def test_SaveSMILESFromFrame(self):
sio = StringIO()
PandasTools.SaveSMILESFromFrame(self.df, sio)
result = sio.getvalue()
self.assertIn(self.df['SMILES'][10], result)
self.assertIn(self.df['ID'][10], result)
sio = StringIO()
PandasTools.SaveSMILESFromFrame(self.df,
sio,
NamesCol='PUBCHEM_IUPAC_INCHIKEY')
result = sio.getvalue()
self.assertIn(self.df['SMILES'][10], result)
self.assertIn(self.df['PUBCHEM_IUPAC_INCHIKEY'][10], result)
def search_pattern(self, inp):
smarts, prefix = inp
pattern = Chem.MolFromSmarts(smarts)
m_df = self.df[self.df.mol >= pattern]
m_df['SMARTS_Match'] = smarts
# Matches = [m for m in self.Mols if m.HasSubstructMatch(pattern)]
print('\n > Molecule matching "{0}": {1}\n'.format(smarts, len(m_df)))
if self.ext == 'sdf':
mol_out = (prefix + '.' + self.ext)
rdpd.WriteSDF(m_df,
mol_out,
molColName='mol',
idName='ID',
properties=list(m_df.columns))
else:
mol_out = (prefix + '.' + self.ext)
rdpd.SaveSMILESFromFrame(m_df,
mol_out,
molCol='mol',
NamesCol='ID',
isomericSmiles=True)
