from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
IPythonConsole.ipython_useSVG = True
mol = Chem.MolFromSmiles("C1NCCC1")
atoms = mol.GetNumAtoms()
for idx in range( atoms ):
mol.GetAtomWithIdx( idx ).SetProp( 'molAtomMapNumber', str(mol.GetAtomWithIdx( idx ).GetAtomicNum()) )
mol
mol = Chem.MolFromSmiles("C1NCCC1")
atoms = mol.GetNumAtoms()
for idx in range( atoms ):
mol.GetAtomWithIdx( idx ).SetProp( 'molAtomMapNumber', str(mol.GetAtomWithIdx( idx ).GetIdx()) )
a = mol.GetAtomWithIdx(0)
mol
def mol_with_atom_index( mol ):
atoms = mol.GetNumAtoms()
for idx in range( atoms ):
mol.GetAtomWithIdx( idx ).SetProp( 'molAtomMapNumber', str( mol.GetAtomWithIdx( idx ).GetIdx() ) )
return mol
mol = Chem.MolFromSmiles( "C1CC2=C3C(=CC=C2)C(=CN3C1)[C@H]4[C@@H](C(=O)NC4=O)C5=CNC6=CC=CC=C65" )
mol
mol_with_atom_index(mol)