linting

environments/community/protein_design/tool_definitions.py

@@ -0,0 +1,92 @@
+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,
+]