Merge pull request #18 from MDAnalysis/parser-and-tests

Extend tests for OpenBabelParser
MDAnalysis · Oct 8, 2024 · cb7466e · cb7466e
2 parents f35c093 + 5a13779
commit cb7466e
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Showing 6 changed files with 313 additions and 195,238 deletions.
diff --git a/mda_openbabel_converter/OpenBabel.py b/mda_openbabel_converter/OpenBabel.py
@@ -51,8 +51,8 @@ def __init__(self, filename: OBMol, **kwargs):
  if filename.NumConformers() == 1:
  coordinates = np.array([
  [(coords := atom.GetVector()).GetX(),
- coords.GetY(),
- coords.GetZ()] for atom in OBMolAtomIter(filename)],
+  coords.GetY(),
+  coords.GetZ()] for atom in OBMolAtomIter(filename)],
  dtype=np.float32)
  else:
  # multiple conformers, such as for a trajectory
@@ -63,16 +63,17 @@ def __init__(self, filename: OBMol, **kwargs):
  for atom in OBMolAtomIter(filename):
  coordinates_inner = np.array([
  [(coords := atom.GetVector()).GetX(),
- coords.GetY(),
- coords.GetZ()] for atom in OBMolAtomIter(filename)],
+  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)
  coordinates[:] = np.nan
- super(OpenBabelReader, self).__init__(coordinates, order='fac', **kwargs)
+ super(OpenBabelReader, self).__init__(coordinates, 
+ order='fac', **kwargs)
 
 class OpenBabelConverter(ConverterBase):
  """

diff --git a/mda_openbabel_converter/OpenBabelParser.py b/mda_openbabel_converter/OpenBabelParser.py
@@ -118,7 +118,6 @@ def parse(self, **kwargs):
  resid = atom.GetResidue()
  resnums.append(resid.GetNum())
  resnames.append(resid.GetName())
- chainids.append(resid.GetChain())
  icodes.append(resid.GetInsertionCode())
 
  aromatics.append(atom.IsAromatic())