +ATOM 256 OW SOL 86 17.720 3.960 5.360 1.00 0.00 +ATOM 257 HW1 SOL 86 17.240 3.880 4.490 1.00 0.00 +ATOM 258 HW2 SOL 86 18.410 3.240 5.430 1.00 0.00 +ATOM 259 OW SOL 87 3.980 6.740 17.460 1.00 0.00 +ATOM 260 HW1 SOL 87 4.080 7.250 16.610 1.00 0.00 +ATOM 261 HW2 SOL 87 4.660 7.060 18.120 1.00 0.00 +ATOM 262 OW SOL 88 13.960 10.070 15.080 1.00 0.00 +ATOM 263 HW1 SOL 88 14.060 10.080 16.080 1.00 0.00 +ATOM 264 HW2 SOL 88 14.860 10.080 14.650 1.00 0.00 +ATOM 265 OW SOL 89 3.660 1.240 0.770 1.00 0.00 +ATOM 266 HW1 SOL 89 3.310 1.830 1.500 1.00 0.00 +ATOM 267 HW2 SOL 89 2.920 1.010 0.140 1.00 0.00 +ATOM 268 OW SOL 90 5.140 5.540 13.900 1.00 0.00 +ATOM 269 HW1 SOL 90 5.110 5.000 14.740 1.00 0.00 +ATOM 270 HW2 SOL 90 5.640 6.390 14.080 1.00 0.00 +ATOM 271 OW SOL 91 15.750 8.850 9.270 1.00 0.00 +ATOM 272 HW1 SOL 91 15.780 9.420 8.440 1.00 0.00 +ATOM 273 HW2 SOL 91 15.430 7.930 9.020 1.00 0.00 +ATOM 274 OW SOL 92 18.380 14.630 7.030 1.00 0.00 +ATOM 275 HW1 SOL 92 17.860 13.840 6.710 1.00 0.00 +ATOM 276 HW2 SOL 92 19.100 14.840 6.370 1.00 0.00 +ATOM 277 OW SOL 93 15.170 10.000 3.740 1.00 0.00 +ATOM 278 HW1 SOL 93 16.160 9.940 3.870 1.00 0.00 +ATOM 279 HW2 SOL 93 14.920 10.960 3.570 1.00 0.00 +ATOM 280 OW SOL 94 9.670 9.890 5.420 1.00 0.00 +ATOM 281 HW1 SOL 94 10.120 9.050 5.140 1.00 0.00 +ATOM 282 HW2 SOL 94 9.300 9.790 6.340 1.00 0.00 +ATOM 283 OW SOL 95 14.220 12.870 14.330 1.00 0.00 +ATOM 284 HW1 SOL 95 14.980 13.360 14.770 1.00 0.00 +ATOM 285 HW2 SOL 95 14.520 11.960 14.050 1.00 0.00 +ATOM 286 OW SOL 96 14.960 7.090 4.950 1.00 0.00 +ATOM 287 HW1 SOL 96 14.530 7.960 5.210 1.00 0.00 +ATOM 288 HW2 SOL 96 15.570 6.790 5.680 1.00 0.00 +ATOM 289 OW SOL 97 15.380 1.610 16.350 1.00 0.00 +ATOM 290 HW1 SOL 97 15.510 2.560 16.650 1.00 0.00 +ATOM 291 HW2 SOL 97 14.420 1.370 16.410 1.00 0.00 +ATOM 292 OW SOL 98 5.540 8.340 16.040 1.00 0.00 +ATOM 293 HW1 SOL 98 5.870 8.730 15.180 1.00 0.00 +ATOM 294 HW2 SOL 98 5.220 9.080 16.640 1.00 0.00 +ATOM 295 OW SOL 99 16.610 16.730 2.860 1.00 0.00 +ATOM 296 HW1 SOL 99 16.350 17.380 2.150 1.00 0.00 +ATOM 297 HW2 SOL 99 17.140 17.200 3.560 1.00 0.00 +ATOM 298 OW SOL 100 3.830 12.250 6.920 1.00 0.00 +ATOM 299 HW1 SOL 100 2.930 11.870 6.680 1.00 0.00 +ATOM 300 HW2 SOL 100 3.870 13.210 6.650 1.00 0.00 +ATOM 301 OW SOL 101 3.280 2.500 3.450 1.00 0.00 +ATOM 302 HW1 SOL 101 3.840 3.310 3.640 1.00 0.00 +ATOM 303 HW2 SOL 101 3.670 1.710 3.930 1.00 0.00 +ATOM 304 OW SOL 102 8.790 1.420 5.340 1.00 0.00 +ATOM 305 HW1 SOL 102 9.150 1.600 4.430 1.00 0.00 +ATOM 306 HW2 SOL 102 9.190 2.070 5.990 1.00 0.00 +ATOM 307 OW SOL 103 6.250 1.740 12.860 1.00 0.00 +ATOM 308 HW1 SOL 103 7.250 1.780 12.920 1.00 0.00 +ATOM 309 HW2 SOL 103 5.910 2.570 12.420 1.00 0.00 +ATOM 310 OW SOL 104 5.120 17.700 1.050 1.00 0.00 +ATOM 311 HW1 SOL 104 5.820 17.640 1.760 1.00 0.00 +ATOM 312 HW2 SOL 104 4.560 18.510 1.190 1.00 0.00 +ATOM 313 OW SOL 105 1.280 17.380 8.350 1.00 0.00 +ATOM 314 HW1 SOL 105 1.570 16.670 7.710 1.00 0.00 +ATOM 315 HW2 SOL 105 1.410 17.060 9.290 1.00 0.00 +ATOM 316 OW SOL 106 15.040 7.710 1.460 1.00 0.00 +ATOM 317 HW1 SOL 106 15.390 8.550 1.050 1.00 0.00 +ATOM 318 HW2 SOL 106 14.690 7.910 2.370 1.00 0.00 +ATOM 319 OW SOL 107 18.790 0.520 1.740 1.00 0.00 +ATOM 320 HW1 SOL 107 18.360 -0.320 1.410 1.00 0.00 +ATOM 321 HW2 SOL 107 18.150 1.020 2.330 1.00 0.00 +ATOM 322 OW SOL 108 13.550 16.420 10.730 1.00 0.00 +ATOM 323 HW1 SOL 108 12.850 16.420 11.440 1.00 0.00 +ATOM 324 HW2 SOL 108 13.120 16.260 9.840 1.00 0.00 +ATOM 325 OW SOL 109 0.880 16.660 11.050 1.00 0.00 +ATOM 326 HW1 SOL 109 0.200 17.080 11.640 1.00 0.00 +ATOM 327 HW2 SOL 109 0.470 15.880 10.570 1.00 0.00 +ATOM 328 OW SOL 110 17.870 14.100 3.490 1.00 0.00 +ATOM 329 HW1 SOL 110 17.290 14.830 3.140 1.00 0.00 +ATOM 330 HW2 SOL 110 18.660 14.500 3.960 1.00 0.00 +ATOM 331 OW SOL 111 1.030 10.340 15.470 1.00 0.00 +ATOM 332 HW1 SOL 111 1.200 10.030 14.530 1.00 0.00 +ATOM 333 HW2 SOL 111 0.600 9.610 16.000 1.00 0.00 +ATOM 334 OW SOL 112 16.810 14.980 11.110 1.00 0.00 +ATOM 335 HW1 SOL 112 15.870 15.220 10.860 1.00 0.00 +ATOM 336 HW2 SOL 112 17.280 14.630 10.310 1.00 0.00 +ATOM 337 OW SOL 113 18.090 3.030 17.920 1.00 0.00 +ATOM 338 HW1 SOL 113 17.960 4.020 18.030 1.00 0.00 +ATOM 339 HW2 SOL 113 17.590 2.550 18.630 1.00 0.00 +ATOM 340 OW SOL 114 11.740 1.260 6.190 1.00 0.00 +ATOM 341 HW1 SOL 114 11.680 2.130 5.700 1.00 0.00 +ATOM 342 HW2 SOL 114 11.730 0.510 5.530 1.00 0.00 +ATOM 343 OW SOL 115 12.190 18.530 4.150 1.00 0.00 +ATOM 344 HW1 SOL 115 12.210 19.400 3.650 1.00 0.00 +ATOM 345 HW2 SOL 115 12.220 17.770 3.510 1.00 0.00 +ATOM 346 OW SOL 116 0.600 14.380 9.350 1.00 0.00 +ATOM 347 HW1 SOL 116 1.390 13.770 9.370 1.00 0.00 +ATOM 348 HW2 SOL 116 0.240 14.430 8.420 1.00 0.00 +ATOM 349 OW SOL 117 6.540 12.430 7.930 1.00 0.00 +ATOM 350 HW1 SOL 117 5.680 12.420 7.410 1.00 0.00 +ATOM 351 HW2 SOL 117 6.680 11.540 8.360 1.00 0.00 +ATOM 352 OW SOL 118 3.020 4.280 15.910 1.00 0.00 +ATOM 353 HW1 SOL 118 3.050 3.290 16.070 1.00 0.00 +ATOM 354 HW2 SOL 118 2.580 4.730 16.680 1.00 0.00 +ATOM 355 OW SOL 119 18.330 5.780 2.370 1.00 0.00 +ATOM 356 HW1 SOL 119 17.440 5.520 2.730 1.00 0.00 +ATOM 357 HW2 SOL 119 18.920 4.970 2.310 1.00 0.00 +ATOM 358 OW SOL 120 10.530 9.330 11.750 1.00 0.00 +ATOM 359 HW1 SOL 120 10.990 10.110 11.330 1.00 0.00 +ATOM 360 HW2 SOL 120 10.770 9.280 12.710 1.00 0.00 +ATOM 361 OW SOL 121 18.420 11.850 10.100 1.00 0.00 +ATOM 362 HW1 SOL 121 17.470 11.990 10.390 1.00 0.00 +ATOM 363 HW2 SOL 121 18.840 12.730 9.900 1.00 0.00 +ATOM 364 OW SOL 122 0.090 11.250 3.750 1.00 0.00 +ATOM 365 HW1 SOL 122 -0.390 10.390 3.930 1.00 0.00 +ATOM 366 HW2 SOL 122 -0.310 11.700 2.950 1.00 0.00 +ATOM 367 OW SOL 123 0.330 1.520 5.440 1.00 0.00 +ATOM 368 HW1 SOL 123 0.770 0.700 5.080 1.00 0.00 +ATOM 369 HW2 SOL 123 0.510 1.580 6.430 1.00 0.00 +ATOM 370 OW SOL 124 12.080 14.370 4.720 1.00 0.00 +ATOM 371 HW1 SOL 124 11.660 13.470 4.750 1.00 0.00 +ATOM 372 HW2 SOL 124 11.410 15.060 5.010 1.00 0.00 +ATOM 373 OW SOL 125 0.450 8.500 17.280 1.00 0.00 +ATOM 374 HW1 SOL 125 -0.220 7.850 16.920 1.00 0.00 +ATOM 375 HW2 SOL 125 0.940 8.080 18.040 1.00 0.00 +ATOM 376 OW SOL 126 18.090 5.800 13.420 1.00 0.00 +ATOM 377 HW1 SOL 126 18.010 6.350 14.250 1.00 0.00 +ATOM 378 HW2 SOL 126 18.990 5.350 13.410 1.00 0.00 +ATOM 379 OW SOL 127 7.230 6.000 0.190 1.00 0.00 +ATOM 380 HW1 SOL 127 6.400 5.880 0.730 1.00 0.00 +ATOM 381 HW2 SOL 127 7.180 5.450 -0.640 1.00 0.00 +ATOM 382 OW SOL 128 18.860 12.130 13.030 1.00 0.00 +ATOM 383 HW1 SOL 128 19.370 11.710 12.280 1.00 0.00 +ATOM 384 HW2 SOL 128 19.500 12.580 13.660 1.00 0.00 +ATOM 385 OW SOL 129 17.940 3.540 10.670 1.00 0.00 +ATOM 386 HW1 SOL 129 17.440 3.060 11.390 1.00 0.00 +ATOM 387 HW2 SOL 129 18.910 3.280 10.710 1.00 0.00 +ATOM 388 OW SOL 130 3.730 12.140 0.260 1.00 0.00 +ATOM 389 HW1 SOL 130 3.890 11.250 -0.160 1.00 0.00 +ATOM 390 HW2 SOL 130 3.910 12.080 1.240 1.00 0.00 +ATOM 391 OW SOL 131 17.390 2.530 8.180 1.00 0.00 +ATOM 392 HW1 SOL 131 17.600 2.890 9.090 1.00 0.00 +ATOM 393 HW2 SOL 131 18.210 2.110 7.790 1.00 0.00 +ATOM 394 OW SOL 132 2.950 12.670 9.730 1.00 0.00 +ATOM 395 HW1 SOL 132 3.470 13.320 10.270 1.00 0.00 +ATOM 396 HW2 SOL 132 3.500 12.350 8.960 1.00 0.00 +ATOM 397 OW SOL 133 11.970 11.510 4.330 1.00 0.00 +ATOM 398 HW1 SOL 133 11.630 11.730 3.420 1.00 0.00 +ATOM 399 HW2 SOL 133 11.280 10.980 4.820 1.00 0.00 +ATOM 400 OW SOL 134 12.800 16.940 17.060 1.00 0.00 +ATOM 401 HW1 SOL 134 13.130 16.740 17.980 1.00 0.00 +ATOM 402 HW2 SOL 134 13.490 16.680 16.390 1.00 0.00 +ATOM 403 OW SOL 135 9.400 15.660 4.740 1.00 0.00 +ATOM 404 HW1 SOL 135 8.990 15.070 5.440 1.00 0.00 +ATOM 405 HW2 SOL 135 9.200 16.610 4.950 1.00 0.00 +ATOM 406 OW SOL 136 14.940 7.190 15.340 1.00 0.00 +ATOM 407 HW1 SOL 136 14.830 6.230 15.070 1.00 0.00 +ATOM 408 HW2 SOL 136 14.570 7.780 14.620 1.00 0.00 +ATOM 409 OW SOL 137 16.650 12.920 5.760 1.00 0.00 +ATOM 410 HW1 SOL 137 15.850 13.510 5.620 1.00 0.00 +ATOM 411 HW2 SOL 137 17.230 12.950 4.950 1.00 0.00 +ATOM 412 OW SOL 138 2.820 6.180 12.480 1.00 0.00 +ATOM 413 HW1 SOL 138 2.110 5.710 12.990 1.00 0.00 +ATOM 414 HW2 SOL 138 3.640 6.270 13.060 1.00 0.00 +ATOM 415 OW SOL 139 1.230 1.380 18.460 1.00 0.00 +ATOM 416 HW1 SOL 139 0.810 1.000 19.280 1.00 0.00 +ATOM 417 HW2 SOL 139 0.600 2.030 18.030 1.00 0.00 +ATOM 418 OW SOL 140 6.250 4.620 16.930 1.00 0.00 +ATOM 419 HW1 SOL 140 6.280 3.680 17.260 1.00 0.00 +ATOM 420 HW2 SOL 140 5.340 5.000 17.100 1.00 0.00 +ATOM 421 OW SOL 141 11.600 15.400 8.260 1.00 0.00 +ATOM 422 HW1 SOL 141 10.720 15.840 8.400 1.00 0.00 +ATOM 423 HW2 SOL 141 12.160 15.970 7.660 1.00 0.00 +ATOM 424 OW SOL 142 13.020 1.810 8.690 1.00 0.00 +ATOM 425 HW1 SOL 142 12.470 1.440 7.930 1.00 0.00 +ATOM 426 HW2 SOL 142 13.550 2.590 8.370 1.00 0.00 +ATOM 427 OW SOL 143 5.730 14.630 4.290 1.00 0.00 +ATOM 428 HW1 SOL 143 5.960 14.750 3.330 1.00 0.00 +ATOM 429 HW2 SOL 143 6.530 14.810 4.850 1.00 0.00 +ATOM 430 OW SOL 144 17.660 5.510 18.710 1.00 0.00 +ATOM 431 HW1 SOL 144 16.720 5.820 18.550 1.00 0.00 +ATOM 432 HW2 SOL 144 17.860 5.560 19.690 1.00 0.00 +ATOM 433 OW SOL 145 5.930 5.730 8.500 1.00 0.00 +ATOM 434 HW1 SOL 145 6.490 5.730 7.670 1.00 0.00 +ATOM 435 HW2 SOL 145 6.470 6.040 9.270 1.00 0.00 +ATOM 436 OW SOL 146 2.920 18.140 15.270 1.00 0.00 +ATOM 437 HW1 SOL 146 2.100 17.570 15.360 1.00 0.00 +ATOM 438 HW2 SOL 146 3.660 17.740 15.800 1.00 0.00 +ATOM 439 OW SOL 147 7.850 14.520 6.900 1.00 0.00 +ATOM 440 HW1 SOL 147 7.540 13.650 7.260 1.00 0.00 +ATOM 441 HW2 SOL 147 8.130 15.120 7.650 1.00 0.00 +ATOM 442 OW SOL 148 8.390 3.320 10.630 1.00 0.00 +ATOM 443 HW1 SOL 148 7.410 3.170 10.500 1.00 0.00 +ATOM 444 HW2 SOL 148 8.660 3.020 11.540 1.00 0.00 +ATOM 445 OW SOL 149 0.580 5.890 5.250 1.00 0.00 +ATOM 446 HW1 SOL 149 0.060 5.110 5.600 1.00 0.00 +ATOM 447 HW2 SOL 149 0.400 6.000 4.270 1.00 0.00 +ATOM 448 OW SOL 150 4.650 14.400 11.350 1.00 0.00 +ATOM 449 HW1 SOL 150 4.050 14.980 11.890 1.00 0.00 +ATOM 450 HW2 SOL 150 5.480 14.190 11.880 1.00 0.00 +ATOM 451 OW SOL 151 7.280 8.460 4.990 1.00 0.00 +ATOM 452 HW1 SOL 151 8.050 9.090 5.060 1.00 0.00 +ATOM 453 HW2 SOL 151 6.500 8.840 5.490 1.00 0.00 +ATOM 454 OW SOL 152 15.540 13.040 0.580 1.00 0.00 +ATOM 455 HW1 SOL 152 16.470 12.760 0.800 1.00 0.00 +ATOM 456 HW2 SOL 152 14.910 12.690 1.270 1.00 0.00 +ATOM 457 OW SOL 153 10.380 13.420 15.400 1.00 0.00 +ATOM 458 HW1 SOL 153 10.950 13.210 14.610 1.00 0.00 +ATOM 459 HW2 SOL 153 10.550 12.750 16.120 1.00 0.00 +ATOM 460 OW SOL 154 1.410 11.440 6.290 1.00 0.00 +ATOM 461 HW1 SOL 154 0.910 10.680 6.700 1.00 0.00 +ATOM 462 HW2 SOL 154 0.970 11.690 5.430 1.00 0.00 +ATOM 463 OW SOL 155 4.870 9.680 5.880 1.00 0.00 +ATOM 464 HW1 SOL 155 4.840 10.670 6.030 1.00 0.00 +ATOM 465 HW2 SOL 155 4.370 9.220 6.610 1.00 0.00 +ATOM 466 OW SOL 156 11.990 12.730 12.670 1.00 0.00 +ATOM 467 HW1 SOL 156 12.200 12.160 11.880 1.00 0.00 +ATOM 468 HW2 SOL 156 12.820 12.900 13.200 1.00 0.00 +ATOM 469 OW SOL 157 15.740 11.790 11.330 1.00 0.00 +ATOM 470 HW1 SOL 157 15.190 10.980 11.510 1.00 0.00 +ATOM 471 HW2 SOL 157 15.590 12.470 12.040 1.00 0.00 +ATOM 