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Don't downcast molecules to single residues and atoms. [closes #16] #19

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merged 1 commit into from
Mar 10, 2023
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Don't downcast molecules to single residues and atoms. [closes #16] #19

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10 changes: 1 addition & 9 deletions python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_search_result.py
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Original file line number Diff line number Diff line change
Expand Up @@ -141,15 +141,7 @@ def __getitem__(self, key):
return _Residue(result)
# Molecule.
elif isinstance(result, _Sire.Mol._Mol.Molecule):
# If the molecule contains a single atom, then convert to an atom.
if result.nAtoms() == 1:
return _Atom(result.atom())
# If there's a single residue, the convert to a residue.
elif result.nResidues() == 1:
return _Residue(result.residue())
# Otherwise, append the molecule.
else:
return _Molecule(result)
return _Molecule(result)
# Bond
elif isinstance(result, _Sire.MM._MM.Bond):
return _Bond(result)
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10 changes: 1 addition & 9 deletions python/BioSimSpace/_SireWrappers/_search_result.py
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Original file line number Diff line number Diff line change
Expand Up @@ -141,15 +141,7 @@ def __getitem__(self, key):
return _Residue(result)
# Molecule.
elif isinstance(result, _Sire.Mol._Mol.Molecule):
# If the molecule contains a single atom, then convert to an atom.
if result.nAtoms() == 1:
return _Atom(result.atom())
# If there's a single residue, the convert to a residue.
elif result.nResidues() == 1:
return _Residue(result.residue())
# Otherwise, append the molecule.
else:
return _Molecule(result)
return _Molecule(result)
# Bond
elif isinstance(result, _Sire.MM._MM.Bond):
return _Bond(result)
Expand Down
6 changes: 3 additions & 3 deletions test/Sandpit/Exscientia/_SireWrappers/test_system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def test_atom_reindexing(system):

def test_residue_reindexing(system):
# Search for all waters by residue name.
results = system.search("resname WAT")
results = system.search("resname WAT").residues()

# There are 3 residues in the alanine-dipeptide, then one in each water
# molecule. This means that residue indexing should start at 3 and
Expand All @@ -89,7 +89,7 @@ def test_residue_reindexing(system):

def test_molecule_reindexing(system):
# Search for all waters by residue name.
results = system.search("resname WAT")
results = system.search("resname WAT").molecules()

# There are 631 molecules in the system: an alanine-dipeptide, followed by
# 630 water molecules. This means that molecule indexing should start at 1
Expand All @@ -103,7 +103,7 @@ def test_molecule_reindexing(system):
# As such, we convert each result to a molecule.
for residue in results:
# Ensure the absolute index matches.
assert system.getIndex(residue.toMolecule()) == index
assert system.getIndex(residue) == index

index += 1

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6 changes: 3 additions & 3 deletions test/_SireWrappers/test_system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def test_atom_reindexing(system):

def test_residue_reindexing(system):
# Search for all waters by residue name.
results = system.search("resname WAT")
results = system.search("resname WAT").residues()

# There are 3 residues in the alanine-dipeptide, then one in each water
# molecule. This means that residue indexing should start at 3 and
Expand All @@ -89,7 +89,7 @@ def test_residue_reindexing(system):

def test_molecule_reindexing(system):
# Search for all waters by residue name.
results = system.search("resname WAT")
results = system.search("resname WAT").molecules()

# There are 631 molecules in the system: an alanine-dipeptide, followed by
# 630 water molecules. This means that molecule indexing should start at 1
Expand All @@ -103,7 +103,7 @@ def test_molecule_reindexing(system):
# As such, we convert each result to a molecule.
for residue in results:
# Ensure the absolute index matches.
assert system.getIndex(residue.toMolecule()) == index
assert system.getIndex(residue) == index

index += 1

Expand Down