From b37c93647e34eb422483a871a0e6fef2e676f366 Mon Sep 17 00:00:00 2001 From: bannanc Date: Tue, 4 Apr 2017 22:59:04 -0700 Subject: [PATCH 1/5] rename to smirnoff and add changes in smarty pull request --- .../__init__.py | 0 .../smirnoff99Frosst.ffxml | 335 ++++++++++-------- 2 files changed, 180 insertions(+), 155 deletions(-) rename {smirff99Frosst => smirnoff99Frosst}/__init__.py (100%) rename smirff99Frosst/smirff99Frosst.ffxml => smirnoff99Frosst/smirnoff99Frosst.ffxml (68%) diff --git a/smirff99Frosst/__init__.py b/smirnoff99Frosst/__init__.py similarity index 100% rename from smirff99Frosst/__init__.py rename to smirnoff99Frosst/__init__.py diff --git a/smirff99Frosst/smirff99Frosst.ffxml b/smirnoff99Frosst/smirnoff99Frosst.ffxml similarity index 68% rename from smirff99Frosst/smirff99Frosst.ffxml rename to smirnoff99Frosst/smirnoff99Frosst.ffxml index 07a99b4..c8fda0c 100644 --- a/smirff99Frosst/smirff99Frosst.ffxml +++ b/smirnoff99Frosst/smirnoff99Frosst.ffxml @@ -1,7 +1,7 @@ - Date: Mar. 3, 2017 + Date: April 4, 2017 C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine @@ -20,25 +20,25 @@ - + - - + + - + - + @@ -47,38 +47,53 @@ - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -100,23 +115,24 @@ - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + @@ -172,107 +188,116 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 8a105bfac3580dd82eaebf3f75d31fd41b81e108 Mon Sep 17 00:00:00 2001 From: Caitlin Bannan Date: Wed, 5 Apr 2017 14:26:19 -0700 Subject: [PATCH 2/5] rename to smirnoff Another note, SMIRKS is already an acronym, it should be capitalized anywhere in our documentation. I'm trying to keep an eye out and fix it when I see smirks or Smirks. --- setup.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/setup.py b/setup.py index 9783f19..93e26cf 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ """ -Setup script to install the smirff99Frosst.ffxml as a python package +Setup script to install the smirnoff99Frosst.ffxml as a python package """ import sys,os @@ -12,19 +12,19 @@ print() descr = """ -This provides the first general-purpose implementation of a Smirks Force Field (SMIRFF) as implemented by SMARTY and its ForceField class (in smarty.forcefield) for parameterizing small molecules for OpenMM. +This provides the first general-purpose implementation of a SMIRKS Native Open Force Field (SMIRNOFF) as implemented by SMARTY and its ForceField class (in smarty.forcefield) for parameterizing small molecules for OpenMM. """ setup( - name = 'smirff99frosst', + name = 'smirnoff99frosst', version = '1.0.5', description = 'SMIRNOFF Forcefield parameters', long_description = descr, - url = 'https://github.com/open-forcefield-group/smirff99Frosst', + url = 'https://github.com/open-forcefield-group/smirnoff99Frosst', author = 'Christopher I. Bayly, Caitlin C. Bannan, David L. Mobley', author_email = 'dmobley@uci.edu', license = 'MIT', platforms = ['Linux-64', 'Mac OSX-64', 'Unix-64'], - packages = find_packages()+['smirff99frosst'], + packages = find_packages()+['smirnoff99frosst'], include_package_data = True ) From 40a005f290163e2b1d8190894b5a02e44e0ddf0a Mon Sep 17 00:00:00 2001 From: Caitlin Bannan Date: Wed, 5 Apr 2017 15:03:56 -0700 Subject: [PATCH 3/5] rename smirnoff and add doc I added a not in a version comment, I can write a more verbose one with all the changes if we need it. --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index de095fd..43c1ac7 100644 --- a/README.md +++ b/README.md @@ -9,11 +9,11 @@ Latest release: [![DOI](https://zenodo.org/badge/68331217.svg)](https://zenodo.o ```bash conda install -c mobleylab smiff99frosst=1.0.4 ``` -(smirnoff99frosst was formerly known as smirff99frosst) +(smirnoff99frosst was formerly known as smirnoff99frosst) ## What it is -The provided smirff99Frosst.xml (forcefield) is a starting point for a general-purpose small molecule force field in [the SMIRFF format](https://github.com/open-forcefield-group/smarty/blob/master/The-SMIRFF-force-field-format.md); it should cover all or almost all of drug-like chemical space, and illustrates some of the major functionality of the SMIRFF format as well as how it simplifies the specification of force field parameters in a compact and chemically sensible way. +The provided smirnoff99Frosst.xml (forcefield) is a starting point for a general-purpose small molecule force field in [the SMIRNOFF format](https://github.com/open-forcefield-group/smarty/blob/master/The-SMIRNOFF-force-field-format.md); it should cover all or almost all of drug-like chemical space, and illustrates some of the major functionality of the SMIRNOFF format as well as how it simplifies the specification of force field parameters in a compact and chemically sensible way. HOWEVER, this is not expected to be (at present) an especially accurate small molecule force field. Its authors (see History, below) expect that while coverage will initially be good, additional refinements will be required (and possibly some expansion of the number of parameters) before it can rival current force fields such as GAFF or OPLS in accuracy. @@ -23,7 +23,7 @@ As with typical members of the AMBER force field family, smirf99Frosst is intend **Differences from parm99 and parm@frosst**: -smirnoff99Frosst/smirff99Frosst is neither parm99 nor parm@frosst exactly, for a number of reasons including