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47 lines
1.6 KiB
Plaintext
47 lines
1.6 KiB
Plaintext
# RFdiffusion3 — Enzyme design examples
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RFD3 contains several knobs and dials for enzyme design.
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- input: the pdb or cif file that contains the input theozyme
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- ligand: any ligand res names that are to be included (comma separated)
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- unindex: which residues should have their index be inferred by the model instead of prespecified
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- length: the length range of the generated protein
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- select_fixed_atoms: dictionary that indicated which atoms should be fixed (can use ALL, BKBN, or TIP for all atoms in the residue, backbone atoms only and tip atoms only)
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If you would like to run the examples below, `enzyme_design.json`, located in this directory, contains the example code. You can run it via:
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```
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rfd3 design out_dir=inference_outputs/enzyme/0 \
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ckpt_path=/path/to/rfd3_latest.ckpt \
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inputs=./enzyme_design.json
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```
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Or, if you have cloned the repo rather than using `pip install`:
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```
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python path/to/foundry/models/rfd3/src/rfd3/run_inference.py \
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out_dir=inference_outputs/enzyme/0 \
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ckpt_path=/path/to/rfd3_latest.ckpt \
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inputs=./enzyme_design.json
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```
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An example script for running these examples in batches is also provided in `run_inf_tutorial.sh`.
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The input files for the different examples are provided in `foundry/models/rfd3/docs/input_pdbs`.
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```json
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{
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"M0255_1mg5_unfixed": {
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"input": "../input_pdbs/M0255_1mg5.pdb",
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"ligand": "NAI,ACT",
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"unindex": "A108,A139,A152,A156",
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"length": "180-200",
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"select_fixed_atoms": {
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"A108": "ND2,CG",
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"A139": "OG,CB,CA",
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"A152": "OH,CZ",
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"A156": "NZ,CE,CD",
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"ACT": "OXT",
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"NAI": ""
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}
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}
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}
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```
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