Hi everyone,
I'm trying to create coordinates for a molecule containing a TRANS double
bond in a ring. However, while I try to create coordinate from the mol
object, the structure that was created is CIS and not TRANS.
I check both options (cis and trans) and check that bond
specificity correctly using FindPotentialStereo, then I use MolToMolBlock
in order to create coordinate, and both structures (cis and trans) are
created as CIS.
any ideas/suggestions?
thanks in advance,
Shani
For example my code:
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
print(rdkit.__version__)
smiles = {'Cis':'C/C1=C\CCCCCCCC1', 'Trans':'C/C1=C/CCCCCCCC1'}
for key in smiles:
mol = Chem.MolFromSmiles(smiles[key])
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)
si = Chem.FindPotentialStereo(mol)
for element in si:
print(f' {key} Type: {element.type}, Descriptor:
{element.descriptor} ')
print(Chem.MolToMolBlock(mol), file=open(str(key)+'.mol', 'w+'))
*the output: *
2021.09.4
Cis Type: Bond_Double, Descriptor: Bond_Cis
Trans Type: Bond_Double, Descriptor: Bond_Trans
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