def __call__(self, smiles: str):
mol = Chem.MolFromSmiles(smiles)
if not (self.rule_dict["MW"][0] <= MolWt(mol) <=
self.rule_dict["MW"][1]):
return False
if not (self.rule_dict["LogP"][0] <= MolLogP(mol) <=
self.rule_dict["LogP"][1]):
return False
if not (self.rule_dict["HBD"][0] <= NumHDonors(mol) <=
self.rule_dict["HBD"][1]):
return False
if not (self.rule_dict["HBA"][0] <= NumHAcceptors(mol) <=
self.rule_dict["HBA"][1]):
return False
if not (self.rule_dict["TPSA"][0] <= TPSA(mol) <=
self.rule_dict["TPSA"][1]):
return False
for row in self.rule_list:
patt, max_val, desc = row
if len(mol.GetSubstructMatches(patt)) > max_val:
return False
return True
def evaluate(self, lst_in):
"""
Evaluate structure alerts on a list of SMILES
:param lst_in: input list of [SMILES, Name]
:return: list of alerts matched or "OK"
"""
smiles, name = lst_in
mol = Chem.MolFromSmiles(smiles)
if mol is None:
return [
smiles, name, 'INVALID', -999, -999, -999, -999, -999, -999
]
desc_list = [
MolWt(mol),
MolLogP(mol),
NumHDonors(mol),
NumHAcceptors(mol),
TPSA(mol),
CalcNumRotatableBonds(mol)
]
for row in self.rule_list:
patt, max_val, desc = row
if len(mol.GetSubstructMatches(patt)) > max_val:
return [smiles, name] + [desc + " > %d" %
(max_val)] + desc_list
return [smiles, name] + ["OK"] + desc_list
canvas.addCanvasText('%s\r\nMolWt: %g\tTPSA: %g' % (s, MolWt(m), TPSA(m)),
pos, font)
with open('xx' + s + '.png', 'w') as f:
canvas.flush()
img.save(f)
if __name__ == '__main__':
drawmol('CN1CCC[C@H]1c2cccnc2')
drawmol('CC(=O)OC1=CC=CC=C1C(=O)O')
drawmol('O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5')
sys.exit(0)
# sample code to use new drawing API (older rdkit do not have DrawString)
from rdkit.Chem.AllChem import EmbedMolecule
assert EmbedMolecule(m) >= 0
x = Draw.rdMolDraw2D.MolDraw2DSVG(200, 250)
x.DrawMolecule(m)
x.DrawString('Test String', 20, 200)
x.FinishDrawing()
print(x.GetDrawingText())
# sample code to generate a legend
legstr = ''
if molname:
legstr += molname + '\n'
legstr += '%s\nWt=%g LogP=%g TPSA=%g\nHBA=%d HBD=%d RotBond=%d\n' % \
(smiles, MolWt(mol), MolLogP(mol), TPSA(mol),
NumHAcceptors(mol), NumHDonors(mol), NumRotatableBonds(mol))
def calc_NumHAcceptors(smiles_string):
"""Given a smiles string (ex. C1CCCCC1), calculate and return the NumHAcceptors"""
mol = Chem.MolFromSmiles(smiles_string)
return NumHAcceptors(mol)
def calc_NumHAcceptors(smiles_string):
mol = Chem.MolFromSmiles(smiles_string)
return NumHAcceptors(mol)