that: +smirnoff99Frosst/smirnoff99Frosst is neither parm99 nor parm@frosst exactly, for a number of reasons including that: - It covers, or should cover with only slight modification, all reasonable organic chemistry, which neither of the above did - It is much simpler (because of parameter consolidation by SMIRKS, because of removing questionably differentiated parameters, and because its goal is to be a "good starting point" than a finished product) @@ -39,7 +39,7 @@ The use of SMIRKS typically means that this is not the case, so many mistakes ar ## History -This forcefield, smirnoff99Frosst/smirff99Frosst, is a logical descendant of AMBER's parm99 forcefield as well as Merck-Frosst's [parm@frosst](http://www.ccl.net/cca/data/parm_at_Frosst/), but is generalized/simplified and put into the SMIRFF format. +This forcefield, smirnoff99Frosst/smirnoff99Frosst, is a logical descendant of AMBER's parm99 forcefield as well as Merck-Frosst's [parm@frosst](http://www.ccl.net/cca/data/parm_at_Frosst/), but is generalized/simplified and put into the SMIRNOFF format. smirnoff99Frosst was created by Christopher I. Bayly (with help from Caitlin C. Bannan and David L. Mobley, UC Irvine) during his sabbatical at UCI during Summer 2016. It was created by hand curation of the original parm99 and parm@frosst parameter and frcmod files (manually creating SMIRKS patterns, condensing parameters, etc.). @@ -51,9 +51,9 @@ We expect to continue to manually expand this to cover more chemical space and, Subsequent versions are expected to build on Bayly's hand created version with some enhancements by Caitlin Bannan by improving specific parameters, further differentiating some chemical functionality, etc. However, derivatives are expected to retain this basic structure and the AMBER legacy/history; a full refitting of bonded parameters would result in a separate force field rather than a new version of this force field. -## Using smirff99Frosst +## Using smirnoff99Frosst -In OpenMM, application of smirff99Frosst to small molecules should be straightforward via `smarty.forcefield`. +In OpenMM, application of smirnoff99Frosst to small molecules should be straightforward via `smarty.forcefield`. Additionally, with ParmEd, it should be possible to convert parameterized OpenMM systems into other formats such as AMBER, CHARMM, or GROMACS, making this forcefield available in a variety of packages. **However**, some development/testing remains to be done on `smarty.forcefield` before this should be applied widely. @@ -61,12 +61,12 @@ Please see the smarty issue tracker for details. ## Versions - Version 1.0/[Version 1.0.1](http://dx.doi.org/10.5281/zenodo.154235) (equivalent): Initial release after hand curation by C. I. Bayly and C. C. Bannan. DOI [10.5281/zenodo.154235](http://dx.doi.org/10.5281/zenodo.154235) -- [Version 1.0.2](http://doi.org/10.5281/zenodo.154555): Fixes an out-of-order generic (bond `[#6X2:1]-[#6:2]`) as per [Issue 4](https://github.com/open-forcefield-group/smirff99Frosst/issues/4). +- [Version 1.0.2](http://doi.org/10.5281/zenodo.154555): Fixes an out-of-order generic (bond `[#6X2:1]-[#6:2]`) as per [Issue 4](https://github.com/open-forcefield-group/smirnoff99Frosst/issues/4). - [Version 1.0.3](http://dx.doi.org/10.5281/zenodo.161616): Bug fixes -- adding one omitted bond length, fixing four torsional smirks patterns, and adding one missing torsional term as detailed in [smarty issue 164](https://github.com/open-forcefield-group/smarty/pull/164) - [Version 1.0.4](http://doi.org/10.5281/zenodo.348165): Bug fixes -- #11: Fix the parm@Frosst-derived C-OS bond length so it does not also match (and thus override) C-OH, switching from SMIRKS of `[#6X3:1](=[#8X1])-[#8X2:2]` to `[#6X3:1](=[#8X1])-[#8X2H0:2]`, which avoids overriding `[#6X3:1]-[#8X2H1:2]`. And then add back in a generic which should have been present (#15, fixing a bug introduced by #11) **Not yet in a version**: - +- Parameters were added and changes made so that the current version would cover an internal set of molecules from DrugBank with only non-metal atoms and less than 200 heavy atoms. Full documentation of changes is available [here](https://github.com/open-forcefield-group/smarty/pull/232). ## Contributors Contributors to the relevant ffxml file include: From 26dbcb38f968327bd8980faba596f95ac4ce2747 Mon Sep 17 00:00:00 2001 From: Caitlin Bannan Date: Wed, 5 Apr 2017 15:12:14 -0700 Subject: [PATCH 4/5] Update MANIFEST.in --- MANIFEST.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/MANIFEST.in b/MANIFEST.in index 7e06319..c1dd67f 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1 +1 @@ -recursive-include smirff99Frosst * +recursive-include smirnoff99Frosst * From 3e4f5df7fdacad661a9aedf3427e39ec1eaba6ac Mon Sep 17 00:00:00 2001 From: Caitlin Bannan Date: Wed, 5 Apr 2017 15:12:41 -0700 Subject: [PATCH 5/5] Update meta.yaml --- conda-recipe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml index 9ae22d8..98983b8 100644 --- a/conda-recipe/meta.yaml +++ b/conda-recipe/meta.yaml @@ -1,5 +1,5 @@ package: - name: smirff99frosst + name: smirnoff99frosst version: "1.0.5" source: @@ -19,6 +19,6 @@ requirements: - python about: - home: https://github.com/open-forcefield-group/smirff99Frosst + home: https://github.com/open-forcefield-group/smirnoff99Frosst license: MIT license_file: LICENSE