cis trans information

[manajit-das]

Hi,
How to check if two atom of interest (let's say I know the indexes) are cis or trans around a double bond?
I tried getting a conformation and measure the dihedral angle to find it, but how to do it without any conformation generation.
Thank you.

[greglandrum]

I'll leave writing the actual code to you, but here's how to get the information you need:

In [35]: m = Chem.MolFromSmiles('C/C(F)=C(Cl)/C')

In [36]: bnd = m.GetBondWithIdx(2)

In [37]: bnd.GetStereo()
Out[37]: rdkit.Chem.rdchem.BondStereo.STEREOE

In [38]: bnd.GetStereoAtoms()
Out[38]: <rdkit.rdBase._vectint at 0x1d8a4d66d60>

In [39]: list(bnd.GetStereoAtoms())
Out[39]: [2, 4]
#   ^^^ Based upon this you know that atoms 2 and 4 are trans ("E") from each other across the double bond

Here's how to find the other atoms connected to the two ends of the bond:

In [40]: beginNbrs = [x for x in bnd.GetBeginAtom().GetNeighbors() if x.GetIdx()!=bnd.GetEndAtomIdx()]

In [41]: beginNbrs = [x.GetIdx() for x in bnd.GetBeginAtom().GetNeighbors() if x.GetIdx()!=bnd.GetEndAtomIdx()]

In [42]: endNbrs = [x.GetIdx() for x in bnd.GetEndAtom().GetNeighbors() if x.GetIdx()!=bnd.GetBeginAtomIdx()]

In [43]: beginNbrs
Out[43]: [0, 2]

In [44]: endNbrs
Out[44]: [4, 5]

[manajit-das]

Thank you so much. I was looking for this.