472 OW SOL 158 11.800 3.050 0.380 1.00 0.00 +ATOM 473 HW1 SOL 158 11.290 2.190 0.260 1.00 0.00 +ATOM 474 HW2 SOL 158 11.150 3.800 0.510 1.00 0.00 +ATOM 475 OW SOL 159 18.220 15.420 13.450 1.00 0.00 +ATOM 476 HW1 SOL 159 17.620 15.260 12.660 1.00 0.00 +ATOM 477 HW2 SOL 159 19.020 14.830 13.370 1.00 0.00 +ATOM 478 OW SOL 160 6.210 8.170 13.090 1.00 0.00 +ATOM 479 HW1 SOL 160 5.320 8.610 12.970 1.00 0.00 +ATOM 480 HW2 SOL 160 6.440 7.640 12.280 1.00 0.00 +ATOM 481 OW SOL 161 15.270 18.010 0.920 1.00 0.00 +ATOM 482 HW1 SOL 161 15.630 18.000 -0.010 1.00 0.00 +ATOM 483 HW2 SOL 161 15.170 18.960 1.220 1.00 0.00 +ATOM 484 OW SOL 162 7.960 16.380 17.830 1.00 0.00 +ATOM 485 HW1 SOL 162 8.870 15.950 17.800 1.00 0.00 +ATOM 486 HW2 SOL 162 7.440 16.100 17.030 1.00 0.00 +ATOM 487 OW SOL 163 13.110 17.170 6.560 1.00 0.00 +ATOM 488 HW1 SOL 163 13.680 17.740 7.150 1.00 0.00 +ATOM 489 HW2 SOL 163 12.550 17.750 5.960 1.00 0.00 +ATOM 490 OW SOL 164 5.830 16.770 15.450 1.00 0.00 +ATOM 491 HW1 SOL 164 5.570 16.500 16.380 1.00 0.00 +ATOM 492 HW2 SOL 164 6.010 17.760 15.440 1.00 0.00 +ATOM 493 OW SOL 165 17.510 17.340 6.770 1.00 0.00 +ATOM 494 HW1 SOL 165 17.530 16.340 6.800 1.00 0.00 +ATOM 495 HW2 SOL 165 18.420 17.690 6.960 1.00 0.00 +ATOM 496 OW SOL 166 18.700 17.320 0.080 1.00 0.00 +ATOM 497 HW1 SOL 166 19.210 16.520 -0.220 1.00 0.00 +ATOM 498 HW2 SOL 166 17.970 17.520 -0.570 1.00 0.00 +ATOM 499 OW SOL 167 6.400 9.870 9.040 1.00 0.00 +ATOM 500 HW1 SOL 167 5.490 9.460 8.920 1.00 0.00 +ATOM 501 HW2 SOL 167 6.660 9.820 10.000 1.00 0.00 +ATOM 502 OW SOL 168 16.030 2.680 12.210 1.00 0.00 +ATOM 503 HW1 SOL 168 15.690 2.170 11.420 1.00 0.00 +ATOM 504 HW2 SOL 168 16.010 2.100 13.020 1.00 0.00 +ATOM 505 OW SOL 169 9.060 16.330 14.580 1.00 0.00 +ATOM 506 HW1 SOL 169 8.750 16.140 13.650 1.00 0.00 +ATOM 507 HW2 SOL 169 9.270 15.470 15.040 1.00 0.00 +ATOM 508 OW SOL 170 11.890 12.500 7.930 1.00 0.00 +ATOM 509 HW1 SOL 170 11.030 12.290 8.410 1.00 0.00 +ATOM 510 HW2 SOL 170 11.930 13.480 7.750 1.00 0.00 +ATOM 511 OW SOL 171 12.380 9.680 0.290 1.00 0.00 +ATOM 512 HW1 SOL 171 11.780 9.730 1.090 1.00 0.00 +ATOM 513 HW2 SOL 171 12.470 8.730 0.000 1.00 0.00 +ATOM 514 OW SOL 172 6.860 15.280 1.710 1.00 0.00 +ATOM 515 HW1 SOL 172 6.690 14.390 1.280 1.00 0.00 +ATOM 516 HW2 SOL 172 7.210 15.920 1.020 1.00 0.00 +ATOM 517 OW SOL 173 16.560 14.050 15.320 1.00 0.00 +ATOM 518 HW1 SOL 173 17.080 14.430 14.560 1.00 0.00 +ATOM 519 HW2 SOL 173 17.190 13.740 16.040 1.00 0.00 +ATOM 520 OW SOL 174 4.230 14.580 14.990 1.00 0.00 +ATOM 521 HW1 SOL 174 4.360 14.240 15.920 1.00 0.00 +ATOM 522 HW2 SOL 174 4.920 15.280 14.800 1.00 0.00 +ATOM 523 OW SOL 175 3.530 10.220 17.100 1.00 0.00 +ATOM 524 HW1 SOL 175 3.390 9.320 17.530 1.00 0.00 +ATOM 525 HW2 SOL 175 2.760 10.410 16.480 1.00 0.00 +ATOM 526 OW SOL 176 9.520 13.550 11.460 1.00 0.00 +ATOM 527 HW1 SOL 176 9.550 12.950 10.660 1.00 0.00 +ATOM 528 HW2 SOL 176 10.250 13.300 12.100 1.00 0.00 +ATOM 529 OW SOL 177 9.670 7.360 4.000 1.00 0.00 +ATOM 530 HW1 SOL 177 8.730 7.400 4.340 1.00 0.00 +ATOM 531 HW2 SOL 177 9.980 6.400 3.980 1.00 0.00 +ATOM 532 OW SOL 178 13.390 10.360 6.410 1.00 0.00 +ATOM 533 HW1 SOL 178 13.200 10.410 5.420 1.00 0.00 +ATOM 534 HW2 SOL 178 12.840 11.050 6.880 1.00 0.00 +ATOM 535 OW SOL 179 12.200 0.370 16.230 1.00 0.00 +ATOM 536 HW1 SOL 179 11.390 0.680 16.730 1.00 0.00 +ATOM 537 HW2 SOL 179 12.470 -0.530 16.560 1.00 0.00 +ATOM 538 OW SOL 180 17.720 9.140 11.980 1.00 0.00 +ATOM 539 HW1 SOL 180 17.330 9.070 11.060 1.00 0.00 +ATOM 540 HW2 SOL 180 18.210 10.010 12.070 1.00 0.00 +ATOM 541 OW SOL 181 3.570 9.170 12.520 1.00 0.00 +ATOM 542 HW1 SOL 181 3.190 10.030 12.190 1.00 0.00 +ATOM 543 HW2 SOL 181 2.840 8.500 12.640 1.00 0.00 +ATOM 544 OW SOL 182 10.950 0.320 1.060 1.00 0.00 +ATOM 545 HW1 SOL 182 10.060 0.050 0.710 1.00 0.00 +ATOM 546 HW2 SOL 182 11.490 -0.500 1.270 1.00 0.00 +ATOM 547 OW SOL 183 16.380 2.410 1.050 1.00 0.00 +ATOM 548 HW1 SOL 183 15.560 2.940 0.850 1.00 0.00 +ATOM 549 HW2 SOL 183 16.540 2.390 2.030 1.00 0.00 +ATOM 550 OW SOL 184 14.240 4.090 0.740 1.00 0.00 +ATOM 551 HW1 SOL 184 13.340 3.670 0.610 1.00 0.00 +ATOM 552 HW2 SOL 184 14.320 4.890 0.130 1.00 0.00 +ATOM 553 OW SOL 185 11.410 3.740 5.070 1.00 0.00 +ATOM 554 HW1 SOL 185 11.110 4.540 5.600 1.00 0.00 +ATOM 555 HW2 SOL 185 12.350 3.870 4.770 1.00 0.00 +ATOM 556 OW SOL 186 14.140 15.600 0.250 1.00 0.00 +ATOM 557 HW1 SOL 186 14.650 14.730 0.220 1.00 0.00 +ATOM 558 HW2 SOL 186 14.750 16.330 0.550 1.00 0.00 +ATOM 559 OW SOL 187 1.620 14.090 14.250 1.00 0.00 +ATOM 560 HW1 SOL 187 2.590 14.230 14.480 1.00 0.00 +ATOM 561 HW2 SOL 187 1.130 13.790 15.060 1.00 0.00 +ATOM 562 OW SOL 188 0.510 7.640 0.940 1.00 0.00 +ATOM 563 HW1 SOL 188 -0.010 8.370 1.390 1.00 0.00 +ATOM 564 HW2 SOL 188 0.260 6.760 1.350 1.00 0.00 +ATOM 565 OW SOL 189 7.800 3.010 1.000 1.00 0.00 +ATOM 566 HW1 SOL 189 7.350 3.350 1.820 1.00 0.00 +ATOM 567 HW2 SOL 189 7.130 2.930 0.260 1.00 0.00 +ATOM 568 OW SOL 190 3.860 16.430 18.040 1.00 0.00 +ATOM 569 HW1 SOL 190 4.240 15.500 17.980 1.00 0.00 +ATOM 570 HW2 SOL 190 4.330 16.930 18.760 1.00 0.00 +ATOM 571 OW SOL 191 7.970 5.160 6.310 1.00 0.00 +ATOM 572 HW1 SOL 191 7.610 5.180 5.380 1.00 0.00 +ATOM 573 HW2 SOL 191 8.950 5.390 6.300 1.00 0.00 +ATOM 574 OW SOL 192 5.180 8.050 3.180 1.00 0.00 +ATOM 575 HW1 SOL 192 5.960 8.240 3.770 1.00 0.00 +ATOM 576 HW2 SOL 192 4.450 8.710 3.360 1.00 0.00 +ATOM 577 OW SOL 193 5.320 4.040 11.630 1.00 0.00 +ATOM 578 HW1 SOL 193 4.760 4.430 10.900 1.00 0.00 +ATOM 579 HW2 SOL 193 5.190 4.560 12.470 1.00 0.00 +ATOM 580 OW SOL 194 9.180 3.220 8.030 1.00 0.00 +ATOM 581 HW1 SOL 194 8.530 3.670 7.420 1.00 0.00 +ATOM 582 HW2 SOL 194 8.850 3.280 8.970 1.00 0.00 +ATOM 583 OW SOL 195 6.250 16.200 9.630 1.00 0.00 +ATOM 584 HW1 SOL 195 6.060 17.150 9.900 1.00 0.00 +ATOM 585 HW2 SOL 195 5.660 15.580 10.150 1.00 0.00 +ATOM 586 OW SOL 196 14.720 3.750 7.690 1.00 0.00 +ATOM 587 HW1 SOL 196 15.690 3.660 7.900 1.00 0.00 +ATOM 588 HW2 SOL 196 14.590 4.500 7.050 1.00 0.00 +ATOM 589 OW SOL 197 8.040 18.930 0.160 1.00 0.00 +ATOM 590 HW1 SOL 197 7.940 18.030 -0.280 1.00 0.00 +ATOM 591 HW2 SOL 197 7.160 19.410 0.120 1.00 0.00 +ATOM 592 OW SOL 198 7.630 6.170 10.510 1.00 0.00 +ATOM 593 HW1 SOL 198 8.420 6.770 10.370 1.00 0.00 +ATOM 594 HW2 SOL 198 7.940 5.260 10.760 1.00 0.00 +ATOM 595 OW SOL 199 16.080 0.490 13.880 1.00 0.00 +ATOM 596 HW1 SOL 199 15.880 0.910 14.770 1.00 0.00 +ATOM 597 HW2 SOL 199 15.350 -0.140 13.630 1.00 0.00 +ATOM 598 OW SOL 200 16.050 10.440 7.050 1.00 0.00 +ATOM 599 HW1 SOL 200 15.090 10.250 6.840 1.00 0.00 +ATOM 600 HW2 SOL 200 16.300 11.330 6.680 1.00 0.00 +ATOM 601 OW SOL 201 5.100 4.680 4.240 1.00 0.00 +ATOM 602 HW1 SOL 201 4.570 5.360 4.760 1.00 0.00 +ATOM 603 HW2 SOL 201 5.260 5.020 3.320 1.00 0.00 +ATOM 604 OW SOL 202 16.610 5.860 7.050 1.00 0.00 +ATOM 605 HW1 SOL 202 17.090 5.260 6.410 1.00 0.00 +ATOM 606 HW2 SOL 202 17.120 5.900 7.910 1.00 0.00 +ATOM 607 OW SOL 203 3.000 8.680 0.620 1.00 0.00 +ATOM 608 HW1 SOL 203 3.400 9.030 1.470 1.00 0.00 +ATOM 609 HW2 SOL 203 2.160 8.180 0.830 1.00 0.00 +ATOM 610 OW SOL 204 16.610 10.290 14.430 1.00 0.00 +ATOM 611 HW1 SOL 204 17.340 10.970 14.460 1.00 0.00 +ATOM 612 HW2 SOL 204 16.800 9.620 13.700 1.00 0.00 +ATOM 613 OW SOL 205 9.800 1.580 17.190 1.00 0.00 +ATOM 614 HW1 SOL 205 9.470 2.390 16.700 1.00 0.00 +ATOM 615 HW2 SOL 205 9.120 1.310 17.880 1.00 0.00 +ATOM 616 OW SOL 206 18.380 0.930 15.570 1.00 0.00 +ATOM 617 HW1 SOL 206 17.890 1.800 15.550 1.00 0.00 +ATOM 618 HW2 SOL 206 18.970 0.900 16.380 1.00 0.00 +ATOM 619 OW SOL 207 11.390 5.050 9.560 1.00 0.00 +ATOM 620 HW1 SOL 207 11.260 4.060 9.490 1.00 0.00 +ATOM 621 HW2 SOL 207 12.210 5.230 10.110 1.00 0.00 +ATOM 622 OW SOL 208 12.910 7.710 13.290 1.00 0.00 +ATOM 623 HW1 SOL 208 12.800 6.820 12.830 1.00 0.00 +ATOM 624 HW2 SOL 208 12.040 7.980 13.700 1.00 0.00 +ATOM 625 OW SOL 209 10.910 1.030 11.220 1.00 0.00 +ATOM 626 HW1 SOL 209 11.680 1.600 11.520 1.00 0.00 +ATOM 627 HW2 SOL 209 10.880 1.010 10.220 1.00 0.00 +ATOM 628 OW SOL 210 14.420 10.650 17.890 1.00 0.00 +ATOM 629 HW1 SOL 210 13.820 10.260 18.590 1.00 0.00 +ATOM 630 HW2 SOL 210 14.530 11.630 18.060 1.00 0.00 +ATOM 631 OW SOL 211 8.290 17.880 5.620 1.00 0.00 +ATOM 632 HW1 SOL 211 8.610 18.830 5.690 1.00 0.00 +ATOM 633 HW2 SOL 211 7.940 17.580 6.500 1.00 0.00 +ATOM 634 OW SOL 212 1.340 15.380 5.440 1.00 0.00 +ATOM 635 HW1 SOL 212 2.310 15.190 5.590 1.00 0.00 +ATOM 636 HW2 SOL 212 1.220 15.820 4.550 1.00 0.00 +ATOM 637 OW SOL 213 1.240 1.480 13.290 1.00 0.00 +ATOM 638 HW1 SOL 213 2.120 1.370 13.760 1.00 0.00 +ATOM 639 HW2 SOL 213 0.500 1.320 13.940 1.00 0.00 +ATOM 640 OW SOL 214 12.890 16.650 2.540 1.00 0.00 +ATOM 641 HW1 SOL 214 13.280 16.550 1.620 1.00 0.00 +ATOM 642 HW2 SOL 214 13.030 15.810 3.060 1.00 0.00 +ATOM 643 OW SOL 215 12.840 2.690 15.130 1.00 0.00 +ATOM 644 HW1 SOL 215 12.270 3.350 15.620 1.00 0.00 +ATOM 645 HW2 SOL 215 12.520 1.760 15.320 1.00 0.00 +ATOM 646 OW SOL 216 1.780 18.470 4.460 1.00 0.00 +ATOM 647 HW1 SOL 216 1.560 18.090 3.560 1.00 0.00 +ATOM 648 HW2 SOL 216 2.760 18.680 4.500 1.00 0.00 +ATOM 649 OW SOL 217 18.060 18.720 12.240 1.00 0.00 +ATOM 650 HW1 SOL 217 17.550 18.920 13.080 1.00 0.00 +ATOM 651 HW2 SOL 217 18.590 19.530 11.980 1.00 0.00 +ATOM 652 OW SOL 218 10.390 9.700 2.370 1.00 0.00 +ATOM 653 HW1 SOL 218 10.400 8.980 3.070 1.00 0.00 +ATOM 654 HW2 SOL 218 9.720 10.400 2.630 1.00 0.00 +ATOM 655 OW SOL 219 5.600 0.860 8.640 1.00 0.00 +ATOM 656 HW1 SOL 219 5.590 0.430 9.540 1.00 0.00 +ATOM 657 HW2 SOL 219 4.900 1.580 8.600 1.00 0.00 +ATOM 658 OW SOL 220 7.910 10.060 12.060 1.00 0.00 +ATOM 659 HW1 SOL 220 8.840 9.730 11.900 1.00 0.00 +ATOM 660 HW2 SOL 220 7.440 9.450 12.690 1.00 0.00 +ATOM 661 OW SOL 221 9.040 11.720 3.400 1.00 0.00 +ATOM 662 HW1 SOL 221 9.210 11.440 4.350 1.00 0.00 +ATOM 663 HW2 SOL 221 9.480 12.600 3.240 1.00 0.00 +TER +ENDMDL diff --git a/tests/data/water.gro b/tests/data/water.gro new file mode 100644 index 0000000..afaa577 --- /dev/null +++ b/tests/data/water.gro @@ -0,0 +1,666 @@ +Generated with MDTraj, t= 0.0 + 663 + 1HOH O 1 0.696 1.330 1.211 + 1HOH H1 2 0.662 1.236 1.203 + 1HOH H2 3 0.790 1.334 1.179 + 2HOH O 4 0.700 0.289 0.376 + 2HOH H1 5 0.714 0.211 0.436 + 2HOH H2 6 0.629 0.348 0.413 + 3HOH O 7 1.480 0.088 0.482 + 3HOH H1 8 1.417 0.022 0.442 + 3HOH H2 9 1.494 0.066 0.579 + 4HOH O 10 0.131 1.339 0.001 + 4HOH H1 11 0.222 1.299 0.000 + 4HOH H2 12 0.129 1.420 -0.058 + 5HOH O 13 0.962 0.163 0.279 + 5HOH H1 14 1.026 0.106 0.228 + 5HOH H2 15 0.890 0.197 0.217 + 6HOH O 16 0.467 1.884 0.461 + 6HOH H1 17 0.481 1.803 0.518 + 6HOH H2 18 0.555 1.922 0.435 + 7HOH O 19 1.823 0.625 0.991 + 7HOH H1 20 1.782 0.683 1.062 + 7HOH H2 21 1.814 0.529 1.018 + 8HOH O 22 0.897 1.672 0.851 + 8HOH H1 23 0.924 1.768 0.859 + 8HOH H2 24 0.855 1.642 0.936 + 9HOH O 25 0.394 1.470 0.608 + 9HOH H1 26 0.405 1.562 0.646 + 9HOH H2 27 0.459 1.457 0.533 + 10HOH O 28 0.885 0.012 1.512 + 10HOH H1 29 0.951 0.045 1.580 + 10HOH H2 30 0.902 -0.085 1.494 + 11HOH O 31 0.593 0.207 1.823 + 11HOH H1 32 0.583 0.161 1.735 + 11HOH