Computed props on non-sanitized molecule interfering with substructure matching

[greglandrum]

In [67]:

db_mol=Chem.MolFromSmiles('C1Cc2ccccc2CN1')
mb="""
  Mrv0541 10251405512D          

 10 11  0  0  1  0            999 V2000
  -17.2624   14.4196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.9768   14.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.9768   13.1821    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -17.2624   12.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5479   14.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5479   13.1821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8334   12.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1189   13.1821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1189   14.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8334   14.4196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  0  0  0  0
  4  6  1  0  0  0  0
  5 10  4  0  0  0  0
  6  5  4  0  0  0  0
  6  7  4  0  0  0  0
  8  7  4  0  0  0  0
  9  8  4  0  0  0  0
 10  9  4  0  0  0  0
M  END
"""
template = Chem.MolFromMolBlock(mb, False)
for atom in template.GetAtoms():
    atom.SetIsAromatic(False)  # set atoms as non-aromatic
for bond in template.GetBonds():
    bond.SetIsAromatic(False)  # set bonds as non-aromatic
    bond.SetBondType(Chem.rdchem.BondType.UNSPECIFIED)
template
print db_mol.HasSubstructMatch(template)
template.ClearComputedProps()
print db_mol.HasSubstructMatch(template)

False
True

[greglandrum]

Further simplification:

In [72]:

db_mol=Chem.MolFromSmiles('C1Cc2ccccc2CN1')
mb="""
  Mrv0541 10251405512D          

 10 11  0  0  1  0            999 V2000
  -17.2624   14.4196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.9768   14.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.9768   13.1821    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -17.2624   12.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5479   14.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5479   13.1821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8334   12.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1189   13.1821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1189   14.0071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8334   14.4196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  0  0  0  0
  4  6  1  0  0  0  0
  5 10  4  0  0  0  0
  6  5  4  0  0  0  0
  6  7  4  0  0  0  0
  8  7  4  0  0  0  0
  9  8  4  0  0  0  0
 10  9  4  0  0  0  0
M  END
"""
template = Chem.MolFromMolBlock(mb, False)
# template
print db_mol.HasSubstructMatch(template)
template.ClearComputedProps()
print db_mol.HasSubstructMatch(template)

False
True