Re: [Rdkit-discuss] Mapping of atom numbering, naming and coordinates for different conformers

ot; Betreff: Re: Re: [Rdkit-discuss] Mapping of atom numbering, naming and coordinates for different conformers If you read the PDBfile RDKit does not guess the atom types, hence the AssignBondOrdersFromTemplate function. If you have SMILES for that PDB, assign bond orders acording to smi and t

Re: [Rdkit-discuss] Mapping of atom numbering, naming and coordinates for different conformers

Hi Max, Have you tried getting the atom map simplu by mathing those molecules? mol2.GetSubstructMatch(mol1) If your molecules dont match this way you can seek inspiration in AssignBondsFromTemplate function here: https://github.com/rdkit/rdkit/blob/83d62a71f28b96b29458bcda225374d7f07f9c82/rdkit

[Rdkit-discuss] Mapping of atom numbering, naming and coordinates for different conformers

Hi everyone,   I am stuck on the following issue: I have two files of different conformers for the same molecule. One is an NMR generated reference PDB, the other one is an sdf with conformers generated in RDKit. I would now like to merge the two files into one PDB preserving the initial atom nu