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darrenwee / drug-discovery

Matchmaking proteins and ligands!
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Implement voxel descriptor feature extraction #1

Closed darrenwee closed 6 years ago

darrenwee commented 6 years ago

Implement a (simplified) version of the voxel feature extraction

Ref: https://github.com/Acellera/htmd/blob/master/htmd/molecule/voxeldescriptors.py

Both protein and ligand are featurized via a voxelized 24 Å representation of the binding site considering eight pharmacophoric-like properties.

Jiménez, J., Skalic, M., Martínez-Rosell, G., & De Fabritiis, G. (2018). K DEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks. Journal of chemical information and modeling, 58(2), 287-296.

alexfjw commented 6 years ago

Note that the mapping in def _getRadii(mol): is quite incomplete. I edited the mappings to fill up the missing matches.

Also, there's a divide by zero error at line 330. I did a quick hack on my side to avoid that problem. (Both the 'C' implementation & numba implementation suffer from this problem. The numba implementation was easier to fix.) https://github.com/Acellera/htmd/blob/330655f6d03a56efe6909c041fb65c5a7ce5ea23/htmd/molecule/voxeldescriptors.py#L330

See following link for the edited file. https://gist.github.com/alexfjw/c49980f7053f1e0b225581e5f410d7f2