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a-r-j / graphein

Protein Graph Library
https://graphein.ai/
MIT License
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Protein-Ligand Interaction Graphs #162

Open a-r-j opened 2 years ago

a-r-j commented 2 years ago

Follow on issue for #155

We'd like to support Protein-Ligand Interaction Graphs eg as shown in this image from this paper.

image

Ideally we can keep this composable under the hood. E.g. we could take a protein graph computed via the graphein.protein API and molecule graph computed with the graphein.molecule API and merge them into one graph (and separate them into two).

The hardest aspect of this is remove non-ligand and non-protein HETATMs from the PDB records. There will be metal ions, crystallographic adjuvants and co-factors that we may wish to exclude. We can maintain common sets of these in our lists of constants and provide an access point for users to supply their own.

A starting point can be this gist from Pat Walters.

yuanqidu commented 2 years ago

I will work on this one :D

BenCree commented 1 year ago

I'm interested in this feature, did you ever end up getting it working?

a-r-j commented 1 year ago

Hi @BenCree , apologies, this slipped through the cracks for me. You can checkout this PR: https://github.com/a-r-j/graphein/pull/164/