Fix ruff lint and formatting across bindmaster/, examples/, tests/

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: damborik22

bindmaster/scoring/unified.py

@@ -14,7 +14,6 @@
 import json
 from dataclasses import asdict, dataclass, field
 from enum import Enum
-from typing import Optional
 
 
 class ToolOrigin(str, Enum):
@@ -49,33 +48,33 @@ class BinderScore:
     binder_length: int
 
     # --- Structural confidence ---
-    plddt_binder: Optional[float] = None
-    iptm: Optional[float] = None
-    ptm: Optional[float] = None
-    ipae: Optional[float] = None
-    pae_interaction: Optional[float] = None
+    plddt_binder: float | None = None
+    iptm: float | None = None
+    ptm: float | None = None
+    ipae: float | None = None
+    pae_interaction: float | None = None
 
     # --- Geometry ---
-    binder_rmsd: Optional[float] = None
-    complex_rmsd: Optional[float] = None
+    binder_rmsd: float | None = None
+    complex_rmsd: float | None = None
 
     # --- Filter pass/fail (PXDesign-style booleans) ---
-    passes_af2ig_easy: Optional[bool] = None
-    passes_af2ig_strict: Optional[bool] = None
-    passes_protenix_basic: Optional[bool] = None
-    passes_protenix_strict: Optional[bool] = None
+    passes_af2ig_easy: bool | None = None
+    passes_af2ig_strict: bool | None = None
+    passes_protenix_basic: bool | None = None
+    passes_protenix_strict: bool | None = None
 
     # --- Ligand-specific (RFDiffusionAA only) ---
-    ligand_ccd_code: Optional[str] = None
-    ligand_contact_residues: Optional[int] = None
+    ligand_ccd_code: str | None = None
+    ligand_contact_residues: int | None = None
 
     # --- Computed composite ---
-    composite_score: Optional[float] = field(default=None, init=False)
+    composite_score: float | None = field(default=None, init=False)
 
     def __post_init__(self):
         self.composite_score = self._compute_composite()
 
-    def _compute_composite(self) -> Optional[float]:
+    def _compute_composite(self) -> float | None:
         """Compute composite score from available metrics."""
         terms = {}
 

bindmaster/tools/base.py

@@ -8,7 +8,6 @@
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Optional
 
 
 @dataclass
@@ -24,9 +23,9 @@ class ToolResult:
     output_dir: Path
     pdb_paths: list[Path]
     log_path: Path
-    error_message: Optional[str] = None
-    raw_scores: Optional[dict] = None  # Tool-specific scores, unmodified
-    metadata: Optional[dict] = None  # Any additional tool-specific info
+    error_message: str | None = None
+    raw_scores: dict | None = None  # Tool-specific scores, unmodified
+    metadata: dict | None = None  # Any additional tool-specific info
 
 
 class ToolAdapter(ABC):

bindmaster/tools/pxdesign/config.py

@@ -5,26 +5,27 @@
 from __future__ import annotations
 
 import hashlib
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from pathlib import Path
-from typing import Optional, Union
 
 import yaml
 
 
 @dataclass
 class ChainConfig:
     """Configuration for a single target chain."""
-    crop: Optional[list[str]] = None
-    hotspots: Optional[list[int]] = None
-    msa: Optional[Path] = None
+
+    crop: list[str] | None = None
+    hotspots: list[int] | None = None
+    msa: Path | None = None
 
 
 @dataclass
 class PXDesignTargetConfig:
     """Target structure configuration."""
+
     file: Path
-    chains: dict[str, Union[ChainConfig, str]]
+    chains: dict[str, ChainConfig | str]
 
     def __post_init__(self):
         if not Path(self.file).exists():
@@ -37,6 +38,7 @@ class PXDesignConfig:
     Complete PXDesign run configuration.
     Generates a YAML file that pxdesign CLI consumes.
     """
+
     target: PXDesignTargetConfig
     binder_length: int
     n_samples: int = 1000
@@ -48,7 +50,7 @@ class PXDesignConfig:
     # BindMaster-specific (not written to YAML)
     gpu_device: int = 0
     conda_env: str = "bindmaster_pxdesign"
-    task_name: Optional[str] = None
+    task_name: str | None = None
 
     def get_task_name(self) -> str:
         if self.task_name:
@@ -75,7 +77,7 @@ def to_yaml(self, output_path: Path) -> Path:
             "target": {
                 "file": str(self.target.file),
                 "chains": {},
-            }
+            },
         }
 
         for chain_id, chain_cfg in self.target.chains.items():
@@ -99,9 +101,12 @@ def to_yaml(self, output_path: Path) -> Path:
     def to_cli_args(self) -> list[str]:
         """Generate the `pxdesign pipeline` CLI argument list."""
         args = [
-            "--preset", self.preset,
-            "--N_sample", str(self.n_samples),
-            "--dtype", self.dtype,
+            "--preset",
+            self.preset,
+            "--N_sample",
+            str(self.n_samples),
+            "--dtype",
+            self.dtype,
         ]
         if self.use_fast_ln:
             args += ["--use_fast_ln", "True"]

