Re: [Open Babel] Converting PDB to SMILES and matching atom orders

David, Thank you very much for the reply, very smart hack! Sam On Wed, Aug 31, 2016 at 7:27 PM, David Hall wrote: > It is a bit of a hack, but for certain applications where I know it is > likely fine, I use networkx to do subgraph isomorphism while considering > only

Re: [Open Babel] Converting PDB to SMILES and matching atom orders

It is a bit of a hack, but for certain applications where I know it is likely fine, I use networkx to do subgraph isomorphism while considering only the elements and not looking at the order of the bonds. I can trivially draw a molecule where this does the wrong thing, but the majority of the

Re: [Open Babel] Converting PDB to SMILES and matching atom orders

Dear Sefano, Thanks for the reply, I was suspecting the same. However I need the PDB 3D coordinates mapped on the original SMILES, that's why I was trying reading the PDB. I am wondering if there are any methods to map the PDB coordinates of a molecule to its original SMILES? Thanks, Sam On

Re: [Open Babel] Converting PDB to SMILES and matching atom orders

Sam, I wouldn't trust the PDB for either bond order or connectivity. In OB the order is inferred from the distances, which are dependent on the quality of the structure and the software used for the model refinement. For example, I found that in structures generated a version of Refmac, the

[Open Babel] Converting PDB to SMILES and matching atom orders

I am trying to read a small molecule from PDB file and match its atom numbers to the same molecule in a SDF file. I have tried both matching SMART patterns and using OBIsomorphismMapper, both work for 70% of cases. However there are cases for which OpenBabel can not simply get the right SMILES