Re: [Rdkit-discuss] RDKit Chem.MolFromPDBFile ignores some files...

Thanks. Yes, I too understood that it should get the connectivity from the distances. I'm using PDB for it being the output from another program. I'll see what I can change then. Thanks, Gustavo. -- Gustavo Seabra From: Alan Kerstjens Medina Sent: Sunday,

[Rdkit-discuss] ?????? How to sort a list of mol objects

Hi, I've tested the code below, and found out that put mol objects into pandas is just straightforward. [code] #SMILES string list into mol objects, and then into dataframe import pandas as pd from rdkit import Chem smiles = ['c1c1', 'c1c1O', 'c1cc(O)ccc1O'] mols =

Re: [Rdkit-discuss] RDKit Chem.MolFromPDBFile ignores some files...

Hi Gustavo, I haven’t looked into the RDKit source code for this but I assume this has to do with the lack of CONECT records in the PDB file you attached (i.e. you are only storing atom coordinates, not connectivity). >From what I could gather from the RDKit documentation, the default

Re: [Rdkit-discuss] How to sort a list of mol objects

Hi Paolo, Your previous reply already helped me. If I need to sort multiple properties, with different directions, What would the code be? Would it be easier to put mols into a pandas dataframe? If so, how to do it? Best regards Zhenting ---Original--- From: "Paolo