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())