Update for external mdahole2 mdakit (#4464)

* update for external mdahole2 mdakit * put deprecation notice at top of docs * update stuff * remove hole duecredit test entries * update changelog * Update package/MDAnalysis/analysis/hole2/__init__.py Co-authored-by: Rocco Meli <[email protected]> * address review comments --------- Co-authored-by: Rocco Meli <[email protected]>
MDAnalysis · Mar 4, 2024 · d366921 · d366921
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diff --git a/.github/actions/setup-deps/action.yaml b/.github/actions/setup-deps/action.yaml
@@ -31,6 +31,8 @@ inputs:
     default: 'hypothesis'
   matplotlib:
     default: 'matplotlib-base'
+  mdahole2:
+    default: 'mdahole2-base'
   mda_xdrlib:
     default: 'mda-xdrlib'
   mmtf-python:
@@ -116,6 +118,7 @@ runs:
           ${{ inputs.griddataformats }}
           ${{ inputs.hypothesis }}
           ${{ inputs.matplotlib }}
+          ${{ inputs.mdahole2 }}
           ${{ inputs.mda_xdrlib }}
           ${{ inputs.mmtf-python }}
           ${{ inputs.numpy }}

diff --git a/maintainer/conda/environment.yml b/maintainer/conda/environment.yml
@@ -29,7 +29,11 @@ dependencies:
   - tidynamics>=1.0.0
   - tqdm>=4.43.0
   - sphinxcontrib-bibtex
+  - mdaencore
+  - waterdynamics
   - pip:
+      - mdahole2
+      - pathsimanalysis
       - duecredit
       - parmed
       - sphinx-sitemap

diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -35,6 +35,9 @@ Enhancements
    `n_initial_contacts` attribute, with documentation. (Issue #2604, PR #4415)
 
 Changes
+ * MDAnalysis.analysis.hole2 is now directly imported from the mdakit
+   mdahole2. This module is deprecated and will be fully removed in
+   MDAnalysis version 3.0 (PR #4464)
  * Testsuite packaging now uses a pyproject.toml file (PR #4463)
  * Improvement of setuptools packaging, including deduplication of
    dependency lists (PR #4424)

diff --git a/package/MDAnalysis/analysis/hole2/__init__.py b/package/MDAnalysis/analysis/hole2/__init__.py
@@ -34,280 +34,14 @@
 :footcite:p:`Smart1993,Smart1996` to analyse an ion channel pore or transporter
 pathway :footcite:p:`Stelzl2014`.
 
