molclaw-fix-pdb

PDBFixer Repair

Note:

• Local files are not directly accessible by the server. Please upload them to the server using molclaw-file-transfer before execution.
• For PDB file inputs, it is recommended to preprocess them using molclaw-pdbfixer before execution.
• Please refer to skill molclaw-scp-server to complete tool invocation.

Usage

1. PDB Repair

The description of tool fix_pdb.

Repair a PDB or mmCIF structure using PDBFixer, optionally clean or model missing parts, write the repaired PDB (unless `dry_run`), and return topology counts.
Args:
    input_path (str): Path to the source PDB or mmCIF file to repair.
    output_path (str|None): Optional output file path for the repaired PDB. If omitted the tool writes to a run-specific folder.
    add_hydrogens (bool): Add missing hydrogens after filling atoms (default: False).
    ph (float): pH value used when adding hydrogens (default: 7.0).
    remove_heterogens (bool): Remove heterogens/ligands (keeps waters unless `remove_water` True).
    remove_water (bool): Remove water molecules (default: False).
    replace_nonstandard (bool): Replace nonstandard residues with standard counterparts (default: False).
    keep_chains (List[str]|None): If provided, retain only these chain IDs.
    add_missing_residues (bool): Attempt to model missing residues before filling atoms (default: False).
    dry_run (bool): Validate operations without writing the repaired file (default: False).
Return:
    status (str): 'success' or 'error'.
    msg (str): Human-readable summary or error message.
    output_dir (str|None): Run-specific directory under tool_result/pdbfixer_result.
    output_file (str|None): Path to the repaired PDB file (None for dry runs or on error).
    atom_count (int|None): Total atoms in the repaired topology when available.
    residue_count (int|None): Total residues in the repaired topology when available.
    chain_count (int|None): Total chains in the repaired topology when available.