H2 33 0.521 0.177 1.885 + 12HOH O 34 0.873 1.618 1.189 + 12HOH H1 35 0.790 1.658 1.150 + 12HOH H2 36 0.882 1.523 1.159 + 13HOH O 37 1.148 0.480 1.640 + 13HOH H1 38 1.052 0.472 1.613 + 13HOH H2 39 1.168 0.418 1.715 + 14HOH O 40 0.564 1.866 1.107 + 14HOH H1 41 0.576 1.942 1.171 + 14HOH H2 42 0.495 1.803 1.142 + 15HOH O 43 1.305 0.250 1.219 + 15HOH H1 44 1.356 0.178 1.170 + 15HOH H2 45 1.330 0.248 1.316 + 16HOH O 46 1.817 1.238 0.153 + 16HOH H1 47 1.799 1.309 0.221 + 16HOH H2 48 1.889 1.269 0.091 + 17HOH O 49 0.082 0.102 0.813 + 17HOH H1 50 0.127 0.143 0.892 + 17HOH H2 51 0.107 0.005 0.808 + 18HOH O 52 1.292 0.522 1.217 + 18HOH H1 53 1.390 0.524 1.196 + 18HOH H2 54 1.263 0.428 1.232 + 19HOH O 55 1.495 0.631 1.810 + 19HOH H1 56 1.486 0.679 1.897 + 19HOH H2 57 1.466 0.691 1.736 + 20HOH O 58 1.416 0.951 1.145 + 20HOH H1 59 1.479 0.900 1.086 + 20HOH H2 60 1.367 0.886 1.203 + 21HOH O 61 0.915 1.185 0.938 + 21HOH H1 62 0.909 1.091 0.905 + 21HOH H2 63 0.834 1.236 0.908 + 22HOH O 64 1.654 1.787 1.011 + 22HOH H1 65 1.720 1.789 1.085 + 22HOH H2 66 1.680 1.716 0.945 + 23HOH O 67 0.345 0.871 0.845 + 23HOH H1 68 0.368 0.800 0.911 + 23HOH H2 69 0.246 0.884 0.843 + 24HOH O 70 1.769 0.692 1.599 + 24HOH H1 71 1.745 0.601 1.632 + 24HOH H2 72 1.686 0.744 1.580 + 25HOH O 73 1.649 1.799 1.744 + 25HOH H1 74 1.599 1.730 1.692 + 25HOH H2 75 1.657 1.882 1.690 + 26HOH O 76 1.592 0.543 0.324 + 26HOH H1 77 1.562 0.621 0.379 + 26HOH H2 78 1.542 0.543 0.237 + 27HOH O 79 0.857 1.079 1.819 + 27HOH H1 80 0.838 0.994 1.867 + 27HOH H2 81 0.954 1.084 1.796 + 28HOH O 82 1.889 1.288 1.639 + 28HOH H1 83 1.900 1.192 1.614 + 28HOH H2 84 1.925 1.302 1.732 + 29HOH O 85 1.249 1.136 1.061 + 29HOH H1 86 1.265 1.182 0.973 + 29HOH H2 87 1.327 1.076 1.081 + 30HOH O 88 0.911 0.389 1.562 + 30HOH H1 89 0.896 0.356 1.468 + 30HOH H2 90 0.844 0.461 1.582 + 31HOH O 91 0.305 1.009 0.316 + 31HOH H1 92 0.216 1.030 0.358 + 31HOH H2 93 0.362 1.091 0.318 + 32HOH O 94 0.357 0.611 0.586 + 32HOH H1 95 0.260 0.605 0.563 + 32HOH H2 96 0.368 0.661 0.672 + 33HOH O 97 0.235 0.159 1.592 + 33HOH H1 98 0.253 0.066 1.560 + 33HOH H2 99 0.217 0.158 1.690 + 34HOH O 100 1.120 1.156 1.750 + 34HOH H1 101 1.141 1.078 1.808 + 34HOH H2 102 1.203 1.208 1.730 + 35HOH O 103 0.884 0.948 0.800 + 35HOH H1 104 0.786 0.946 0.819 + 35HOH H2 105 0.929 0.871 0.845 + 36HOH O 106 0.697 1.207 0.172 + 36HOH H1 107 0.683 1.177 0.077 + 36HOH H2 108 0.771 1.154 0.213 + 37HOH O 109 0.366 1.702 1.207 + 37HOH H1 110 0.277 1.682 1.166 + 37HOH H2 111 0.354 1.760 1.287 + 38HOH O 112 1.675 0.923 1.880 + 38HOH H1 113 1.749 0.906 1.816 + 38HOH H2 114 1.605 0.980 1.836 + 39HOH O 115 0.889 0.173 1.293 + 39HOH H1 116 0.898 0.118 1.376 + 39HOH H2 117 0.967 0.156 1.233 + 40HOH O 118 0.826 0.670 1.527 + 40HOH H1 119 0.755 0.718 1.580 + 40HOH H2 120 0.904 0.731 1.514 + 41HOH O 121 0.164 1.077 1.118 + 41HOH H1 122 0.071 1.067 1.082 + 41HOH H2 123 0.217 1.138 1.059 + 42HOH O 124 0.794 0.860 0.062 + 42HOH H1 125 0.863 0.853 0.134 + 42HOH H2 126 0.768 0.768 0.032 + 43HOH O 127 0.935 0.466 0.351 + 43HOH H1 128 1.010 0.418 0.398 + 43HOH H2 129 0.863 0.400 0.328 + 44HOH O 130 1.042 1.515 1.774 + 44HOH H1 131 1.051 1.431 1.721 + 44HOH H2 132 1.106 1.584 1.739 + 45HOH O 133 0.732 1.279 1.647 + 45HOH H1 134 0.762 1.206 1.708 + 45HOH H2 135 0.796 1.286 1.570 + 46HOH O 136 0.202 0.654 0.985 + 46HOH H1 137 0.218 0.645 1.083 + 46HOH H2 138 0.109 0.688 0.969 + 47HOH O 139 1.778 0.898 0.424 + 47HOH H1 140 1.723 0.868 0.502 + 47HOH H2 141 1.814 0.818 0.376 + 48HOH O 142 1.077 0.576 0.664 + 48HOH H1 143 1.114 0.666 0.685 + 48HOH H2 144 1.068 0.523 0.748 + 49HOH O 145 1.148 1.766 1.268 + 49HOH H1 146 1.119 1.843 1.210 + 49HOH H2 147 1.067 1.722 1.307 + 50HOH O 148 0.703 1.844 0.294 + 50HOH H1 149 0.751 1.830 0.380 + 50HOH H2 150 0.766 1.884 0.227 + 51HOH O 151 1.011 1.451 0.236 + 51HOH H1 152 0.929 1.478 0.185 + 51HOH H2 153 1.006 1.488 0.329 + 52HOH O 154 0.494 0.588 0.166 + 52HOH H1 155 0.486 0.655 0.240 + 52HOH H2 156 0.411 0.591 0.110 + 53HOH O 157 1.009 0.049 0.824 + 53HOH H1 158 0.952 0.129 0.805 + 53HOH H2 159 1.079 0.040 0.753 + 54HOH O 160 0.024 1.703 1.550 + 54HOH H1 161 -0.002 1.798 1.534 + 54HOH H2 162 -0.019 1.645 1.480 + 55HOH O 163 1.513 1.624 1.564 + 55HOH H1 164 1.507 1.674 1.478 + 55HOH H2 165 1.554 1.534 1.547 + 56HOH O 166 1.414 1.776 1.318 + 56HOH H1 167 1.316 1.781 1.295 + 56HOH H2 168 1.465 1.739 1.241 + 57HOH O 169 1.124 0.979 1.432 + 57HOH H1 170 1.222 0.978 1.452 + 57HOH H2 171 1.081 1.057 1.478 + 58HOH O 172 1.430 0.630 0.950 + 58HOH H1 173 1.428 0.541 0.904 + 58HOH H2 174 1.479 0.621 1.037 + 59HOH O 175 1.710 0.176 0.380 + 59HOH H1 176 1.786 0.168 0.443 + 59HOH H2 177 1.630 0.127 0.417 + 60HOH O 178 0.508 1.384 1.751 + 60HOH H1 179 0.459 1.312 1.800 + 60HOH H2 180 0.595 1.349 1.718 + 61HOH O 181 1.402 0.376 0.412 + 61HOH H1 182 1.474 0.439 0.384 + 61HOH H2 183 1.443 0.295 0.454 + 62HOH O 184 0.530 1.733 0.710 + 62HOH H1 185 0.502 1.819 0.754 + 62HOH H2 186 0.572 1.674 0.778 + 63HOH O 187 1.169 1.247 0.181 + 63HOH H1 188 1.124 1.336 0.179 + 63HOH H2 189 1.119 1.183 0.123 + 64HOH O 190 0.987 0.755 0.963 + 64HOH H1 191 1.033 0.667 0.952 + 64HOH H2 192 1.048 0.818 1.011 + 65HOH O 193 1.473 0.090 1.065 + 65HOH H1 194 1.427 0.098 0.976 + 65HOH H2 195 1.544 0.020 1.059 + 66HOH O 196 1.340 1.311 1.703 + 66HOH H1 197 1.394 1.384 1.746 + 66HOH H2 198 1.355 1.311 1.605 + 67HOH O 199 0.071 0.349 0.244 + 67HOH H1 200 0.156 0.331 0.294 + 67HOH H2 201 0.040 0.265 0.200 + 68HOH O 202 1.491 0.458 1.481 + 68HOH H1 203 1.530 0.429 1.393 + 68HOH H2 204 1.410 0.404 1.501 + 69HOH O 205 0.326 1.525 0.182 + 69HOH H1 206 0.383 1.604 0.158 + 69HOH H2 207 0.353 1.447 0.126 + 70HOH O 208 1.511 0.008 0.720 + 70HOH H1 209 1.531 0.083 0.784 + 70HOH H2 210 1.583 -0.060 0.725 + 71HOH O 211 1.207 0.721 1.830 + 71HOH H1 212 1.147 0.665 1.887 + 71HOH H2 213 1.218 0.677 1.740 + 72HOH O 214 1.883 0.995 0.795 + 72HOH H1 215 1.882 1.055 0.875 + 72HOH H2 216 1.789 0.979 0.765 + 73HOH O 217 1.261 0.202 0.278 + 73HOH H1 218 1.234 0.226 0.185 + 73HOH H2 219 1.309 0.279 0.320 + 74HOH O 220 0.138 0.431 1.384 + 74HOH H1 221 0.202 0.439 1.460 + 74HOH H2 222 0.135 0.337 1.352 + 75HOH O 223 1.231 0.791 0.752 + 75HOH H1 224 1.275 0.878 0.732 + 75HOH H2 225 1.293 0.734 0.806 + 76HOH O 226 0.071 1.631 0.269 + 76HOH H1 227 0.033 1.670 0.185 + 76HOH H2 228 0.147 1.570 0.246 + 77HOH O 229 0.160 0.236 1.047 + 77HOH H1 230 0.255 0.252 1.021 + 77HOH H2 231 0.157 0.185 1.133 + 78HOH O 232 1.458 1.448 0.464 + 78HOH H1 233 1.484 1.543 0.444 + 78HOH H2 234 1.360 1.444 0.481 + 79HOH O 235 0.449 1.250 0.283 + 79HOH H1 236 0.546 1.228 0.272 + 79HOH H2 237 0.439 1.336 0.332 + 80HOH O 238 0.113 1.558 1.755 + 80HOH H1 239 0.072 1.613 1.682 + 80HOH H2 240 0.208 1.587 1.770 + 81HOH O 241 0.365 0.421 0.927 + 81HOH H1 242 0.451 0.449 0.882 + 81HOH H2 243 0.301 0.498 0.925 + 82HOH O 244 1.439 1.232 0.277 + 82HOH H1 245 1.462 1.288 0.357 + 82HOH H2 246 1.339 1.227 0.268 + 83HOH O 247 1.019 0.524 0.076 + 83HOH H1 248 0.951 0.563 0.013 + 83HOH H2 249 0.975 0.501 0.163 + 84HOH O 250 1.564 0.546 1.174 + 84HOH H1 251 1.584 0.451 1.150 + 84HOH H2 252 1.636 0.581 1.234 + 85HOH O 253 0.617 0.087 1.548 + 85HOH H1 254 0.706 0.051 1.577 + 85HOH H2 255 0.630 0.143 1.465 + 86HOH O 256 1.772 0.396 0.536 + 86HOH H1 257 1.724 0.388 0.449 + 86HOH H2 258 1.841 0.324 0.543 + 87HOH O 259 0.398 0.674 1.746 + 87HOH H1 260 0.408 0.725 1.661 + 87HOH H2 261 0.466 0.706 1.812 + 88HOH O 262 1.396 1.007 1.508 + 88HOH H1 263 1.406 1.008 1.608 + 88HOH H2 264 1.486 1.008 1.465 + 89HOH O 265 0.366 0.124 0.077 + 89HOH H1 266 0.331 0.183 0.150 + 89HOH H2 267 0.292 0.101 0.014 + 90HOH O 268 0.514 0.554 1.390 + 90HOH H1 269 0.511 0.500 1.474 + 90HOH H2 270 0.564 0.639 1.408 + 91HOH O 271 1.575 0.885 0.927 + 91HOH H1 272 1.578 0.942 0.844 + 91HOH H2 273 1.543 0.793 0.902 + 92HOH O 274 1.838 1.463 0.703 + 92HOH H1 275 1.786 1.384 0.671 + 92HOH H2 276 1.910 1.484 0.637 + 93HOH O 277 1.517 1.000 0.374 + 93HOH H1 278 1.616 0.994 0.387 + 93HOH H2 279 1.492 1.096 0.357 + 94HOH O 280 0.967 0.989 0.542 + 94HOH H1 281 1.012 0.905 0.514 + 94HOH H2 282 0.930 0.979 0.634 + 95HOH O 283 1.422 1.287 1.433 + 95HOH H1 284 1.498 1.336 1.477 + 95HOH H2 285 1.452 1.196 1.405 + 96HOH O 286 1.496 0.709 0.495 + 96HOH H1 287 1.453 0.796 0.521 + 96HOH H2 288 1.557 0.679 0.568 + 97HOH O 289 1.538 0.161 1.635 + 97HOH H1 290 1.551 0.256 1.665 + 97HOH H2 291 1.442 0.137 1.641 + 98HOH O 292 0.554 0.834 1.604 + 98HOH H1 293 0.587 0.873 1.518 + 98HOH H2 294 0.522 0.908 1.664 + 99HOH O 295 1.661 1.673 0.286 + 99HOH H1 296 1.635 1.738 0.215 + 99HOH H2 297 1.714 1.720 0.356 + 100HOH O 298 0.383 1.225 0.692 + 100HOH H1 299 0.293 1.187 0.668 + 100HOH H2 300 0.387 1.321 0.665 + 101HOH O 301 0.328 0.250 0.345 + 101HOH H1 302 0.384 0.331 0.364 + 101HOH H2 303 0.367 0.171 0.393 + 102HOH O 304 0.879 0.142 0.534 + 102HOH H1 305 0.915 0.160 0.443 + 102HOH H2 306 0.919 0.207 0.599 + 103HOH O 307 0.625 0.174 1.286 + 103HOH H1 308 0.725 0.178 1.292 + 103HOH H2 309 0.591 0.257 1.242 + 104HOH O 310 0.512 1.770 0.105 + 104HOH H1 311 0.582 1.764 0.176 + 104HOH H2 312 0.456 1.851 0.119 + 105HOH O 313 0.128 1.738 0.835 + 105HOH H1 314 0.157 1.667 0.771 + 105HOH H2 315 0.141 1.706 0.929 + 106HOH O 316 1.504 0.771 0.146 + 106HOH H1 317 1.539 0.855 0.105 + 106HOH H2 318 1.469 0.791 0.237 + 107HOH O 319 1.879 0.052 0.174 + 107HOH H1 320 1.836 -0.032 0.141 + 107HOH H2 321 1.815 0.102 0.233 + 108HOH O 322 1.355 1.642 1.073 + 108HOH H1 323 1.285 1.642 1.144 + 108HOH H2 324 1.312 1.626 0.984 + 109HOH O 325 0.088 1.666 1.105 + 109HOH H1 326 0.020 1.708 1.164 + 109HOH H2 327 0.047 1.588 1.057 + 110HOH O 328 1.787 1.410 0.349 + 110HOH H1 329 1.729 1.483 0.314 + 110HOH H2 330 1.866 1.450 0.396 + 111HOH O 331 0.103 1.034 1.547 + 111HOH H1 332 0.120 1.003 1.453 + 111HOH H2 333 0.060 0.961 1.600 + 112HOH O 334 1.681 1.498 1.111 + 112HOH H1 335 1.587 1.522 1.086 + 112HOH H2 336 1.728 1.463 1.031 + 113HOH O 337 1.809 0.303 1.792 + 113HOH H1 338 1.796 0.402 1.803 + 113HOH H2 339 1.759 0.255 1.863 + 114HOH O 340 1.174 0.126 0.619 + 114HOH H1 341 1.168 0.213 0.570 + 114HOH H2 342 1.173 0.051 0.553 + 115HOH O 343 1.219 1.853 0.415 + 115HOH H1 344 1.221 1.940 0.365 + 115HOH H2 345 1.222 1.777 0.351 + 116HOH O 346 0.060 1.438 0.935 + 116HOH H1 347 0.139 1.377 0.937 + 116HOH H2 348 0.024 1.443 0.842 + 117HOH O 349 0.654 1.243 0.793 + 117HOH H1 350 0.568 1.242 0.741 + 117HOH H2 351 0.668 1.154 0.836 + 118HOH O 352 0.302 0.428 1.591 + 118HOH H1 353 0.305 0.329 1.607 + 118HOH H2 354 0.258 0.473 1.668 + 119HOH O 355 1.833 0.578 0.237 + 119HOH H1 356 1.744 0.552 0.273 + 119HOH H2 357 1.892 0.497 0.231 + 120HOH O 358 1.053 0.933 1.175 + 120HOH H1 359 1.099 1.011 1.133 + 120HOH H2 360 1.077 0.928 1.271 + 121HOH O 361 1.842 1.185 1.010 + 121HOH H1 362 1.747 1.199 1.039 + 121HOH H2 363 1.884 1.273 0.990 + 122HOH O 364 0.009 1.125 0.375 + 122HOH H1 365 -0.039 1.039 0.393 + 122HOH H2 366 -0.031 1.170 0.295 + 123HOH O 367 0.033 0.152 0.544 + 123HOH H1 368 0.077 0.070 0.508 + 123HOH H2 369 0.051 0.158 