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Fix issue #332 #333

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merged 1 commit into from
Sep 6, 2024
Merged

Fix issue #332 #333

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24 changes: 3 additions & 21 deletions python/BioSimSpace/Align/_align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1547,17 +1547,11 @@ def _rmsdAlign(molecule0, molecule1, mapping=None, property_map0={}, property_ma
mol0 = molecule0._getSireObject()
mol1 = molecule1._getSireObject()

# Do we have a monatomic ion?
if (molecule0.nAtoms() == 1) or (molecule1.nAtoms() == 1):
is_ion = True
else:
is_ion = False

# Convert the mapping to AtomIdx key:value pairs.
sire_mapping = _to_sire_mapping(mapping)

# Perform the alignment, mol0 to mol1.
if len(mapping) == 1 and is_ion:
if len(mapping) == 1:
idx0 = list(mapping.keys())[0]
idx1 = list(mapping.values())[0]
# Replace the coordinates of the mapped atom with those of the reference.
Expand Down Expand Up @@ -2534,12 +2528,6 @@ def _score_rdkit_mappings(
.commit()
)

# Do we have a monatomic ion?
if (molecule0.nAtoms() == 1) or (molecule1.nAtoms() == 1):
is_ion = True
else:
is_ion = False

# Get the set of matching substructures in each molecule. For some reason
# setting uniquify to True removes valid matches, in some cases even the
# best match! As such, we set uniquify to False and account for duplicate
Expand Down Expand Up @@ -2608,7 +2596,7 @@ def _score_rdkit_mappings(
if is_valid:
# If there is only a single atom in the mapping and one molecule
# has one atom, e.g. an ion, then skip the alignment.
if len(mapping) == 1 and is_ion:
if len(mapping) == 1:
mappings.append(mapping)
scores.append(0.0)
else:
Expand Down Expand Up @@ -2770,12 +2758,6 @@ def _score_sire_mappings(
.commit()
)

# Do we have a monatomic ion?
if (molecule0.nAtoms() == 1) or (molecule1.nAtoms() == 1):
is_ion = True
else:
is_ion = False

# Initialise a list to hold the mappings.
mappings = []

Expand All @@ -2797,7 +2779,7 @@ def _score_sire_mappings(
if is_valid:
# If there is only a single atom in the mapping and one molecule
# has one atom, e.g. an ion, then skip the alignment.
if len(mapping) == 1 and is_ion:
if len(mapping) == 1:
mappings.append(mapping)
scores.append(0.0)
else:
Expand Down
24 changes: 3 additions & 21 deletions python/BioSimSpace/Sandpit/Exscientia/Align/_align.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1151,14 +1151,8 @@ def rmsdAlign(molecule0, molecule1, mapping=None, property_map0={}, property_map
# Convert the mapping to AtomIdx key:value pairs.
sire_mapping = _to_sire_mapping(mapping)

# Do we have a monatomic ion?
if (molecule0.nAtoms() == 1) or (molecule1.nAtoms() == 1):
is_ion = True
else:
is_ion = False

# Perform the alignment, mol0 to mol1.
if len(mapping) == 1 and is_ion:
if len(mapping) == 1:
idx0 = list(mapping.keys())[0]
idx1 = list(mapping.values())[0]
# Replace the coordinates of the mapped atom with those of the reference.
Expand Down Expand Up @@ -1785,12 +1779,6 @@ def _score_rdkit_mappings(
.commit()
)

# Do we have a monatomic ion?
if (molecule0.nAtoms() == 1) or (molecule1.nAtoms() == 1):
is_ion = True
else:
is_ion = False

# Get the set of matching substructures in each molecule. For some reason
# setting uniquify to True removes valid matches, in some cases even the
# best match! As such, we set uniquify to False and account for duplicate
Expand Down Expand Up @@ -1859,7 +1847,7 @@ def _score_rdkit_mappings(
if is_valid:
# If there is only a single atom in the mapping and one molecule
# has one atom, e.g. an ion, then skip the alignment.
if len(mapping) == 1 and is_ion:
if len(mapping) == 1:
mappings.append(mapping)
scores.append(0.0)
else:
Expand Down Expand Up @@ -2021,12 +2009,6 @@ def _score_sire_mappings(
.commit()
)

# Do we have a monatomic ion?
if (molecule0.nAtoms() == 1) or (molecule1.nAtoms() == 1):
is_ion = True
else:
is_ion = False

# Initialise a list to hold the mappings.
mappings = []

Expand All @@ -2048,7 +2030,7 @@ def _score_sire_mappings(
if is_valid:
# If there is only a single atom in the mapping and one molecule
# has one atom, e.g. an ion, then skip the alignment.
if len(mapping) == 1 and is_ion:
if len(mapping) == 1:
mappings.append(mapping)
scores.append(0.0)
else:
Expand Down
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