-Using HOLE on a PDB file
-------------------------
-
-Use the :func:``hole`` function to run `HOLE`_ on a single PDB file. For example,
-the code below runs the `HOLE`_ program installed at '~/hole2/exe/hole' ::
-
-    from MDAnalysis.tests.datafiles import PDB_HOLE
-    from MDAnalysis.analysis import hole2
-    profiles = hole2.hole(PDB_HOLE, executable='~/hole2/exe/hole')
-    # to create a VMD surface of the pore
-    hole2.create_vmd_surface(filename='hole.vmd')
-
-``profiles`` is a dictionary of HOLE profiles, indexed by the frame number. If only
-a PDB file is passed to the function, there will only be one profile at frame 0.
-You can visualise the pore by loading your PDB file into VMD, and in
-Extensions > Tk Console, type::
-
-    source hole.vmd
-
-You can also pass a DCD trajectory with the same atoms in the same order as
-your PDB file with the ``dcd`` keyword argument. In that case, ``profiles`` will
-contain multiple HOLE profiles, indexed by frame.
-
-The HOLE program will create some output files:
-
-* an output file (default name: hole.out)
-* an sphpdb file (default name: hole.sph)
-* a file of van der Waals' radii
-    (if not specified with ``vdwradii_file``. Default name: simple2.rad)
-* a symlink of your PDB or DCD files (if the original name is too long)
-* the input text (if you specify ``infile``)
-
-By default (`keep_files=True`), these files are kept. If you would like to
-delete the files after the function is wrong, set `keep_files=False`. Keep in
-mind that if you delete the sphpdb file, you cannot then create a VMD surface.
-
-
-Using HOLE on a trajectory
---------------------------
-
-You can also run HOLE on a trajectory through the :class:`HoleAnalysis` class.
-This behaves similarly to the ``hole`` function, although arguments such as ``cpoint``
-and ``cvect`` become runtime arguments for the :meth:`~HoleAnalysis.run` function.
-
-The class can be set-up and run like a normal MDAnalysis analysis class::
-
-    import MDAnalysis as mda
-    from MDAnalysis.tests.datafiles import MULTIPDB_HOLE
-    from MDAnalysis.analysis import hole2
-
-    u = mda.Universe(MULTIPDB_HOLE)
-
-    ha = hole2.HoleAnalysis(u, executable='~/hole2/exe/hole') as h2:
-    ha.run()
-    ha.create_vmd_surface(filename='hole.vmd')
-
-The VMD surface created by the class updates the pore for each frame of the trajectory.
-Use it as normal by loading your trajectory in VMD and sourcing the file in the Tk Console.
-
-You can access the actual profiles generated in the ``results`` attribute::
-
-    print(ha.results.profiles)
-
-Again, HOLE writes out files for each frame. If you would like to delete these files
-after the analysis, you can call :meth:`~HoleAnalysis.delete_temporary_files`::
-
-    ha.delete_temporary_files()
-
-Alternatively, you can use HoleAnalysis as a context manager that deletes temporary
-files when you are finished with the context manager::
-
-    with hole2.HoleAnalysis(u, executable='~/hole2/exe/hole') as h2:
-        h2.run()
-        h2.create_vmd_surface()
-
-
-Using HOLE with VMD
--------------------
-
-The :program:`sos_triangle` program that is part of HOLE_ can write an input
-file for VMD_ to display a triangulated surface of the pore found by
-:program:`hole`. This functionality is available with the
-:meth:`HoleAnalysis.create_vmd_surface` method
-[#create_vmd_surface_function]_. For an input trajectory MDAnalysis writes a
-*trajectory* of pore surfaces that can be animated in VMD together with the
-frames from the trajectory.
-
-
-Analyzing a full trajectory
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-To analyze a full trajectory and write pore surfaces for all frames to file
-:file:`hole_surface.vmd`, use ::
-
-    import MDAnalysis as mda
-    from MDAnalysis.analysis import hole2
-
-    # load example trajectory MULTIPDB_HOLE
-    from MDAnalysis.tests.datafiles import MULTIPDB_HOLE
-
-    u = mda.Universe(MULTIPDB_HOLE)
-
-    with hole2.HoleAnalysis(u, executable='~/hole2/exe/hole') as h2:
-        h2.run()
-        h2.create_vmd_surface(filename="hole_surface.vmd")
-
-In VMD, load your trajectory and then in the tcl console
-(e.g.. :menuselection:`Extensions --> Tk Console`) load the surface
-trajectory:
-
-.. code-block:: tcl
-
-   source hole_surface.vmd
-
-If you only want to *subsample the trajectory* and only show the surface at
-specific frames then you can either load the trajectory with the same
-subsampling into VMD or create a subsampled trajectory.
-
-
-Creating subsampled HOLE surface
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-For example, if we want to start displaying at frame 1 (i.e., skip frame 0), stop at frame 7, and
-only show every other frame (step 2) then the HOLE analysis will be ::
-
-    with hole2.HoleAnalysis(u, executable='~/hole2/exe/hole') as h2:
-        h2.run(start=1, stop=9, step=2)
-        h2.create_vmd_surface(filename="hole_surface_subsampled.vmd")
-
-The commands produce the file ``hole_surface_subsampled.vmd`` that can be loaded into VMD.
-
-.. Note::
-
-   Python (and MDAnalysis) stop indices are *exclusive* so the parameters
-   ``start=1``, ``stop=9``, and ``step=2`` will analyze frames 1, 3, 5, 7.
-
-.. _Loading-a-trajectory-into-VMD-with-subsampling:
-
-Loading a trajectory into VMD with subsampling
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Load your system into VMD. This can mean to load the topology file with
-:menuselection:`File --> New Molecule` and adding the trajectory with
-:menuselection:`File --> Load Data into Molecule` or just :menuselection:`File
---> New Molecule`.
-