0.643 + 124HOH O 370 1.208 1.437 0.472 + 124HOH H1 371 1.166 1.347 0.475 + 124HOH H2 372 1.141 1.506 0.501 + 125HOH O 373 0.045 0.850 1.728 + 125HOH H1 374 -0.022 0.785 1.692 + 125HOH H2 375 0.094 0.808 1.804 + 126HOH O 376 1.809 0.580 1.342 + 126HOH H1 377 1.801 0.635 1.425 + 126HOH H2 378 1.899 0.535 1.341 + 127HOH O 379 0.723 0.600 0.019 + 127HOH H1 380 0.640 0.588 0.073 + 127HOH H2 381 0.718 0.545 -0.064 + 128HOH O 382 1.886 1.213 1.303 + 128HOH H1 383 1.937 1.171 1.228 + 128HOH H2 384 1.950 1.258 1.366 + 129HOH O 385 1.794 0.354 1.067 + 129HOH H1 386 1.744 0.306 1.139 + 129HOH H2 387 1.891 0.328 1.071 + 130HOH O 388 0.373 1.214 0.026 + 130HOH H1 389 0.389 1.125 -0.016 + 130HOH H2 390 0.391 1.208 0.124 + 131HOH O 391 1.739 0.253 0.818 + 131HOH H1 392 1.760 0.289 0.909 + 131HOH H2 393 1.821 0.211 0.779 + 132HOH O 394 0.295 1.267 0.973 + 132HOH H1 395 0.347 1.332 1.027 + 132HOH H2 396 0.350 1.235 0.896 + 133HOH O 397 1.197 1.151 0.433 + 133HOH H1 398 1.163 1.173 0.342 + 133HOH H2 399 1.128 1.098 0.482 + 134HOH O 400 1.280 1.694 1.706 + 134HOH H1 401 1.313 1.674 1.798 + 134HOH H2 402 1.349 1.668 1.639 + 135HOH O 403 0.940 1.566 0.474 + 135HOH H1 404 0.899 1.507 0.544 + 135HOH H2 405 0.920 1.661 0.495 + 136HOH O 406 1.494 0.719 1.534 + 136HOH H1 407 1.483 0.623 1.507 + 136HOH H2 408 1.457 0.778 1.462 + 137HOH O 409 1.665 1.292 0.576 + 137HOH H1 410 1.585 1.351 0.562 + 137HOH H2 411 1.723 1.295 0.495 + 138HOH O 412 0.282 0.618 1.248 + 138HOH H1 413 0.211 0.571 1.299 + 138HOH H2 414 0.364 0.627 1.306 + 139HOH O 415 0.123 0.138 1.846 + 139HOH H1 416 0.081 0.100 1.928 + 139HOH H2 417 0.060 0.203 1.803 + 140HOH O 418 0.625 0.462 1.693 + 140HOH H1 419 0.628 0.368 1.726 + 140HOH H2 420 0.534 0.500 1.710 + 141HOH O 421 1.160 1.540 0.826 + 141HOH H1 422 1.072 1.584 0.840 + 141HOH H2 423 1.216 1.597 0.766 + 142HOH O 424 1.302 0.181 0.869 + 142HOH H1 425 1.247 0.144 0.793 + 142HOH H2 426 1.355 0.259 0.837 + 143HOH O 427 0.573 1.463 0.429 + 143HOH H1 428 0.596 1.475 0.333 + 143HOH H2 429 0.653 1.481 0.485 + 144HOH O 430 1.766 0.551 1.871 + 144HOH H1 431 1.672 0.582 1.855 + 144HOH H2 432 1.786 0.556 1.969 + 145HOH O 433 0.593 0.573 0.850 + 145HOH H1 434 0.649 0.573 0.767 + 145HOH H2 435 0.647 0.604 0.927 + 146HOH O 436 0.292 1.814 1.527 + 146HOH H1 437 0.210 1.757 1.536 + 146HOH H2 438 0.366 1.774 1.580 + 147HOH O 439 0.785 1.452 0.690 + 147HOH H1 440 0.754 1.365 0.726 + 147HOH H2 441 0.813 1.512 0.765 + 148HOH O 442 0.839 0.332 1.063 + 148HOH H1 443 0.741 0.317 1.050 + 148HOH H2 444 0.866 0.302 1.154 + 149HOH O 445 0.058 0.589 0.525 + 149HOH H1 446 0.006 0.511 0.560 + 149HOH H2 447 0.040 0.600 0.427 + 150HOH O 448 0.465 1.440 1.135 + 150HOH H1 449 0.405 1.498 1.189 + 150HOH H2 450 0.548 1.419 1.188 + 151HOH O 451 0.728 0.846 0.499 + 151HOH H1 452 0.805 0.909 0.506 + 151HOH H2 453 0.650 0.884 0.549 + 152HOH O 454 1.554 1.304 0.058 + 152HOH H1 455 1.647 1.276 0.080 + 152HOH H2 456 1.491 1.269 0.127 + 153HOH O 457 1.038 1.342 1.540 + 153HOH H1 458 1.095 1.321 1.461 + 153HOH H2 459 1.055 1.275 1.612 + 154HOH O 460 0.141 1.144 0.629 + 154HOH H1 461 0.091 1.068 0.670 + 154HOH H2 462 0.097 1.169 0.543 + 155HOH O 463 0.487 0.968 0.588 + 155HOH H1 464 0.484 1.067 0.603 + 155HOH H2 465 0.437 0.922 0.661 + 156HOH O 466 1.199 1.273 1.267 + 156HOH H1 467 1.220 1.216 1.188 + 156HOH H2 468 1.282 1.290 1.320 + 157HOH O 469 1.574 1.179 1.133 + 157HOH H1 470 1.519 1.098 1.151 + 157HOH H2 471 1.559 1.247 1.204 + 158HOH O 472 1.180 0.305 0.038 + 158HOH H1 473 1.129 0.219 0.026 + 158HOH H2 474 1.115 0.380 0.051 + 159HOH O 475 1.822 1.542 1.345 + 159HOH H1 476 1.762 1.526 1.266 + 159HOH H2 477 1.902 1.483 1.337 + 160HOH O 478 0.621 0.817 1.309 + 160HOH H1 479 0.532 0.861 1.297 + 160HOH H2 480 0.644 0.764 1.228 + 161HOH O 481 1.527 1.801 0.092 + 161HOH H1 482 1.563 1.800 -0.001 + 161HOH H2 483 1.517 1.896 0.122 + 162HOH O 484 0.796 1.638 1.783 + 162HOH H1 485 0.887 1.595 1.780 + 162HOH H2 486 0.744 1.610 1.703 + 163HOH O 487 1.311 1.717 0.656 + 163HOH H1 488 1.368 1.774 0.715 + 163HOH H2 489 1.255 1.775 0.596 + 164HOH O 490 0.583 1.677 1.545 + 164HOH H1 491 0.557 1.650 1.638 + 164HOH H2 492 0.601 1.776 1.544 + 165HOH O 493 1.751 1.734 0.677 + 165HOH H1 494 1.753 1.634 0.680 + 165HOH H2 495 1.842 1.769 0.696 + 166HOH O 496 1.870 1.732 0.008 + 166HOH H1 497 1.921 1.652 -0.022 + 166HOH H2 498 1.797 1.752 -0.057 + 167HOH O 499 0.640 0.987 0.904 + 167HOH H1 500 0.549 0.946 0.892 + 167HOH H2 501 0.666 0.982 1.000 + 168HOH O 502 1.603 0.268 1.221 + 168HOH H1 503 1.569 0.217 1.142 + 168HOH H2 504 1.601 0.210 1.302 + 169HOH O 505 0.906 1.633 1.458 + 169HOH H1 506 0.875 1.614 1.365 + 169HOH H2 507 0.927 1.547 1.504 + 170HOH O 508 1.189 1.250 0.793 + 170HOH H1 509 1.103 1.229 0.841 + 170HOH H2 510 1.193 1.348 0.775 + 171HOH O 511 1.238 0.968 0.029 + 171HOH H1 512 1.178 0.973 0.109 + 171HOH H2 513 1.247 0.873 0.000 + 172HOH O 514 0.686 1.528 0.171 + 172HOH H1 515 0.669 1.439 0.128 + 172HOH H2 516 0.721 1.592 0.102 + 173HOH O 517 1.656 1.405 1.532 + 173HOH H1 518 1.708 1.443 1.456 + 173HOH H2 519 1.719 1.374 1.604 + 174HOH O 520 0.423 1.458 1.499 + 174HOH H1 521 0.436 1.424 1.592 + 174HOH H2 522 0.492 1.528 1.480 + 175HOH O 523 0.353 1.022 1.710 + 175HOH H1 524 0.339 0.932 1.753 + 175HOH H2 525 0.276 1.041 1.648 + 176HOH O 526 0.952 1.355 1.146 + 176HOH H1 527 0.955 1.295 1.066 + 176HOH H2 528 1.025 1.330 1.210 + 177HOH O 529 0.967 0.736 0.400 + 177HOH H1 530 0.873 0.740 0.434 + 177HOH H2 531 0.998 0.640 0.398 + 178HOH O 532 1.339 1.036 0.641 + 178HOH H1 533 1.320 1.041 0.542 + 178HOH H2 534 1.284 1.105 0.688 + 179HOH O 535 1.220 0.037 1.623 + 179HOH H1 536 1.139 0.068 1.673 + 179HOH H2 537 1.247 -0.053 1.656 + 180HOH O 538 1.772 0.914 1.198 + 180HOH H1 539 1.733 0.907 1.106 + 180HOH H2 540 1.821 1.001 1.207 + 181HOH O 541 0.357 0.917 1.252 + 181HOH H1 542 0.319 1.003 1.219 + 181HOH H2 543 0.284 0.850 1.264 + 182HOH O 544 1.095 0.032 0.106 + 182HOH H1 545 1.006 0.005 0.071 + 182HOH H2 546 1.149 -0.050 0.127 + 183HOH O 547 1.638 0.241 0.105 + 183HOH H1 548 1.556 0.294 0.085 + 183HOH H2 549 1.654 0.239 0.203 + 184HOH O 550 1.424 0.409 0.074 + 184HOH H1 551 1.334 0.367 0.061 + 184HOH H2 552 1.432 0.489 0.013 + 185HOH O 553 1.141 0.374 0.507 + 185HOH H1 554 1.111 0.454 0.560 + 185HOH H2 555 1.235 0.387 0.477 + 186HOH O 556 1.414 1.560 0.025 + 186HOH H1 557 1.465 1.473 0.022 + 186HOH H2 558 1.475 1.633 0.055 + 187HOH O 559 0.162 1.409 1.425 + 187HOH H1 560 0.259 1.423 1.448 + 187HOH H2 561 0.113 1.379 1.506 + 188HOH O 562 0.051 0.764 0.094 + 188HOH H1 563 -0.001 0.837 0.139 + 188HOH H2 564 0.026 0.676 0.135 + 189HOH O 565 0.780 0.301 0.100 + 189HOH H1 566 0.735 0.335 0.182 + 189HOH H2 567 0.713 0.293 0.026 + 190HOH O 568 0.386 1.643 1.804 + 190HOH H1 569 0.424 1.550 1.798 + 190HOH H2 570 0.433 1.693 1.876 + 191HOH O 571 0.797 0.516 0.631 + 191HOH H1 572 0.761 0.518 0.538 + 191HOH H2 573 0.895 0.539 0.630 + 192HOH O 574 0.518 0.805 0.318 + 192HOH H1 575 0.596 0.824 0.377 + 192HOH H2 576 0.445 0.871 0.336 + 193HOH O 577 0.532 0.404 1.163 + 193HOH H1 578 0.476 0.443 1.090 + 193HOH H2 579 0.519 0.456 1.247 + 194HOH O 580 0.918 0.322 0.803 + 194HOH H1 581 0.853 0.367 0.742 + 194HOH H2 582 0.885 0.328 0.897 + 195HOH O 583 0.625 1.620 0.963 + 195HOH H1 584 0.606 1.715 0.990 + 195HOH H2 585 0.566 1.558 1.015 + 196HOH O 586 1.472 0.375 0.769 + 196HOH H1 587 1.569 0.366 0.790 + 196HOH H2 588 1.459 0.450 0.705 + 197HOH O 589 0.804 1.893 0.016 + 197HOH H1 590 0.794 1.803 -0.028 + 197HOH H2 591 0.716 1.941 0.012 + 198HOH O 592 0.763 0.617 1.051 + 198HOH H1 593 0.842 0.677 1.037 + 198HOH H2 594 0.794 0.526 1.076 + 199HOH O 595 1.608 0.049 1.388 + 199HOH H1 596 1.588 0.091 1.477 + 199HOH H2 597 1.535 -0.014 1.363 + 200HOH O 598 1.605 1.044 0.705 + 200HOH H1 599 1.509 1.025 0.684 + 200HOH H2 600 1.630 1.133 0.668 + 201HOH O 601 0.510 0.468 0.424 + 201HOH H1 602 0.457 0.536 0.476 + 201HOH H2 603 0.526 0.502 0.332 + 202HOH O 604 1.661 0.586 0.705 + 202HOH H1 605 1.709 0.526 0.641 + 202HOH H2 606 1.712 0.590 0.791 + 203HOH O 607 0.300 0.868 0.062 + 203HOH H1 608 0.340 0.903 0.147 + 203HOH H2 609 0.216 0.818 0.083 + 204HOH O 610 1.661 1.029 1.443 + 204HOH H1 611 1.734 1.097 1.446 + 204HOH H2 612 1.680 0.962 1.370 + 205HOH O 613 0.980 0.158 1.719 + 205HOH H1 614 0.947 0.239 1.670 + 205HOH H2 615 0.912 0.131 1.788 + 206HOH O 616 1.838 0.093 1.557 + 206HOH H1 617 1.789 0.180 1.555 + 206HOH H2 618 1.897 0.090 1.638 + 207HOH O 619 1.139 0.505 0.956 + 207HOH H1 620 1.126 0.406 0.949 + 207HOH H2 621 1.221 0.523 1.011 + 208HOH O 622 1.291 0.771 1.329 + 208HOH H1 623 1.280 0.682 1.283 + 208HOH H2 624 1.204 0.798 1.370 + 209HOH O 625 1.091 0.103 1.122 + 209HOH H1 626 1.168 0.160 1.152 + 209HOH H2 627 1.088 0.101 1.022 + 210HOH O 628 1.442 1.065 1.789 + 210HOH H1 629 1.382 1.026 1.859 + 210HOH H2 630 1.453 1.163 1.806 + 211HOH O 631 0.829 1.788 0.562 + 211HOH H1 632 0.861 1.883 0.569 + 211HOH H2 633 0.794 1.758 0.650 + 212HOH O 634 0.134 1.538 0.544 + 212HOH H1 635 0.231 1.519 0.559 + 212HOH H2 636 0.122 1.582 0.455 + 213HOH O 637 0.124 0.148 1.329 + 213HOH H1 638 0.212 0.137 1.376 + 213HOH H2 639 0.050 0.132 1.394 + 214HOH O 640 1.289 1.665 0.254 + 214HOH H1 641 1.328 1.655 0.162 + 214HOH H2 642 1.303 1.581 0.306 + 215HOH O 643 1.284 0.269 1.513 + 215HOH H1 644 1.227 0.335 1.562 + 215HOH H2 645 1.252 0.176 1.532 + 216HOH O 646 0.178 1.847 0.446 + 216HOH H1 647 0.156 1.809 0.356 + 216HOH H2 648 0.276 1.868 0.450 + 217HOH O 649 1.806 1.872 1.224 + 217HOH H1 650 1.755 1.892 1.308 + 217HOH H2 651 1.859 1.953 1.198 + 218HOH O 652 1.039 0.970 0.237 + 218HOH H1 653 1.040 0.898 0.307 + 218HOH H2 654 0.972 1.040 0.263 + 219HOH O 655 0.560 0.086 0.864 + 219HOH H1 656 0.559 0.043 0.954 + 219HOH H2 657 0.490 0.158 0.860 + 220HOH O 658 0.791 1.006 1.206 + 220HOH H1 659 0.884 0.973 1.190 + 220HOH H2 660 0.744 0.945 1.269 + 221HOH O 661 0.904 1.172 0.340 + 221HOH H1 662 0.921 1.144 0.435 + 221HOH H2 663 0.948 1.260 0.324 + 1.89868 1.89868 1.89868 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/test/data/water.map b/tests/data/water.map similarity index 100% rename from test/data/water.map rename to tests/data/water.map diff --git a/test/data/water.pdb b/tests/data/water.pdb similarity index 100% rename from test/data/water.pdb rename to tests/data/water.pdb diff --git a/test/data/water.xtc b/tests/data/water.xtc similarity index 100% rename from test/data/water.xtc rename to tests/data/water.xtc diff --git a/tests/data/water_double_weight.map b/tests/data/water_double_weight.map new file mode 100644 index 0000000..d147162 --- /dev/null +++ b/tests/data/water_double_weight.map @@ -0,0 +1,2 @@ +[SOL] +W P4 OW HW1 HW1 HW2 HW2 diff --git a/tests/test_bondset.py b/tests/test_bondset.py new file mode 100644 index 0000000..b4bf52c --- /dev/null +++ b/tests/test_bondset.py @@ -0,0 +1,304 @@ +import math +import os +import pathlib +import tempfile +import unittest + +from pycgtool.bondset import BondSet +from pycgtool.frame import Frame +from pycgtool.mapping import Mapping +from pycgtool.util import