Add mmcif compatibility to mdanalysis library

CHANGELOG.rst

@@ -10,6 +10,9 @@ Upon version 0.8, and before version 1, SV2 major version increments are reflect
 Changelog
 =========
 
+* Add support for CIF topologies in libmda using openmm.app.pdbxfile
+* removes the install*.yml gitactions
+
 v0.10.0 (2021-11-24)
 ------------------------------------------------------------
 

README.rst

@@ -50,7 +50,7 @@ taurenmd
     :target: https://pypistats.org/packages/taurenmd
 
 **A command-line interface for analysis routines of Molecular Dynamics data.**
-  
+
 **Taurenmd** provides an easy, flexible and extensible, **command-line** interface for the most common *(and not so common)* routines of analysis and representation of Molecular Dynamics (MD) data.
 
 It bridges the gap between the highly complex (and powerful) Python libraries available for analysis of MD data and the *non-developer* users that lack the programming skills to perform a thorough and proficient use those libraries. *But not only*, **taurenmd** also facilitates high throughput operations, even to those proficient *devs*, because complex executions are reduced to single argument-rich command-lines that can be concatenated or aliased.

src/taurenmd/libs/libmda.py

@@ -17,7 +17,7 @@
 from taurenmd import Path
 from taurenmd import core as tcore
 from taurenmd import log
-from taurenmd.libs import libcli, libio
+from taurenmd.libs import libcli, libio, libopenmm
 from taurenmd.logger import S, T
 
 
@@ -73,11 +73,17 @@ def load_universe(
         trajectories = libio.sort_numbered_input(*trajectories)
 
     libio.report_input(topology, trajectories)
-    universe = mda.Universe(
-        Path(topology).str(),
-        [Path(i).str() for i in trajectories],
-        **universe_args,
-        )
+
+    topo_path = Path(topology).str()
+    traj_path = [Path(i).str() for i in trajectories],
+
+    try:
+        universe = mda.Universe(topo_path, traj_path, **universe_args)
+
+    except ValueError:
+        pdbx = libopenmm.attempt_to_load_top_from_simtk(topo_path)
+        universe = mda.Universe(pdbx, traj_path, **universe_args)
+
     report(universe)
     return universe
 

src/taurenmd/libs/libmdt.py

@@ -15,36 +15,16 @@
 .. _Simtk OpenMM: http://openmm.org/
 """
 import os
-import sys
 
 import mdtraj
 
 from taurenmd import Path
 from taurenmd import core as tcore
 from taurenmd import log
-from taurenmd.libs import libcli, libio
+from taurenmd.libs import libcli, libio, libopenmm
 from taurenmd.logger import S, T
 
 
-try:
-    from simtk.openmm.app import PDBxFile
-    SIMTK = True
-except ImportError:
-    SIMTK = False
-
-
-def _log_simtkimport_error():
-    msg = (
-        "To use .cif files as Topologies taurenmd requires OpenMM, "
-        "which is currently not installed. "
-        "Please visit our Installation instruction at "
-        "https://taurenmd.readthedocs.io/"
-        )
-    log.error(T('Dependency Error'))
-    log.error(S(msg))
-    sys.exit(0)
-
-
 @libcli.add_reference(tcore.ref_mdt)
 def load_traj(topology, trajectories, insort=False):
     """
@@ -65,7 +45,8 @@ def load_traj(topology, trajectories, insort=False):
     trajectory : str or Path
         Path to the trajectory file. Accepts MDTraj compatible `files <http://mdtraj.org/1.9.3/load_functions.html#trajectory-reference>`_
 
-    Returns -------
+    Returns
+    -------
     MDTraj trajectory
         `Trajectory object <http://mdtraj.org/1.9.3/api/generated/mdtraj.Trajectory.html#mdtraj-trajectory>`_.
     """  # noqa: E501
@@ -79,41 +60,16 @@ def load_traj(topology, trajectories, insort=False):
         trajs = os.fspath(trajectories)
 
     libio.report_input(topology, trajs)
-    top = attempt_to_load_top_from_simtk(topology)
-    mdtrajectory = mdtraj.load(trajs, top=top)
-
-    return mdtrajectory
-
-
-@libcli.add_reference(tcore.ref_openmm)
-def attempt_to_load_top_from_simtk(topology):
-    """
-    Load topology from SIMTK.
 
