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a-r-j / graphein

Protein Graph Library
https://graphein.ai/
MIT License
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mesh with surface descriptors? #251

Open johnnytam100 opened 1 year ago

johnnytam100 commented 1 year ago

Hi @a-r-j Happy 2023, I wish you great success with graphein and more!

I am trying to build a protein mesh with surface descriptors (e.g. hydrophobicity).

As an example, like what HTMD from Acellera can do (though it is voxelization but not meshing)

image

Does graphein have this functionality already?

a-r-j commented 1 year ago

Hi @johnnytam100, happy new year to you too!

At present, no, I don’t see an easy way to do that in Graphein. You could check out masif however. The original surface-based model used MSMS to compute the surface & then map features on to it.

See here: https://github.com/LPDI-EPFL/masif/blob/2a370518e0d0d0b0d6f153f2f10f6630ae91f149/source/triangulation/computeMSMS.py#L13

https://github.com/LPDI-EPFL/masif/blob/2a370518e0d0d0b0d6f153f2f10f6630ae91f149/source/triangulation/computeHydrophobicity.py#L27

If you end up writing a nice solution feel free to make a PR! It’d be a great feature.