cmp_file_whitespace_float + + +class DummyOptions: + constr_threshold = 100000 + map_center = "geom" + virtual_map_center = "geom" + angle_default_fc = False + generate_angles = True + generate_dihedrals = False + + +class DummyBond: + def __init__(self, atoms, eqm, fconst, values=None): + self.atoms = atoms + self.eqm = eqm + self.fconst = fconst + self.values = [] if values is None else values + + def __iter__(self): + return iter(self.atoms) + + +# TODO add setup and teardown to put all files in a tmp directory +class BondSetTest(unittest.TestCase): + base_dir = pathlib.Path(__file__).absolute().parent + data_dir = base_dir.joinpath("data") + invert_test_ref_data = [ + ( 0.220474419132, 72658.18163, 1250), + ( 0.221844516963, 64300.01188, 1250), + ( 0.216313356504, 67934.93368, 1250), + ( 0.253166204438, 19545.27388, 1250), + ( 0.205958461836, 55359.06367, 1250), + ( 0.180550961226, 139643.66601, 1250), + ( 1.359314249473, 503.24211, 25), + ( 2.026002746003, 837.76904, 25), + ( 1.937848056214, 732.87969, 25), + ( 1.453592079716, 945.32633, 25), + ( 2.504189933347, 771.63691, 25), + ( 1.733002945619, 799.82825, 25), + ( 1.695540843207, 253.75691, 50), + (-2.074156183261, 125.04591, 50), + ( 2.768063749729, 135.50927, 50), + (-2.213755550432, 51.13975, 50), + ( 1.456495664734, 59.38162, 50), + (-1.826134298998, 279.80889, 50), + ] # fmt: skip + + def test_bondset_create(self): + measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions) + self.assertEqual(1, len(measure)) + self.assertTrue("ALLA" in measure) + self.assertEqual(18, len(measure["ALLA"])) + + def test_bondset_apply(self): + measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions) + frame = Frame(self.data_dir.joinpath("sugar-cg.gro")) + measure.apply(frame) + + # First six are bond lengths + self.assertEqual(1, len(measure["ALLA"][0].values)) + self.assertAlmostEqual( + 0.2225376, measure["ALLA"][0].values[0], delta=0.2225376 / 500 + ) + # Second six are angles + self.assertEqual(1, len(measure["ALLA"][6].values)) + expected = math.radians(77.22779289) + self.assertAlmostEqual( + expected, measure["ALLA"][6].values[0], delta=expected / 500 + ) + # Final six are dihedrals + self.assertEqual(1, len(measure["ALLA"][12].values)) + expected = math.radians(-89.5552903) + self.assertAlmostEqual( + expected, measure["ALLA"][12].values[0], delta=abs(expected) / 500 + ) + + def test_bondset_remove_triangles(self): + bondset = BondSet(self.data_dir.joinpath("triangle.bnd"), DummyOptions) + angles = bondset.get_bond_angles("TRI", exclude_triangle=False) + self.assertEqual(3, len(angles)) + angles = bondset.get_bond_angles("TRI", exclude_triangle=True) + self.assertEqual(0, len(angles)) + + def support_check_mean_fc(self, mol_bonds, fc_column_number): + # Require accuracy to 0.5% + # Allows for slight modifications to code + accuracy = 0.005 + + for i, bond in enumerate(mol_bonds): + ref = self.invert_test_ref_data + self.assertAlmostEqual(ref[i][0], bond.eqm, delta=abs(ref[i][0] * accuracy)) + self.assertAlmostEqual( + ref[i][fc_column_number], + bond.fconst, + delta=abs(ref[i][fc_column_number] * accuracy), + ) + + def test_bondset_boltzmann_invert(self): + measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions) + frame = Frame( + self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc") + ) + mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions) + + cg_frame = mapping.apply(frame) + + measure.apply(cg_frame) + measure.boltzmann_invert() + + self.support_check_mean_fc(measure["ALLA"], 1) + + def test_bondset_boltzmann_invert_default_fc(self): + class DefaultOptions(DummyOptions): + default_fc = True + + measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DefaultOptions) + frame = Frame( + self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc") + ) + mapping = Mapping(self.data_dir.joinpath("sugar.map"), DefaultOptions) + + cg_frame = mapping.apply(frame) + + measure.apply(cg_frame) + measure.boltzmann_invert() + + self.support_check_mean_fc(measure["ALLA"], 2) + + def test_bondset_boltzmann_invert_manual_default_fc(self): + class FuncFormOptions(DummyOptions): + length_form = "MartiniDefaultLength" + angle_form = "MartiniDefaultAngle" + dihedral_form = "MartiniDefaultDihedral" + + measure = BondSet(self.data_dir.joinpath("sugar.bnd"), FuncFormOptions) + frame = Frame( + self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc") + ) + mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions) + + cg_frame = mapping.apply(frame) + + measure.apply(cg_frame) + measure.boltzmann_invert() + + self.support_check_mean_fc(measure["ALLA"], 2) + + def test_bondset_polymer(self): + bondset = BondSet(self.data_dir.joinpath("polyethene.bnd"), DummyOptions) + frame = Frame(self.data_dir.joinpath("polyethene.gro")) + bondset.apply(frame) + + self.assertEqual(5, len(bondset["ETH"][0].values)) + self.assertEqual(4, len(bondset["ETH"][1].values)) + self.assertEqual(4, len(bondset["ETH"][2].values)) + self.assertEqual(4, len(bondset["ETH"][3].values)) + + bondset.boltzmann_invert() + + self.assertAlmostEqual(0.107, bondset["ETH"][0].eqm, delta=0.107 / 500) + self.assertAlmostEqual(0.107, bondset["ETH"][1].eqm, delta=0.107 / 500) + + def test_bondset_pbc(self): + bondset = BondSet(self.data_dir.joinpath("polyethene.bnd"), DummyOptions) + frame = Frame(self.data_dir.joinpath("pbcpolyethene.gro")) + + bondset.apply(frame) + bondset.boltzmann_invert() + + for bond in bondset.get_bond_lengths("ETH", True): + self.assertAlmostEqual(1.0, bond.eqm) + self.assertEqual(math.inf, bond.fconst) + + def test_full_itp_sugar(self): + measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions) + frame = Frame( + self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc") + ) + mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions) + + cg_frame = mapping.apply(frame) + + measure.apply(cg_frame) + measure.boltzmann_invert() + + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + + measure.write_itp(tmp_path.joinpath("sugar_out.itp"), mapping) + + self.assertTrue( + cmp_file_whitespace_float( + tmp_path.joinpath("sugar_out.itp"), + self.data_dir.joinpath("sugar_out.itp"), + rtol=0.005, + verbose=True, + ) + ) + + def test_full_itp_vsites(self): + """Test full operation to output of .itp file for molecule with vsites.""" + options = DummyOptions() + options.generate_angles = False + + measure = BondSet(self.data_dir.joinpath("martini3/naphthalene.bnd"), options) + frame = Frame(self.data_dir.joinpath("martini3/naphthalene.gro")) + mapping = Mapping(self.data_dir.joinpath("martini3/naphthalene.map"), options) + + cg_frame = mapping.apply(frame) + + measure.apply(cg_frame) + measure.boltzmann_invert() + + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + measure.write_itp(tmp_path.joinpath("naphthalene_out.itp"), mapping) + + self.assertTrue( + cmp_file_whitespace_float( + tmp_path.joinpath("naphthalene_out.itp"), + self.data_dir.joinpath("martini3/naphthalene_out.itp"), + rtol=0.005, + verbose=True, + ) + ) + + def test_duplicate_atoms_in_bond(self): + with self.assertRaises(ValueError): + _ = BondSet(self.data_dir.joinpath("duplicate_atoms.bnd"), DummyOptions) + + def test_dump_bonds(self): + measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions) + frame = Frame( + self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.xtc") + ) + mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions) + + cg_frame = mapping.apply(frame) + + measure.apply(cg_frame) + measure.boltzmann_invert() + measure.dump_values() + + filenames = ("ALLA_length.dat", "ALLA_angle.dat", "ALLA_dihedral.dat") + for filename in filenames: + self.assertTrue( + cmp_file_whitespace_float( + self.data_dir.joinpath(filename), filename, rtol=0.008, verbose=True + ) + ) + os.remove(filename) + + def test_get_lines_for_bond_dump(self): + expected = [ + " 0.00000 1.00000 2.00000", + " 1.00000 2.00000 3.00000", + " 2.00000 3.00000 4.00000", + " 3.00000 4.00000 5.00000", + ] + + bonds = [ + DummyBond(None, None, None, values=[0, 1, 2, 3]), + DummyBond(None, None, None, values=[1, 2, 3, 4]), + DummyBond(None, None, None, values=[2, 3, 4, 5]), + ] + + output = BondSet._get_lines_for_bond_dump(bonds) + + self.assertListEqual(expected, output) + + def test_get_lines_for_bond_dump_sample(self): + expected = [ + " 0.00000 1.00000 2.00000", + " 1.00000 2.00000 3.00000", + " 2.00000 3.00000 4.00000", + " 3.00000 4.00000 5.00000", + ] + + bonds = [ + DummyBond(None, None, None, values=[0, 1, 2, 3]), + DummyBond(None, None, None, values=[1, 2, 3, 4]), + DummyBond(None, None, None, values=[2, 3, 4, 5]), + ] + + nlines = 2 + output = BondSet._get_lines_for_bond_dump(bonds, target_number=nlines) + + self.assertEqual(nlines, len(output)) + + seen = set() + for line in output: + self.assertIn(line, expected) + self.assertNotIn(line, seen) + seen.add(line) diff --git a/tests/test_forcefield.py b/tests/test_forcefield.py new file mode 100644 index 0000000..30e0c11 --- /dev/null +++ b/tests/test_forcefield.py @@ -0,0 +1,143 @@ +import collections +import pathlib +import tempfile +import unittest + +from pycgtool.forcefield import ForceField + +DummyBMap = collections.namedtuple("DummyBMap", ["name", "type", "charge"]) + + +class DummyBond: + def __init__(self, atoms, eqm, fconst): + self.atoms = atoms + self.eqm = eqm + self.fconst = fconst + + def __iter__(self): + return iter(self.atoms) + + +class DummyBondSet: + def __init__(self, bonds, name): + self.bonds = bonds + self.name = name + + def __contains__(self, item): + return self.name == item + + def get_bonds(self, mol, natoms, select=lambda x: True): + if natoms == -1: + return [bond for bond in self.bonds if select(bond)] + return [ + bond for bond in self.bonds if len(bond.atoms) == natoms and select(bond) + ] + + def get_bond_lengths(self, *args, **kwargs): + return self.get_bonds(None, 2) + + def get_bond_angles(self, *args, **kwargs): + return self.get_bonds(None, 3) + + def get_bond_dihedrals(self, *args, **kwargs): + return self.get_bonds(None, 4) + + +class ForceFieldTest(unittest.TestCase): + def setUp(self): + self.bonds = [ + DummyBond(["a", "b"], 1, 100), + DummyBond(["b", "c"], 2, 50), + DummyBond(["c", "+a"], 3, 20), + ] + + self.mapping = { + "Dummy": [ + DummyBMap("a", "a1", 1), + DummyBMap("b", "b2", -1), + DummyBMap("c", "c3", 0), + ] + } + + self.bondset = DummyBondSet(self.bonds, "Dummy") + + def test_create(self): + with tempfile.TemporaryDirectory() as t: + tmp_dir = pathlib.Path(t) + + name = "test" + ff_dir = tmp_dir.joinpath("fftest.ff") + + ForceField(name, dir_path=tmp_dir) + self.assertTrue(ff_dir.exists()) + self.assertTrue(ff_dir.is_dir()) + + # Makes a backup of the existing ff and replaces it + ForceField(name, dir_path=tmp_dir) + + def test_bond_section(self): + expected = [ + " [ section ]", + " a b 1.00000 100.00000", + " b c 2.00000 50.00000", + " c +a 3.00000 20.00000", + ] + + self.assertListEqual(expected, ForceField.bond_section(self.bonds, "section")) + + def test_r2b(self): + nter = {"a", "b", "d"} + cter = {"a", "c", "d"} + + expected = [ + "; rtp residue to rtp building block table", + "; main N-ter C-ter 2-ter", + "a a Na Ca 2a ", + "b b Nb - - ", + "c c - Cc - ", + "d d Nd Cd 2d ", + ] + + output = ForceField.write_r2b(nter, cter) + self.assertListEqual(expected, output) + + def test_rtp(self): + expected = [ + "[ bondedtypes ]", + " 1 1 1 1 1 1 0 0", + "[ Dummy ]", + " [ atoms ]", + " a a1 1.000000 0", + " b b2 -1.000000 0", + " c c3 0.000000 0", + " [ bonds ]", + " a b 1.00000 100.00000", + " b c 2.00000 50.00000", + " c +a 3.00000 20.00000", + "[ CDummy ]", + " [ atoms ]", + " a a1 1.000000 0", + " b b2 -1.000000 0", + " c c3 0.000000 0", + " [ bonds ]", + " a b 1.00000 100.00000", + " b c 2.00000 50.00000", + ] + + output, nter, cter = ForceField.write_rtp(self.mapping, self.bondset) + + self.maxDiff = None + self.assertListEqual(expected, output) + + self.assertFalse(nter) + self.assertEqual({"Dummy"}, cter) + + def test_needs_terminal_entries(self): + nter, cter = ForceField.needs_terminal_entries(self.mapping, self.bondset) + + self.assertFalse(nter) + self.assertTrue(cter) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/test_frame.py b/tests/test_frame.py new file mode 100644 index 0000000..fafb8db --- /dev/null +++ b/tests/test_frame.py @@ -0,0 +1,183 @@ +import filecmp +import os +import pathlib +import unittest +import tempfile + +import numpy as np + +from pycgtool.frame import NonMatchingSystemError, UnsupportedFormatException +from pycgtool.frame import Frame +from pycgtool import util + + +def try_remove(filename) -> None: + try: + os.remove(filename) + + except IOError: + pass + + +# TODO add ITP parsing tests +class FrameTest(unittest.TestCase): + base_dir = pathlib.Path(__file__).absolute().parent + data_dir = base_dir.joinpath("data") + + def check_reference_topology(self, frame, skip_names=True): + self.assertEqual(663, frame.natoms) + + residue = frame.residue(0) + + self.assertEqual(221, len(list(frame.residues))) + self.assertEqual(3, residue.n_atoms) + + if not skip_names: # MDTraj renames water + self.assertEqual("SOL", residue.name) + self.assertEqual("OW", residue.atom(0).name) + + def check_reference_frame(self, frame, check_box: bool = True): + self.check_reference_topology(frame) + + atom0_coords = np.array([[0.696, 1.330, 1.211]]) + box_vectors = np.array([[1.89868, 1.89868, 1.89868]]) + + np.testing.assert_allclose(atom0_coords, frame.atom(0).coords) + if check_box: + np.testing.assert_allclose( + box_vectors, frame.unitcell_lengths, rtol=1e-4 + ) # PDB files are f9.3 + + def check_reference_trajectory(self, frame): + self.check_reference_topology(frame) + atom0_coords = np.array( + [ + [1.176 , 1.1520001 , 1.5860001 ], + [1.1220001 , 1.13 , 1.534 ], + [1.0580001 , 1.1620001 , 1.462 ], + [0.91600007, 1.276 , 1.5580001 ], + [0.73200005, 1.1240001 , 1.286 ], + [0.64000005, 1.2160001 , 1.258 ], + [0.632 , 1.312 , 1.2520001 ], + [0.606 , 1.284 , 1.246 ], + [0.582 , 1.312 , 1.1600001 ], + [0.68200004, 1.22 , 1.25 ], + [0.69600004, 1.33 , 1.21 ], + ], + dtype=np.float32, + ) # fmt: skip + unitcell_lengths = np.array( + [ + [1.9052 , 1.9052 , 1.9052 ], + [1.9032527, 1.9032527, 1.9032527], + [1.9040661, 1.9040661, 1.9040661], + [1.896811 , 1.896811 , 1.896811 ], + [1.8985983, 1.8985983, 1.8985983], + [1.9033976, 1.9033976, 1.9033976], + [1.8904614, 1.8904614, 1.8904614], + [1.9013108, 1.9013108, 1.9013108], + [1.8946321, 1.8946321, 1.8946321], + [1.898091 , 1.898091 , 1.898091 ], + [1.898684 , 1.898684 , 1.898684 ], + ], + dtype=np.float32, + ) # fmt: skip + + np.testing.assert_allclose(atom0_coords, frame.atom(0).coords) + np.testing.assert_allclose( + unitcell_lengths, frame.unitcell_lengths, rtol=1e-4 + ) # PDB files are f9.3 + + def test_frame_create(self): + Frame() + + def test_frame_add_residue(self): + frame = Frame() + residue = frame.add_residue("TEST_RESIDUE") + + self.assertTrue(residue is frame.residue(0)) + + def test_frame_read_gro(self): + frame = Frame(self.data_dir.joinpath("water.gro")) + + self.check_reference_frame(frame) + + def test_frame_read_pdb(self): + frame = Frame(self.data_dir.joinpath("water.pdb")) + + self.check_reference_frame(frame) + + def test_frame_read_pdb_nobox(self): + """Test reading a PDB with zero box volume.""" + frame = Frame(self.data_dir.joinpath("water-nobox.pdb")) + + self.check_reference_frame(frame, check_box=False) + + def test_frame_read_zero_box(self): + frame = Frame(self.data_dir.joinpath("polyethene.gro")) + self.assertIsNone(frame.unitcell_lengths) + + def test_frame_any_read_unsupported(self): + with self.assertRaises(UnsupportedFormatException): + _ = Frame(self.data_dir.joinpath("dppc.map")) + + def test_frame_output_gro(self): + frame = Frame(self.data_dir.joinpath("water.gro")) + + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + + frame.save(tmp_path.joinpath("water-out.gro")) + self.assertTrue( + filecmp.cmp( + self.data_dir.joinpath("water.gro"), + tmp_path.joinpath("water-out.gro"), + ) + ) + + def test_frame_read_xtc_numframes(self): + frame = Frame( + self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("water.xtc") + ) + self.assertEqual(11, frame.n_frames) + + def test_frame_read_xtc(self): + frame = Frame( + self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("water.xtc") + ) + + self.check_reference_trajectory(frame) + + def test_frame_accept_path(self): + """Test that Frame accepts :class:`pathlib.Path` arguments.""" + _ = Frame( + self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("water.xtc") + ) + + def test_frame_write_xtc(self): + """Test that :class:`Frame` can save a trajectory file.""" + frame = Frame( + self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("water.xtc") + ) + + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + + frame.save(tmp_path.joinpath("water.xtc")) + self.assertTrue( + util.compare_trajectories( + self.data_dir.joinpath("water.xtc"), + tmp_path.joinpath("water.xtc"), + topology_file=self.data_dir.joinpath("water.gro"), + ) + ) + + def test_raise_nonmatching_system_mdtraj(self): + with self.assertRaises(NonMatchingSystemError): + _ = Frame( + self.data_dir.joinpath("water.gro"), self.data_dir.joinpath("sugar.xtc") + ) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/test_functionalforms.py b/tests/test_functionalforms.py new file mode 100644 index 0000000..f8b13d6 --- /dev/null +++ b/tests/test_functionalforms.py @@ -0,0 +1,68 @@ +import unittest + +import numpy as np + +from pycgtool.functionalforms import FunctionalForm, get_functional_forms +from pycgtool.util import circular_mean, circular_variance + + +class FunctionalFormTest(unittest.TestCase): + def test_functional_form(self): + funcs = get_functional_forms() + + harmonic_form = funcs.Harmonic + self.assertIsNotNone(harmonic_form) + + cos_harmonic_form = funcs.CosHarmonic + self.assertIsNotNone(cos_harmonic_form) + + def test_functional_form_new(self): + class TestFunc(FunctionalForm): + gromacs_type_ids = (None, None, None) + + @staticmethod + def eqm(values, temp): + return "TestResultEqm" + + @staticmethod + def fconst(values, temp): + return "TestResultFconst" + + funcs = get_functional_forms() + test_func = funcs["TestFunc"].value + + self.assertEqual("TestResultEqm", test_func.eqm(None, None)) + self.assertEqual("TestResultFconst", test_func.fconst(None, None)) + + def test_inject_mean_function(self): + """ + Test injecting mean function into Boltzmann Inversion + """ + funcs = get_functional_forms() + vals = [0.25 * np.pi, 1.75 * np.pi] + + func = funcs["Harmonic"].value() + + np.testing.assert_allclose(func.eqm(vals, None), np.pi) + + func = funcs["Harmonic"].value(mean_func=circular_mean) + + np.testing.assert_allclose(func.eqm(vals, None), 0, atol=1e-6) + + def test_inject_variance_function(self): + """ + Test injecting variance function into Boltzmann Inversion + """ + funcs = get_functional_forms() + + func = funcs["Harmonic"].value(variance_func=circular_variance) + + vals = [0, 0.5 * np.pi] + ref = func.fconst(vals, 300) + + vals = [0.25 * np.pi, 1.75 * np.pi] + np.testing.assert_allclose(func.fconst(vals, 300), ref, atol=0) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/test_mapping.py b/tests/test_mapping.py new file mode 100644 index 0000000..273f647 --- /dev/null +++ b/tests/test_mapping.py @@ -0,0 +1,258 @@ +import filecmp +import os +import pathlib +import unittest + +import numpy as np + +from pycgtool.mapping import BeadMap, Mapping, VirtualMap +from pycgtool.frame import Frame + + +class DummyOptions: + map_center = "geom" + virtual_map_center = "geom" + + +class BeadMapTest(unittest.TestCase): + def test_beadmap_create(self): + """Test that a BeadMap can be created.""" + bead = BeadMap("BEAD", 1, atoms=["ATOM1", "ATOM2"]) + + self.assertEqual("BEAD", bead.name) + self.assertEqual(1, bead.num) + + self.assertEqual(2, len(bead)) + self.assertEqual("ATOM1", bead[0]) + self.assertEqual("ATOM2", bead[1]) + + def test_beadmap_guess_masses(self): + """Test that masses can be assigned from atom names.""" + bead = BeadMap("BEAD", 1, atoms=["C1", "H1", "H2"]) + bead.guess_atom_masses() + + # Total mass of bead + self.assertEqual(14, int(bead.mass)) + + # Contribution of each atom to bead mass + np.testing.assert_allclose( + np.array([12, 1, 1]) / 14, bead.weights_dict["mass"], rtol=0.01 + ) # Account for 1% error in approximate masses + + +class MappingTest(unittest.TestCase): + base_dir = pathlib.Path(__file__).absolute().parent + data_dir = base_dir.joinpath("data") + + def test_mapping_create(self): + """Test that a mapping can be correctly read from a file.""" + mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions) + self.assertEqual(2, len(mapping)) # SOL and HOH + self.assertTrue("SOL" in mapping) + + sol_map = mapping["SOL"] + + self.assertEqual(1, len(sol_map)) + self.assertEqual(3, len(sol_map[0].atoms)) + self.assertEqual("OW", sol_map[0].atoms[0]) + self.assertEqual("HW1", sol_map[0].atoms[1]) + self.assertEqual("HW2", sol_map[0].atoms[2]) + + def test_mapping_rename(self): + """Test that an alternate mapping is created using MDTraj conventions.""" + mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions) + self.assertEqual(2, len(mapping)) # SOL and HOH + self.assertTrue("HOH" in mapping) + + sol_map = mapping["HOH"] + + self.assertEqual(1, len(sol_map)) + self.assertEqual(3, len(sol_map[0].atoms)) + self.assertEqual("O", sol_map[0].atoms[0]) + self.assertEqual("H1", sol_map[0].atoms[1]) + self.assertEqual("H2", sol_map[0].atoms[2]) + + def test_virtual_mapping_create(self): + mapping = Mapping( + self.data_dir.joinpath("martini3/naphthalene.map"), DummyOptions + ) + self.assertEqual(1, len(mapping)) + self.assertTrue("NAPH" in mapping) + self.assertEqual(5, len(mapping["NAPH"])) + self.assertTrue(isinstance(mapping["NAPH"][2], VirtualMap)) + self.assertEqual(4, len(mapping["NAPH"][2].atoms)) + self.assertEqual("R1", mapping["NAPH"][2].atoms[0]) + self.assertEqual( + 1, [isinstance(bead, VirtualMap) for