Finalise test and handling for multi-conformer (aka trajectory) conta…

…ining OBMols

mda_openbabel_converter/OpenBabel.py

@@ -46,15 +46,28 @@ def __init__(self, filename: OBMol, **kwargs):
  """
  Converts file to OBMol to AtomGroup
  """
- n_conf = filename.NumConformers()
- if n_conf > 1:
- raise("Reader does not support OBMol's with more than one conformer")
  n_atoms = filename.NumAtoms()
- coordinates = np.array([
- [(coords := atom.GetVector()).GetX(),
- coords.GetY(),
- coords.GetZ()] for atom in OBMolAtomIter(filename)],
- dtype=np.float32)
+ # single position
+ if filename.NumConformers() == 1:
+ coordinates = np.array([
+ [(coords := atom.GetVector()).GetX(),
+ coords.GetY(),
+ coords.GetZ()] for atom in OBMolAtomIter(filename)],
+ dtype=np.float32)
+ else:
+ # multiple conformers, such as for a trajectory
+ numConf = filename.NumConformers()
+ coordinates = np.zeros((numConf, n_atoms, 3))
+ for conf_id in range(numConf):
+ filename.SetConformer(conf_id)
+ for atom in OBMolAtomIter(filename):
+ coordinates_inner = np.array([
+ [(coords := atom.GetVector()).GetX(),
+ coords.GetY(),
+ coords.GetZ()] for atom in OBMolAtomIter(filename)],
+ dtype=np.float32)
+ coordinates[conf_id] = coordinates_inner
+ # no coordinates present
  if not np.any(coordinates):
  warnings.warn("No coordinates found in the OBMol")
  coordinates = np.empty((1, n_atoms, 3), dtype=np.float32)

mda_openbabel_converter/tests/test_openbabel_reader.py

@@ -67,27 +67,31 @@ def test_coordinates_complex(self, n_frames):
  dtype=np.float32)
  assert_equal(expected, universe.trajectory.coordinate_array[0])
 
- # def test_multiple_conformer(self):
- # obconversion = ob.OBConversion()
- # obconversion.SetInFormat("xyz")
- # obmol = ob.OBMol()
- # notatend = obconversion.ReadFile(obmol, MET_ENKAPH_MOVIE.as_posix())
- # obmol_master = ob.OBMol()
- # obconversion.ReadFile(obmol_master, MET_ENKAPH_MOVIE.as_posix())
- # index = 0
- # while notatend:
- # # temp = obmol_master.GetConformer(0)
- # # obmol.CopyConformer(temp, 0)
- # #obmol_master.AddConformer(temp)
+ def test_multiple_conformer(self):
+ ob_conversion = ob.OBConversion()
+ ob_conversion.SetInFormat("smi")
+ mol = ob.OBMol()
+ ob_conversion.ReadString(mol, "CC(=O)OC1=CC=CC=C1C(=O)O")
+ assert mol.AddHydrogens()
 
- # print(obmol.GetConformer(0))
- # temp = obmol.GetConformer(0)
- # obmol_master.AddConformer(temp)
-
- # obmol = ob.OBMol()
- # notatend = obconversion.Read(obmol)
- # print(obmol_master.NumConformers())
- # assert 1 == 0
+ # build basic 3D coordinates
+ builder = ob.OBBuilder()
+ assert builder.Build(mol)
+
+ # generate multiconfs
+ confsearch = ob.OBConformerSearch()
+ num_conformers = 3
+ confsearch.Setup(mol, num_conformers)
+ confsearch.Search()
+ confsearch.GetConformers(mol)
+ assert mol.NumConformers() == 3
+
+ # convert to Universe
+ universe = mda.Universe(mol)
+ n_atoms = mol.NumAtoms()
+ expected_coordinates = np.empty((mol.NumConformers(), n_atoms, 3))
+ expected_shape = expected_coordinates.shape
+ assert_equal(universe.trajectory.coordinate_array.shape, expected_shape)
 
  def test_no_coordinates(self):
  obConversion = ob.OBConversion()