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Extend tests for OpenBabelParser #18

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merged 12 commits into from
Oct 8, 2024
Merged

Extend tests for OpenBabelParser #18

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8228671
Update gh-ci.yaml
IAlibay Jul 22, 2024
81507e8
Update gh-ci.yaml
IAlibay Jul 22, 2024
b5def69
Fixing new error take 8
lunamorrow Jul 18, 2024
040a525
final commit before moving to new branch for new PR
lunamorrow Jul 24, 2024
ada522c
Rebase done
lunamorrow Jul 24, 2024
6f758ed
Getting things straightened up
lunamorrow Jul 24, 2024
6a40a7c
Extend testse for the OpenBabel Parser, but without support for chainids
lunamorrow Sep 23, 2024
ddbaf65
Empty commit to rebase with main again
lunamorrow Sep 23, 2024
c0d23a6
Clean up excess comments
lunamorrow Sep 23, 2024
209c53a
Replace parser sdf test with correctly formatted file
lunamorrow Sep 30, 2024
905dd9f
Coaxing pep8 to comment
lunamorrow Oct 1, 2024
5a13779
Remove stray comment
lunamorrow Oct 8, 2024
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11 changes: 6 additions & 5 deletions mda_openbabel_converter/OpenBabel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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):
"""
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1 change: 0 additions & 1 deletion mda_openbabel_converter/OpenBabelParser.py
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Expand Up @@ -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())
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