bead in mapping["NAPH"]].count(True) + ) + + def test_mapping_apply(self): + mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions) + frame = Frame(self.data_dir.joinpath("water.gro")) + cg_frame = mapping.apply(frame) + + self.assertEqual(frame.natoms / 3, cg_frame.natoms) + + cg_frame.save("water-cg.gro") + + self.assertTrue( + filecmp.cmp(self.data_dir.joinpath("water-cg.gro"), "water-cg.gro") + ) + os.remove("water-cg.gro") + + def test_mapping_duplicate_atom_weight(self): + """Test that an atom can be duplicated in a bead specification to act as a weighting.""" + frame = Frame(self.data_dir.joinpath("water.gro")) + + mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[0.716, 1.300, 1.198]]), + cg_frame.residue(0).atom(0).coords, + atol=0.0005, + ) + + mapping = Mapping( + self.data_dir.joinpath("water_double_weight.map"), DummyOptions + ) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[0.720, 1.294, 1.195]]), + cg_frame.residue(0).atom(0).coords, + atol=0.0005, + ) + + def test_mapping_charges(self): + mapping = Mapping(self.data_dir.joinpath("dppc.map"), DummyOptions) + self.assertEqual(1, mapping["DPPC"][0].charge) + self.assertEqual(-1, mapping["DPPC"][1].charge) + + def test_mapping_pbc(self): + frame = Frame(self.data_dir.joinpath("pbcwater.gro")) + + mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose(frame.atom(0).coords, cg_frame.atom(0).coords) + + def test_mapping_weights_geom(self): + frame = Frame(self.data_dir.joinpath("two.gro")) + + mapping = Mapping(self.data_dir.joinpath("two.map"), DummyOptions) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[1.5, 1.5, 1.5]]), cg_frame.residue(0).atom(0).coords + ) + + def test_virtual_mapping_weights_geom(self): + frame = Frame(self.data_dir.joinpath("martini3/four.gro")) + + mapping = Mapping(self.data_dir.joinpath("martini3/four.map"), DummyOptions) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[2.5, 2.5, 2.5]]), cg_frame.residue(0).atom(2).coords + ) + + def test_mapping_weights_mass(self): + frame = Frame(self.data_dir.joinpath("two.gro")) + options = DummyOptions() + options.map_center = "mass" + + mapping = Mapping( + self.data_dir.joinpath("two.map"), + options, + itp_filename=self.data_dir.joinpath("two.itp"), + ) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[2.0, 2.0, 2.0]]), cg_frame.residue(0).atom(0).coords + ) + + def test_virtual_mapping_weights_mass(self): + frame = Frame(self.data_dir.joinpath("martini3/four.gro")) + options = DummyOptions() + options.virtual_map_center = "mass" + + mapping = Mapping( + self.data_dir.joinpath("martini3/four.map"), + options, + itp_filename=self.data_dir.joinpath("martini3/four.itp"), + ) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[3.0, 3.0, 3.0]]), cg_frame.residue(0).atom(2).coords + ) + + def test_mapping_weights_guess_mass(self): + frame = Frame(self.data_dir.joinpath("two.gro")) + options = DummyOptions() + options.map_center = "mass" + + mapping = Mapping(self.data_dir.joinpath("two.map"), options) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[1.922575, 1.922575, 1.922575]], dtype=np.float32), + cg_frame.residue(0).atom(0).coords, + rtol=0.01, + ) + + def test_virtual_mapping_weights_guess_mass(self): + frame = Frame(self.data_dir.joinpath("martini3/four.gro")) + options = DummyOptions() + options.virtual_map_center = "mass" + + mapping = Mapping(self.data_dir.joinpath("martini3/four.map"), options) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[2.83337, 2.83337, 2.83337]], dtype=np.float32), + cg_frame.residue(0).atom(2).coords, + rtol=0.01, + ) + + def test_mapping_weights_first(self): + frame = Frame(self.data_dir.joinpath("two.gro")) + options = DummyOptions() + options.map_center = "first" + + mapping = Mapping( + self.data_dir.joinpath("two.map"), + options, + itp_filename=self.data_dir.joinpath("two.itp"), + ) + cg_frame = mapping.apply(frame) + + np.testing.assert_allclose( + np.array([[1.0, 1.0, 1.0]]), cg_frame.residue(0).atom(0).coords + ) + + def test_mapping_itp_multi(self): + mapping = Mapping( + self.data_dir.joinpath("membrane/membrane.map"), + DummyOptions, + itp_filename=self.data_dir.joinpath("membrane/membrane.top"), + ) + self.assertAlmostEqual(-1.2, mapping["POPE"][0].charge, delta=0.0001) + self.assertAlmostEqual(0, mapping["POPG"][0].charge, delta=0.0001) + + self.assertAlmostEqual(94.9716, mapping["POPE"][0].mass, delta=0.0001) + + def test_empty_result_frame(self): + """Test that no error is raised when an empty output frame is encountered. + + This is instead checked and logged as a warning in the outer script. + """ + frame = Frame(self.data_dir.joinpath("sugar.gro")) + mapping = Mapping(self.data_dir.joinpath("water.map"), DummyOptions) + + cg_frame = mapping.apply(frame) + + self.assertEqual(0, cg_frame.natoms) + self.assertEqual((1, 0, 3), cg_frame._trajectory.xyz.shape) diff --git a/test/test_parsers_cfg.py b/tests/test_parsers_cfg.py similarity index 53% rename from test/test_parsers_cfg.py rename to tests/test_parsers_cfg.py index 1d481bd..ea20a4a 100644 --- a/test/test_parsers_cfg.py +++ b/tests/test_parsers_cfg.py @@ -1,3 +1,4 @@ +import pathlib import unittest from pycgtool.parsers.cfg import DuplicateSectionError, NoSectionError @@ -5,43 +6,47 @@ class TestParsersCFG(unittest.TestCase): + base_dir = pathlib.Path(__file__).absolute().parent + data_dir = base_dir.joinpath("data") + + water_name = "SOL" watline = ("W", "P4", "OW", "HW1", "HW2") def test_cfg_with(self): - with CFG("test/data/water.map"): + with CFG(self.data_dir.joinpath("water.map")): pass def test_cfg_iterate_sections(self): - with CFG("test/data/water.map") as cfg: + with CFG(self.data_dir.joinpath("water.map")) as cfg: for name in cfg: - self.assertEqual("SOL", name) + self.assertEqual(self.water_name, name) def test_cfg_iterate_lines(self): - with CFG("test/data/water.map") as cfg: + with CFG(self.data_dir.joinpath("water.map")) as cfg: for name, section in cfg.items(): - self.assertEqual("SOL", name) + self.assertEqual(self.water_name, name) for line in section: self.assertEqual(self.watline, line) def test_cfg_get_section(self): - with CFG("test/data/water.map") as cfg: - self.assertTrue("SOL" in cfg) - for line in cfg["SOL"]: + with CFG(self.data_dir.joinpath("water.map")) as cfg: + self.assertTrue(self.water_name in cfg) + for line in cfg[self.water_name]: self.assertEqual(self.watline, line) def test_cfg_duplicate_error(self): with self.assertRaises(DuplicateSectionError): - CFG("test/data/twice.cfg") + CFG(self.data_dir.joinpath("twice.cfg")) def test_include_file(self): - with CFG("test/data/martini.map") as cfg: + with CFG(self.data_dir.joinpath("martini.map")) as cfg: self.assertTrue("DOPC" in cfg) self.assertTrue("GLY" in cfg) def test_error_no_sections(self): with self.assertRaises(NoSectionError): - CFG("test/data/nosections.cfg") + CFG(self.data_dir.joinpath("nosections.cfg")) -if __name__ == '__main__': +if __name__ == "__main__": unittest.main() diff --git a/tests/test_parsers_topology.py b/tests/test_parsers_topology.py new file mode 100644 index 0000000..289230d --- /dev/null +++ b/tests/test_parsers_topology.py @@ -0,0 +1,46 @@ +import pathlib +import unittest + +from pycgtool.parsers.cfg import DuplicateSectionError, NoSectionError +from pycgtool.parsers import ITP + + +class TestParsersITP(unittest.TestCase): + base_dir = pathlib.Path(__file__).absolute().parent + data_dir = base_dir.joinpath("data") + + def test_empty_itp(self): + itp = ITP() + self.assertEqual(0, len(itp)) + + def test_itp_with(self): + with ITP(self.data_dir.joinpath("membrane/membrane.top")): + pass + + def test_itp_duplicate_error(self): + with self.assertRaises(DuplicateSectionError): + ITP(self.data_dir.joinpath("membrane/twice.itp")) + + def test_itp_include(self): + with ITP(self.data_dir.joinpath("membrane/membrane.top")) as itp: + self.assertIn("CDL2", itp) + self.assertIn("POPE", itp) + + def test_read_section(self): + pii_line = ["1", "CC3161", "1", "PII", "C13", "1", "0.1400", "12.0110"] + + with ITP(self.data_dir.joinpath("membrane/membrane.top")) as itp: + self.assertEqual(len(itp["PII"]["atoms"]), 283) + self.assertListEqual(list(itp["PII"]["atoms"][0]), pii_line) + + def test_double_sections(self): + with ITP(self.data_dir.joinpath("two_double_section.itp")) as itp: + self.assertEqual(len(itp["TWO"]["atoms"]), 2) + + def test_unknown_sections(self): + with ITP(self.data_dir.joinpath("two_unknown_section.itp")) as itp: + self.assertEqual(len(itp["TWO"]["atoms"]), 2) + + def test_error_no_sections(self): + with self.assertRaises(NoSectionError): + ITP(self.data_dir.joinpath("nosections.cfg")) diff --git a/tests/test_pycgtool.py b/tests/test_pycgtool.py new file mode 100644 index 0000000..8eb365c --- /dev/null +++ b/tests/test_pycgtool.py @@ -0,0 +1,207 @@ +"""Tests of the full application workflows.""" + +import itertools +import pathlib +import subprocess +import tempfile +import typing +import unittest + +from pycgtool import util +import pycgtool.__main__ as main + + +def get_args(name, out_dir, extra: typing.Optional[typing.Mapping] = None): + base_dir = pathlib.Path(__file__).absolute().parent + data_dir = base_dir.joinpath("data") + + args = [ + data_dir.joinpath(f"{name}.gro"), + data_dir.joinpath(f"{name}.xtc"), + ] + + kwargs = { + "-m": data_dir.joinpath(f"{name}.map"), + "-b": data_dir.joinpath(f"{name}.bnd"), + "--out-dir": out_dir, + } + + parsed_args = main.parse_arguments( + itertools.chain( + map(str, args), *[[key, str(value)] for key, value in kwargs.items()] + ) + ) + + if extra is not None: + for key, value in extra.items(): + setattr(parsed_args, key, value) + + # Re-validate after manual changes + return main.validate_arguments(parsed_args) + + +class PycgtoolTest(unittest.TestCase): + base_dir = pathlib.Path(__file__).absolute().parent + data_dir = base_dir.joinpath("data") + + def test_pycgtool_help(self): + subprocess.check_call(["python", "-m", "pycgtool", "-h"]) + subprocess.check_call(["python", "-m", "pycgtool", "--help"]) + + def test_pycgtool_version(self): + subprocess.check_call(["python", "-m", "pycgtool", "-v"]) + subprocess.check_call(["python", "-m", "pycgtool", "--version"]) + + def test_parse_arguments(self): + args = main.parse_arguments( + [ + "TOPOLOGY", + "-m", + "MAP", + "--begin", + "1000", + ] + ) + + self.assertEqual("TOPOLOGY", args.topology) + self.assertEqual("MAP", args.mapping) + self.assertEqual(1000, args.begin) + + def test_map_only(self): + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + args = get_args( + "sugar", + tmp_path, + extra={ + "output_xtc": True, + "bnd": None, + }, + ) + + # Equivalent to + # pycgtool -m --output-xtc + main.PyCGTOOL(args) + + self.assertTrue( + util.compare_trajectories( + self.data_dir.joinpath("sugar_out.xtc"), + tmp_path.joinpath("out.xtc"), + topology_file=self.data_dir.joinpath("sugar_out.gro"), + ) + ) + + def test_full(self): + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + args = get_args("sugar", tmp_path) + + # Equivalent