-When loading the trajectory, subsample the frames by setting parametes in in
-the :guilabel:`Frames` section. Select *First: 1*, *Last: 7*, *Stride: 2*. Then
-:guilabel:`Load` everything.
-
-.. Note::
-
-   VMD considers the stop/last frame to be *inclusive* so you need to typically
-   choose one less than the ``stop`` value that you selected in MDAnalysis.
-
-Then load the surface trajectory:
-
-.. code-block:: tcl
-
-   source hole_surface_subsampled.vmd
-
-You should see a different surface for each frame in the trajectory. [#vmd_extra_frame]_
-
-
-Creating a subsampled trajectory
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Instead of having VMD subsample the trajectory as described in
-:ref:`Loading-a-trajectory-into-VMD-with-subsampling` we can write a subsampled
-trajectory to a file. Although it requires more disk space, it can be
-convenient if we want to visualize the system repeatedly.
-
-The example trajectory comes as a multi-PDB file so we need a suitable topology
-file. If you already have a topology file such as a PSF, TPR, or PRMTOP file
-then skip this step. We write frame 0 as a PDB :file:`frame0.pdb` (which we
-will use as the topology in VMD)::
-
-    u.atoms.write("frame0.pdb")
-
-Then write the actual trajectory in a convenient format such as TRR (or
-DCD). Note that we apply the same slicing (``start=1``, ``stop=9``, ``step=2``)
-to the trajectory itself and then use it as the value for the ``frames``
-parameter of :meth:`AtomGroup.write<MDAnalysis.core.groups.AtomGroup.write>`
-method::
-
-    u.atoms.write("subsampled.trr", frames=u.trajectory[1:9:2])
-
-This command creates the subsampled trajectory file :file:`subsampled.trr` in
-TRR format.
-
-In VMD we load the topology and the trajectory and then load the surface. In
-our example we have a PDB file (:file:`frame0.pdb`) as topology so we need to
-remove the first frame [#vmd_extra_frame]_ (skip the "trim" step below if you
-are using a true topology file such as PSF, TPR, or PRMTOP). To keep this
-example compact, we are using the tcl command line interface in VMD_
-(:menuselection:`Extensions --> Tk Console`) for loading and trimming the
-trajectory; you can use the menu commands if you prefer.
-
-.. code-block:: tcl
-
-   # load topology and subsampled trajectory
-   mol load pdb frame0.pdb trr subsampled.trr
-
-   # trim first frame (frame0) -- SKIP if using PSF, TPR, PRMTOP
-   animate delete beg 0 end 0
-
-   # load the HOLE surface trajectory
-   source hole_surface_subsampled.vmd
-
-You can now animate your molecule together with the surface and render it.
-
-
-.. _HOLE: http://www.holeprogram.org
-.. _VMD: https://www.ks.uiuc.edu/Research/vmd/
-
-Functions and classes
----------------------
-
-.. autofunction:: hole
-
-.. autoclass:: HoleAnalysis
-   :members:
-
-
-.. rubric:: References
-
-.. footbibliography::
-
-.. rubric:: Footnotes
-
-.. Footnotes
-
-.. [#create_vmd_surface_function] If you use the :class:`hole` class to run
-              :program:`hole` on a single PDB file then you can use
-              :func:`MDAnalysis.analysis.hole2.utils.create_vmd_surface`
-              function to manually run :program:`sph_process` and
-              :program:`sos_triangle` on the output files andcr eate a surface
-              file.
-
-.. [#vmd_extra_frame] If you loaded your system in VMD_ from separate topology
-              and trajectory files and the topology file contained coordinates
-              (such as a PDB or GRO) file then your trajectory will have an
-              extra initial frame containing the coordinates from your topology
-              file. Delete the initial frame with :menuselection:`Molecule -->
-              Delete Frames` by setting *First* to 0 and *Last* to 0 and
-              selecting :guilabel:`Delete`.
-
-.. [#HOLEDCD] PDB files are not the only files that :program:`hole` can
-              read. In principle, it is also able to read CHARMM DCD
-              trajectories and generate a hole profile for each frame. However,
-              native support for DCD in :program:`hole` is patchy and not every
-              DCD is recognized. In particular, At the moment, DCDs generated
-              with MDAnalysis are not accepted by HOLE. To overcome this
-              PDB / DCD limitation, use :class:`HoleAnalysis` which creates
-              temporary PDB files for each frame of a
-              :class:`~MDAnalysis.core.universe.Universe` or
-              :class:`~MDAnalysis.core.universe.AtomGroup` and runs
-              :func:``hole`` on each of them.
-
 """
-from ...due import due, Doi
-from .hole import hole, HoleAnalysis
-from .utils import create_vmd_surface
-
-due.cite(Doi("10.1016/S0006-3495(93)81293-1"),
-         description="HOLE program",
-         path="MDAnalysis.analysis.hole2",
-         cite_module=True)
-due.cite(Doi("10.1016/S0263-7855(97)00009-X"),
-         description="HOLE program",
-         path="MDAnalysis.analysis.hole2",
-         cite_module=True)
-due.cite(Doi("10.1016/j.jmb.2013.10.024"),
-         description="HOLE trajectory analysis with orderparameters",
-         path="MDAnalysis.analysis.hole2",
-         cite_module=True)
-del Doi
+import warnings
+from mdahole2.analysis.hole import hole, HoleAnalysis
+from mdahole2.analysis import utils, templates
+from mdahole2.analysis.utils import create_vmd_surface
+
+wmsg = ("Deprecated in version 2.8.0\n"
+        "MDAnalysis.analysis.hole2 is deprecated in favour of the "
+        "MDAKit madahole2 (https://www.mdanalysis.org/mdahole2/) "
+        "and will be removed in MDAnalysis version 3.0.0")
+warnings.warn(wmsg, category=DeprecationWarning)