openai4s/mcp_servers/protein_design/service.py

• DesignToolError · class · L56-L57 — class DesignToolError(RuntimeError)
• InterruptedAttempt · class · L60-L61 — class InterruptedAttempt(DesignToolError)
• Residue · class · L65-L73 — class Residue
• label · method · L72-L73 — def label(self) -> str
• _canonical · function · L76-L79 — def _canonical(value: Any) -> bytes
• _digest_json · function · L82-L83 — def _digest_json(value: Any) -> str
• _sha256 · function · L86-L91 — def _sha256(path: Path) -> str
• _utc_now · function · L94-L95 — def _utc_now() -> str
• _atomic_json · function · L98-L105 — def _atomic_json(path: Path, value: Any) -> None
• _clean_error · function · L108-L110 — def _clean_error(error: BaseException) -> str
• _sequence · function · L113-L123 — def _sequence(value: Any, field: str = "sequence") -> str
• _read_pdb_residues · function · L126-L160 — def _read_pdb_residues(path: Path) -> dict[str, list[Residue]]
• _chain_sequences · function · L163-L167 — def _chain_sequences(chains: dict[str, list[Residue]]) -> dict[str, str]
• _target_contig · function · L170-L190 — def _target_contig(residues: list[Residue]) -> str
• _parse_json_array_env · function · L193-L207 — def _parse_json_array_env(name: str) -> list[str]
• _mpnn_chain_order · function · L210-L226 — def _mpnn_chain_order(header: str) -> list[str] | None
• _tail_text · function · L229-L247 — def _tail_text(path: Path, limit: int) -> str
• _network_isolation_prefix · function · L250-L303 — def _network_isolation_prefix() -> list[str]
• ProteinDesignService · class · L306-L1466 — class ProteinDesignService
• init · method · L309-L324 — def init(self, *, root: str | Path | None = None, timeout: float | None = None)
• _path · method · L326-L345 — def _path( self, raw: Any, *, existing: bool = False, directory: bool = False ) -> Path
• _prepare · method · L347-L393 — def _prepare( self, name: str, args: dict[str, Any] ) -> tuple[str, int, Path, float, str]
• _operator_path · method · L395-L409 — def _operator_path(self, variable: str, default: str) -> Path
• _admission_key · method · L411-L417 — def _admission_key(self, name: str, args: dict[str, Any]) -> str | None
• _verify_checkpoint · method · L419-L429 — def _verify_checkpoint(self, args: dict[str, Any]) -> tuple[Path, str]
• _verify_checkpoint_bundle · method · L431-L528 — def _verify_checkpoint_bundle( self, args: dict[str, Any] ) -> tuple[Path, Path, str, list[dict[str, str]]]
• _verify_revision · method · L530-L554 — def _verify_revision( self, backend: str, expected: str, repository: Path | None = None ) -> str
• _run · method · L556-L627 — def _run( self, command: list[str], output: Path, *, cwd: Path | None = None, offline: bool = False, ) -> dict[str, Any]
• _base_record · method · L642-L664 — def _base_record( self, name: str, args: dict[str, Any], attempt: str, seed: int, started_at: str, start: float, ) -> dict[str, Any]: # Named redacted while redacting nothing, which is worse than no name # at all: the next author to add a credential-shaped tool field would # read it and assume the digest already excludes the value.
• call · method · L666-L826 — def call(self, name: str, args: dict[str, Any]) -> dict[str, Any]
• _tool_generate_backbone · method · L828-L956 — def _tool_generate_backbone( self, args: dict[str, Any], output: Path ) -> dict[str, Any]
• _tool_design_sequence · method · L958-L1125 — def _tool_design_sequence( self, args: dict[str, Any], output: Path ) -> dict[str, Any]
• _validate_mpnn_fasta · method · L1127-L1194 — def _validate_mpnn_fasta( self, path: Path, source: dict[str, str], residues: dict[str, list[Residue]], design_chains: list[str], fixed_indexes: dict[str, set[int]], expected: int, ) -> list[dict[str, Any]]
• prediction · method · L1196-L1343 — def _prediction( self, args: dict[str, Any], output: Path, *, complex: bool ) -> dict[str, Any]
• _mean · method · L1346-L1350 — def _mean(values: Any) -> float | None
• _interface_pae · method · L1353-L1372 — def _interface_pae(pae: list[Any], lengths: list[int]) -> float
• _tool_predict_structure · method · L1374-L1377 — def _tool_predict_structure( self, args: dict[str, Any], output: Path ) -> dict[str, Any]
• _tool_predict_complex · method · L1379-L1382 — def _tool_predict_complex( self, args: dict[str, Any], output: Path ) -> dict[str, Any]
• _scientific_worker · method · L1384-L1445 — def _scientific_worker( self, name: str, args: dict[str, Any], output: Path ) -> dict[str, Any]
• _tool_rosetta_score · method · L1447-L1448 — def _tool_rosetta_score(self, args: dict[str, Any], output: Path) -> dict[str, Any]
• _tool_rosetta_relax · method · L1450-L1451 — def _tool_rosetta_relax(self, args: dict[str, Any], output: Path) -> dict[str, Any]
• _tool_rosetta_interface_score · method · L1453-L1456 — def _tool_rosetta_interface_score( self, args: dict[str, Any], output: Path ) -> dict[str, Any]
• _tool_score_stability · method · L1458-L1461 — def _tool_score_stability( self, args: dict[str, Any], output: Path ) -> dict[str, Any]
• _tool_energy_minimize · method · L1463-L1466 — def _tool_energy_minimize( self, args: dict[str, Any], output: Path ) -> dict[str, Any]