-    Parameters
-    ----------
-    topology : str or Path
-
-    Returns
-    -------
-    topology from mdtraj.Topology.from_openmm`
-
-    Raises
-    ------
-    Dependency error from :func:`_log_simtkimport_error`, program
-    halts.
-    """
-    topp = Path(topology)
-
-    if topp.suffix == '.cif' and SIMTK:
-        mol = PDBxFile(topp.str())
-        return mdtraj.Topology.from_openmm(mol.topology)
+    if Path(topology).suffix == '.cif':
+        _top = libopenmm.attempt_to_load_top_from_simtk(topology)
+        top = mdtraj.Topology.from_openmm(_top.topology)
+    else:
+        top = Path(topology).str()
 
-    elif topp.suffix == '.cif' and not SIMTK:
-        _log_simtkimport_error()
+    mdtrajectory = mdtraj.load(trajs, top=top)
 
-    else:
-        return topp.str()
+    return mdtrajectory
 
 
 @libcli.add_reference(tcore.ref_mdt)

src/taurenmd/libs/libopenmm.py

@@ -0,0 +1,67 @@
+"""
+Functions that wrap around `OpenMM library`_.
+
+Read our `citing documentation`_ to understand how to cite multiple
+libraries.
+
+.. _citing documentation: https://taurenmd.readthedocs.io/en/latest/citing.html
+.. _OpenMM library: http://openmm.org/
+"""
+import sys
+
+
+try:
+    from openmm.app.pdbxfile import PDBxFile
+    SIMTK = True
+except ImportError:
+    SIMTK = False
+
+
+from taurenmd import Path
+from taurenmd import core as tcore
+from taurenmd import log
+from taurenmd.libs import libcli
+from taurenmd.logger import S, T
+
+
+@libcli.add_reference(tcore.ref_openmm)
+def attempt_to_load_top_from_simtk(topology):
+    """
+    Load topology from SIMTK.
+
+    Parameters
+    ----------
+    topology : str or Path
+
+    Returns
+    -------
+    topology from mdtraj.Topology.from_openmm`
+
+    Raises
+    ------
+    Dependency error from :func:`_log_simtkimport_error`, program
+    halts.
+    """
+    topp = Path(topology)
+
+    if topp.suffix == '.cif' and SIMTK:
+        mol = PDBxFile(topp.str())
+        return mol
+
+    elif topp.suffix == '.cif' and not SIMTK:
+        _log_simtkimport_error()
+
+    else:
+        raise ValueError(f'`topology` suffix is not CIF: {topp.suffix!r}')
+
+
+def _log_simtkimport_error():
+    msg = (
+        "To use .cif files as Topologies taurenmd requires OpenMM, "
+        "which is currently not installed. "
+        "Please visit our Installation instruction at "
+        "https://taurenmd.readthedocs.io/"
+        )
+    log.error(T('Dependency Error'))
+    log.error(S(msg))
+    sys.exit(0)

tests/test_libmda.py

@@ -7,7 +7,7 @@
 
 from taurenmd.libs import libmda as la
 
-from . import toptest, trajtest
+from . import toptest, toptest_cif, trajtest
 
 
 def test_load_universe_1():
@@ -20,6 +20,16 @@ def test_load_universe_1():
     assert len(universe.trajectory) == 10
 
 
+def test_load_universe_1_cif():
+    """Test load MDA Universe."""
+    universe = la.load_universe(
+        toptest_cif,
+        trajtest,
+        )
+    assert isinstance(universe, mda.Universe)
+    assert len(universe.trajectory) == 10
+
+
 def test_load_universe_2():
     """Test load MDA Universe multiple trajs."""
     universe = la.load_universe(

tests/test_libmdt.py

@@ -1,9 +1,5 @@
 """Test libmdt."""
-import importlib
-import sys
-
 import mdtraj as md
-import pytest
 
 from taurenmd.libs import libmdt
 
@@ -33,36 +29,7 @@ def test_load_traj_pdb_3():
 
 def test_load_traj_cif():
     """Test loading traj."""
+    assert toptest_cif.suffix == '.cif'
     traj = libmdt.load_traj(toptest_cif, trajtest)
     assert isinstance(traj, md.Trajectory)
     assert len(traj) == 10
-
-
-def test_attempt_load_cif_SIMTK_1():
-    """Test attempt load CIF."""
-    libmdt.attempt_to_load_top_from_simtk(toptest_cif)
-
-
-def test_attempt_load_cif_SIMTK_2():
-    """Test attempt load CIF."""
-    assert toptest.str() == libmdt.attempt_to_load_top_from_simtk(toptest)
-
-
-def test_load_traj_cif_import_error():
-    """Test loadtraj_cif import error as if simtk was not installed."""
-    sys.modules['simtk.openmm.app'] = None
-    importlib.reload(libmdt)
-    """Test loading traj."""
-    with pytest.raises(SystemExit) as err:
-        libmdt.load_traj(toptest_cif, trajtest)
-    assert err.type == SystemExit
-    assert err.value.code == 0
-
-
-def test_simtk_import_error():
-    """Test import error message."""
-    with pytest.raises(SystemExit) as err:
-        libmdt._log_simtkimport_error()
-
-    assert err.type == SystemExit
-    assert err.value.code == 0