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refactor, full run

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based-tachikoma 2025-05-20 20:11:52 -07:00
parent de9dfff221
commit 1ee67de035
12 changed files with 1039 additions and 1127 deletions
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environments/hack0/protein_design_env/tool_definitions.py Normal file
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PREDICT_TARGET_STRUCTURE_TOOL = {
"type": "function",
"function": {
"name": "predict_target_structure_alphafold2",
"description": "Predicts the 3D structure of the target protein sequence using AlphaFold2.",
"parameters": {
"type": "object",
"properties": {
"sequence": {"type": "string", "description": "Amino acid sequence of the target protein."},
},
"required": ["sequence"]
}
}
}
DESIGN_BINDER_BACKBONE_TOOL = {
"type": "function",
"function": {
"name": "design_binder_backbone_rfdiffusion",
"description": "Generates a novel protein binder backbone using RFDiffusion, conditioned on the target protein structure.",
"parameters": {
"type": "object",
"properties": {
"contigs": {"type": "string", "description": "RFDiffusion contigs (e.g., 'A1-100/0 50-70')."},
"hotspot_residues": {"type": "array", "items": {"type": "string"}, "description": "Optional hotspot residues (e.g., ['A50', 'A52'])."},
},
"required": ["contigs"]
}
}
}
DESIGN_BINDER_SEQUENCE_TOOL = {
"type": "function",
"function": {
"name": "design_binder_sequence_proteinmpnn",
"description": "Designs an amino acid sequence for the generated binder backbone.",
"parameters": {
"type": "object",
"properties": {
"sampling_temp": {"type": "array", "items": {"type": "number"}, "description": "Sampling temperatures (e.g., [0.1, 0.2]). Default [0.1]."}
},
"required": []
}
}
}
EVALUATE_COMPLEX_TOOL = {
"type": "function",
"function": {
"name": "evaluate_binder_complex_alphafold2_multimer",
"description": "Predicts the complex structure of target and designed binder, providing quality scores.",
"parameters": {
"type": "object",
"properties": {
"relax_prediction": {"type": "boolean", "description": "Whether to relax the prediction. Default True."}
},
"required": []
}
}
}
ALL_TOOLS_LIST = [
PREDICT_TARGET_STRUCTURE_TOOL,
DESIGN_BINDER_BACKBONE_TOOL,
DESIGN_BINDER_SEQUENCE_TOOL,
EVALUATE_COMPLEX_TOOL
]