pharmacophore alignment using RDKit

One of the my favorite paper is “SAR NEWS 19”.
link here
I wrote some script for p4core align and uploaded to my repository . makes pharmacophore object from input file and dump it. aligns input sdf to pharmacophore from But I must improve this script ASAP.

Basic usage…

To Get Pharmacophore.

iwatobipen$ python  query_mol.sdf

You could make query_mol.sdf from your interested PDB file or any .
And after run the script, you could get pharmacophore object named query_mol_pcophore.pkl.

To Get Align molecules to the p4core.

iwatobipen$ python -i mols.sdf -p query_mol_pcophore.pkl -o output.sdf

-o is option. default output file name is res.sdf.

At first this script reads input sdf and pharmacophore object.
Then it tries to generate 3D conf that satisfies the pharmacophore and optimize conf using universal force field.
Finally all generated conformers are aligned and write to sdf.
I tested these scripts, but does not work well. 😦
If anyone who has any advices, please post comment or advice for me.


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