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Layne-Huang / PMDM

MIT License
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How to generate bond #26

Closed HITzhongyu closed 1 month ago

HITzhongyu commented 5 months ago

Hi，Layne-Huang Thank you very much for your work, and I want to know in your work, only generate the atom and atom coordinate, and use the 'open babel' tools to generate the final drug stucture? I wonder how to generate the bond? thanks! Zhongyu

HITzhongyu commented 5 months ago

I also have another questios in your MDM_pocket_coor_shared.py line 374-378, I want to know why here ligand atom add context? Thanks! Zhongyu

Layne-Huang commented 4 months ago

Hi,

We build the bonds according to the distance and types of the atoms. We have a dictionary to store the distance of different chemical bonds, for example, C-C. If the distance of the generated two carbon atoms is shorter than the stored value, then we build the C-C chemical bond.