bindmaster/tools/pxdesign/msa_manager.py

@@ -10,7 +10,7 @@
 import time
 from pathlib import Path
 
-from bindmaster.tools.pxdesign.config import PXDesignConfig, ChainConfig
+from bindmaster.tools.pxdesign.config import ChainConfig, PXDesignConfig
 
 
 class MSAManager:
@@ -28,10 +28,7 @@ def is_cached(self, config: PXDesignConfig) -> bool:
         cache_path = self.cache_dir / key
         if not cache_path.exists():
             return False
-        for chain_id in config.target.chains:
-            if not (cache_path / chain_id).exists():
-                return False
-        return True
+        return all((cache_path / chain_id).exists() for chain_id in config.target.chains)
 
     def get_msa_paths(self, config: PXDesignConfig) -> dict[str, Path]:
         key = self.cache_key(config)
@@ -41,8 +38,7 @@ def get_msa_paths(self, config: PXDesignConfig) -> dict[str, Path]:
             chain_msa = cache_path / chain_id
             if not chain_msa.exists():
                 raise FileNotFoundError(
-                    f"MSA not cached for chain {chain_id} "
-                    f"(target_hash={key}). Run compute_msa() first."
+                    f"MSA not cached for chain {chain_id} (target_hash={key}). Run compute_msa() first."
                 )
             paths[chain_id] = chain_msa
         return paths
@@ -68,8 +64,17 @@ def compute_msa(
 
         t0 = time.time()
         proc = subprocess.run(
-            ["conda", "run", "-n", conda_env, "--no-capture-output",
-             "pxdesign", "prepare-msa", "--yaml", str(tmp_yaml)],
+            [
+                "conda",
+                "run",
+                "-n",
+                conda_env,
+                "--no-capture-output",
+                "pxdesign",
+                "prepare-msa",
+                "--yaml",
+                str(tmp_yaml),
+            ],
             capture_output=True,
             text=True,
         )

bindmaster/tools/pxdesign/results_parser.py

@@ -7,7 +7,6 @@
 import csv
 from pathlib import Path
 
-
 COLUMN_MAP = {
     "af2_ipTM": "af2_iptm",
     "af2_ipAE": "af2_ipae",
@@ -89,10 +88,7 @@ def get_passing_designs(
     }.get(filter_name)
 
     if not filter_key:
-        raise ValueError(
-            f"Unknown filter '{filter_name}'. "
-            f"Choose from: AF2-IG-easy, AF2-IG, Protenix-basic, Protenix"
-        )
+        raise ValueError(f"Unknown filter '{filter_name}'. Choose from: AF2-IG-easy, AF2-IG, Protenix-basic, Protenix")
 
     return [r for r in records if r.get(filter_key) is True]
 
@@ -112,13 +108,21 @@ def summarize_run(summary_csv: Path) -> dict:
 
     print(f"\n[pxdesign] Run summary ({summary_csv.parent.name}):")
     print(f"  Total designs:      {n_total:>6}")
-    print(f"  AF2-IG easy pass:   {summary['passes_af2ig_easy']:>6} "
-          f"({100*summary['passes_af2ig_easy']/max(n_total,1):.1f}%)")
-    print(f"  AF2-IG strict pass: {summary['passes_af2ig_strict']:>6} "
-          f"({100*summary['passes_af2ig_strict']/max(n_total,1):.1f}%)")
-    print(f"  Protenix basic:     {summary['passes_protenix_basic']:>6} "
-          f"({100*summary['passes_protenix_basic']/max(n_total,1):.1f}%)")
-    print(f"  Protenix strict:    {summary['passes_protenix_strict']:>6} "
-          f"({100*summary['passes_protenix_strict']/max(n_total,1):.1f}%)")
+    print(
+        f"  AF2-IG easy pass:   {summary['passes_af2ig_easy']:>6} "
+        f"({100 * summary['passes_af2ig_easy'] / max(n_total, 1):.1f}%)"
+    )
+    print(
+        f"  AF2-IG strict pass: {summary['passes_af2ig_strict']:>6} "
+        f"({100 * summary['passes_af2ig_strict'] / max(n_total, 1):.1f}%)"
+    )
+    print(
+        f"  Protenix basic:     {summary['passes_protenix_basic']:>6} "
+        f"({100 * summary['passes_protenix_basic'] / max(n_total, 1):.1f}%)"
+    )
+    print(
+        f"  Protenix strict:    {summary['passes_protenix_strict']:>6} "
+        f"({100 * summary['passes_protenix_strict'] / max(n_total, 1):.1f}%)"
+    )
 
     return summary