to + # pycgtool -m -b + main.PyCGTOOL(args) + + self.assertTrue( + util.cmp_file_whitespace_float( + tmp_path.joinpath("out.itp"), + self.data_dir.joinpath("sugar_out.itp"), + rtol=0.001, + verbose=True, + ) + ) + + self.assertTrue( + util.compare_trajectories( + self.data_dir.joinpath("sugar_out.gro"), + tmp_path.joinpath("out.gro"), + rtol=0.001, + ) + ) + + def test_full_no_traj(self): + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + args = get_args( + "sugar", + tmp_path, + extra={ + "trajectory": None, + }, + ) + + # Equivalent to + # pycgtool -m -b + main.PyCGTOOL(args) + + self.assertFalse(tmp_path.joinpath("out.itp").exists()) + + self.assertTrue( + util.compare_trajectories( + self.data_dir.joinpath("sugar_out.gro"), + tmp_path.joinpath("out.gro"), + rtol=0.001, + ) + ) + + def test_measure_only(self): + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + args = get_args( + "sugar", + tmp_path, + extra={ + "mapping": None, + "trajectory": None, + }, + ) + + # Equivalent to + # pycgtool -b + main.PyCGTOOL(args) + + # Does not produce itp file + self.assertFalse(tmp_path.joinpath("out.itp").exists()) + + # Check bond dump files against reference + for bond_type in ["length", "angle", "dihedral"]: + out_file = tmp_path.joinpath(f"ALLA_{bond_type}.dat") + self.assertTrue(out_file.exists()) + + self.assertTrue( + util.cmp_file_whitespace_float( + self.data_dir.joinpath(f"ALLA_{bond_type}_one.dat"), out_file + ) + ) + + def test_forcefield(self): + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = pathlib.Path(tmpdir) + args = get_args( + "sugar", + tmp_path, + extra={ + "output_forcefield": True, + }, + ) + + # Equivalent to + # pycgtool -m -b --output-forcefield + main.PyCGTOOL(args) + + # Does not produce itp file + self.assertFalse(tmp_path.joinpath("out.itp").exists()) + + out_ff_dir = tmp_path.joinpath("ffout.ff") + self.assertTrue(out_ff_dir.is_dir()) + + # Compare all files in ffout.ff to reference versions + for out_file in out_ff_dir.iterdir(): + ref_file = self.data_dir.joinpath(out_file) + + self.assertTrue(util.cmp_file_whitespace_float(ref_file, out_file)) + + # TODO more tests + # TODO test wrong args.end + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/test_util.py b/tests/test_util.py new file mode 100644 index 0000000..2015c3a --- /dev/null +++ b/tests/test_util.py @@ -0,0 +1,265 @@ +import logging +import os +import pathlib +import shutil +import tempfile +import unittest + +import numpy as np + +from pycgtool import util +from pycgtool.util import extend_graph_chain, transpose_and_sample +from pycgtool.util import dir_up, backup_file, sliding +from pycgtool.util import file_write_lines, cmp_whitespace_float +from pycgtool.util import circular_mean, circular_variance + + +class UtilTest(unittest.TestCase): + def test_triplets_from_pairs(self): + pairs = [(0, 1), (1, 2), (2, 3)] + result = [(0, 1, 2), (1, 2, 3)] + self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs))) + pairs = [(0, 1), (1, 2), (2, 3), (3, 0)] + result = [(0, 1, 2), (1, 0, 3), (1, 2, 3), (2, 3, 0)] + self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs))) + + def test_triplets_from_pairs_multires(self): + pairs = [("a", "b"), ("b", "c"), ("c", "d"), ("d", "+a")] + result = [("a", "b", "c"), ("b", "c", "d"), ("c", "d", "+a"), ("d", "+a", "+b")] + self.assertEqual(result, sorted(extend_graph_chain(pairs, pairs))) + + def test_quadruplets_from_pairs(self): + pairs = [(0, 1), (1, 2), (2, 3)] + result = [(0, 1, 2, 3)] + triplets = extend_graph_chain(pairs, pairs) + self.assertEqual(result, sorted(extend_graph_chain(triplets, pairs))) + pairs = [(0, 1), (1, 2), (2, 3), (3, 0)] + triplets = extend_graph_chain(pairs, pairs) + result = [(0, 1, 2, 3), (1, 0, 3, 2), (1, 2, 3, 0), (2, 1, 0, 3)] + self.assertEqual(result, sorted(extend_graph_chain(triplets, pairs))) + + def test_dir_up(self): + path = os.path.realpath(__file__) + self.assertEqual(path, dir_up(path, 0)) + self.assertEqual(os.path.dirname(path), dir_up(path)) + self.assertEqual(os.path.dirname(os.path.dirname(path)), dir_up(path, 2)) + + def test_backup_file(self): + with tempfile.TemporaryDirectory() as t: + tmp_dir = pathlib.Path(t) + + paths = [ + tmp_dir.joinpath("testfile"), + tmp_dir.joinpath("#testfile.1#"), + tmp_dir.joinpath("#testfile.2#"), + ] + path = paths[0] + + logging.disable(logging.WARNING) + + path.touch() + self.assertTrue(path.exists()) + + # Backup file with no existing backups + new_path = backup_file(path) + + self.assertEqual(paths[1], new_path) + self.assertFalse(path.exists()) + self.assertTrue(paths[1].exists()) + + path.touch() + self.assertTrue(path.exists()) + + # Backup file that already has a backup + new_path = backup_file(path) + + self.assertEqual(paths[2], new_path) + self.assertFalse(path.exists()) + self.assertTrue(paths[1].exists()) + self.assertTrue(paths[2].exists()) + + logging.disable(logging.NOTSET) + + def test_backup_directory(self): + with tempfile.TemporaryDirectory() as t: + tmp_dir = pathlib.Path(t) + + paths = [ + tmp_dir.joinpath("testfile"), + tmp_dir.joinpath("#testfile.1#"), + tmp_dir.joinpath("#testfile.2#"), + ] + path = paths[0] + + logging.disable(logging.WARNING) + + path.mkdir() + self.assertTrue(path.exists()) + self.assertTrue(path.is_dir()) + + # Backup directory with no existing backups + new_path = backup_file(path) + + self.assertEqual(paths[1], new_path) + self.assertFalse(path.exists()) + self.assertTrue(paths[1].exists()) + self.assertTrue(paths[1].is_dir()) + + path.mkdir() + self.assertTrue(path.exists()) + self.assertTrue(path.is_dir()) + + # Backup directory that already has a backup + new_path = backup_file(path) + + self.assertEqual(paths[2], new_path) + self.assertFalse(path.exists()) + self.assertTrue(paths[1].exists()) + self.assertTrue(paths[1].is_dir()) + self.assertTrue(paths[2].exists()) + self.assertTrue(paths[2].is_dir()) + + logging.disable(logging.NOTSET) + + def test_sliding(self): + test_list = [0, 1, 2, 3, 4] + res = [(None, 0, 1), (0, 1, 2), (1, 2, 3), (2, 3, 4), (3, 4, None)] + for res, pair in zip(res, sliding(test_list)): + self.assertEqual(res, pair) + + def test_sliding_empty(self): + """Test that an exception is raised when trying to iterate over empty iterable.""" + with self.assertRaises(ValueError): + for _, _, _ in sliding([]): + pass + + def test_transpose_and_sample_no_sample(self): + test_list = [(1, 2), (3, 4), (5, 6)] + test_list_transpose = [(1, 3, 5), (2, 4, 6)] + self.assertEqual(test_list_transpose, transpose_and_sample(test_list, None)) + + def test_transpose_and_sample(self): + test_list = [(1, 2), (3, 4), (5, 6)] + test_list_transpose = [(1, 3, 5), (2, 4, 6)] + + result = transpose_and_sample(test_list, n=1) + self.assertEqual(1, len(result)) + self.assertIn(result[0], test_list_transpose) + + def test_cmp_whitespace_text(self): + ref = ["Hello World"] + test = ["Hello World"] + self.assertTrue(cmp_whitespace_float(ref, test)) + test = ["Hello PyCGTOOL"] + self.assertFalse(cmp_whitespace_float(ref, test)) + + def test_cmp_whitespace_float(self): + ref = ["8.3 1.00 -3 0"] + test = ["8.3 1.00 -3 0.0"] + self.assertTrue(cmp_whitespace_float(ref, test)) + test = ["8.3 1.01 -3 0"] + self.assertFalse(cmp_whitespace_float(ref, test)) + self.assertTrue(cmp_whitespace_float(ref, test, rtol=0.1)) + + test = ["8.3 1.00 -2.999 0"] + self.assertTrue(cmp_whitespace_float(ref, test)) + test = ["8.3 1.00 -3.001 0"] + self.assertTrue(cmp_whitespace_float(ref, test)) + + def test_cmp_whitespace_float_diff_lengths(self): + """Test that lists of different lengths are considered different.""" + ref = ["1"] + test = ["1", "2"] + + self.assertFalse(cmp_whitespace_float(ref, test)) + + def test_circular_mean(self): + values = np.deg2rad(np.array([-175, 165], dtype=np.float32)) + test = np.deg2rad(175.0) + self.assertAlmostEqual(circular_mean(values), test, delta=test / 500.0) + + values = np.deg2rad(np.array([165, 145], dtype=np.float32)) + test = np.deg2rad(155.0) + self.assertAlmostEqual(circular_mean(values), test, delta=test / 500.0) + + def test_circular_variance(self): + values = np.deg2rad(np.array([165, 145], dtype=np.float32)) + test_var = np.var(values) + self.assertAlmostEqual( + circular_variance(values), test_var, delta=test_var / 500.0 + ) + + values = np.deg2rad(np.array([-175, 165], dtype=np.float32)) + self.assertAlmostEqual( + circular_variance(values), test_var, delta=test_var / 500.0 + ) + + +class UtilFileWriteLinesTest(unittest.TestCase): + def setUp(self): + self.test_dir = tempfile.mkdtemp() + + def tearDown(self): + shutil.rmtree(self.test_dir) + + def test_file_write_lines_empty(self): + filename = os.path.join(self.test_dir, "empty") + file_write_lines(filename) + with open(filename) as f: + self.assertFalse(f.readlines()) + + def test_file_write_lines_list(self): + lines = ["a", "b c", " ", "123 d", "", " %-+# "] + + filename = os.path.join(self.test_dir, "list") + file_write_lines(filename, lines) + with open(filename) as f: + self.assertListEqual(lines, f.read().splitlines()) + + def test_file_write_lines_append(self): + lines = ["a", "b c", "d ", " ef"] + + filename = os.path.join(self.test_dir, "append") + file_write_lines(filename, lines[:2]) + file_write_lines(filename, lines[2:], append=True) + with open(filename) as f: + self.assertListEqual(lines, f.read().splitlines()) + + +class CompareTrajectoryTest(unittest.TestCase): + base_dir = pathlib.Path(__file__).absolute().parent + data_dir = base_dir.joinpath("data") + + def test_compare_trajectory_single(self): + self.assertTrue( + util.compare_trajectories( + self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("sugar.gro") + ) + ) + + def test_compare_trajectory_single_false(self): + with self.assertRaises(ValueError): + util.compare_trajectories( + self.data_dir.joinpath("sugar.gro"), self.data_dir.joinpath("water.gro") + ) + + def test_compare_trajectory(self): + self.assertTrue( + util.compare_trajectories( + self.data_dir.joinpath("sugar.xtc"), + self.data_dir.joinpath("sugar.xtc"), + topology_file=self.data_dir.joinpath("sugar.gro"), + ) + ) + + def test_compare_trajectory_false(self): + with self.assertRaises(ValueError): + util.compare_trajectories( + self.data_dir.joinpath("sugar.xtc"), + self.data_dir.joinpath("water.xtc"), + topology_file=self.data_dir.joinpath("sugar.gro"), + ) + + +if __name__ == "__main__": + unittest.main() diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..6a14acf --- /dev/null +++ b/tox.ini @@ -0,0 +1,26 @@ +[tox] +isolated_build = true +envlist = lint,py3 + +[testenv:lint] +deps = + black + flake8 +commands = + black --check pycgtool/ tests/ + flake8 pycgtool/ tests/ + +[testenv] +deps = + coverage + pytest +commands = + coverage run --source=pycgtool -m pytest tests/ + coverage report --skip-covered --fail-under=80 + +[flake8] +max-line-length = 120 +; Ignore lint errors with formatted blocks of numbers in test code +per-file-ignores = + tests/test_bondset.py: E201 + tests/test_frame.py: E202, E203