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williamgilpin / pypdb

A Python API for the RCSB Protein Data Bank (PDB)
MIT License
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PyPDB for fetching .sdf (or .mol2) ligand coordinate #42

Open areyesromero opened 3 years ago

areyesromero commented 3 years ago

Dear William, Thanks for creating 'pypdb' module for such a large range of protein data.

As you can see from the picture, the PDB allows downloading either ideal CCDs or instance coordinates.

picture

In the current state of pypdb development, do you think there is/will be a possibility to download specifically only ligands coordinates (.sdf of .mol2) similarly to the "get_pdb_file" function? This would speed up the process of collecting crystallographic reference libraries. In addition, I noticed that these coordinates are already represented in Kekulè form without therefore adding an extra step of preparing the downstream molecules. Best regards Atilio

williamgilpin commented 3 years ago

Hi Atilio, I will take a look at this to see if I can figure it out. I'll warn that I'm a bit slow to add new features these days, but I will leave this open in case any of our other contributors knows how to do it.

danny305 commented 3 years ago

I have some scripts that will download mol2 files for ligands within a particular PDB. Does this sound like the functionality you guys want? If so I can make a PR and commit my scripts.

I have never used this repo and came by this issue in passing and just happen to already have code that does something similar.