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Metal3D and Metal3D-Cat

The manuscript scores P(catalytic metal) with Metal3D-Cat. That is just another --models entry. The same wrapper runs Metal3D (any metal site) or Metal3D-Cat (catalytic metal site).

metal3d_model scans through the current PDB and predicts based on the local chemical enviornments the probability and position of a metal site. It writes pmetal (higher is better).

Which weights

Same yaml block. Only model_path changes.

weights use when
metal3d_cat.pth Metal3D-Cat for predicting a catalytic metal (the paper)
metal3d_clean.pth Metal3D-Clean for predicting a generic metal site 
models:
  metal3d:
    model_path: ./models/metal3d/weights/metal3d_cat.pth
    max_metal_p: 0.2
    threshold: 5

The CLI name is metal3d_model. The config section is metal3d.

python run.py -c configs/your_run.yml \
  --models seq_model metal3d_model

Add pocket shape, physics, pKa, or anything else on the same line. A demo that combines both Metal3D-Cat and pocket shape is available in example_substrate.md.

Files

file role
models/metal3d_model.py the dEVA wrapper
models/metal3d/weights/metal3d_cat.pth Metal3D-Cat
models/metal3d/weights/metal3d_clean.pth Metal3D-Clean
models/metal3d/weights/metal_0.5A_v3_d0.2_16Abox.pth Metal3D OG