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Repair a protein PDB file with PDBFixer: fix missing atoms/residues, add hydrogens, remove heterogens, etc.
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Basé sur la classification professionnelle SOC
| name | molclaw-pdbfixer |
| description | Repair a protein PDB file with PDBFixer: fix missing atoms/residues, add hydrogens, remove heterogens, etc. |
Note:
molclaw-file-transfer before execution.molclaw-pdbfixer before execution.molclaw-scp-server to complete tool invocation.Use tool fix_pdb to repair the protein structure file (pdb format) as below:
Tool description:
Repair a PDB file with PDBFixer: fix missing atoms/residues, add hydrogens, remove heterogens, etc.
Args:
input_path (str): Path to the source PDB file to repair (required)
add_hydrogens (bool): Add missing hydrogens after atom completion (default: False)
ph (float): pH value used when adding hydrogens (default: 7.0)
remove_heterogens (bool): Remove heterogens/ligands; keeps waters if remove_water is False (default: False)
remove_water (bool): Remove water molecules even if heterogens are retained (default: False)
replace_nonstandard (bool): Replace nonstandard residues with standard counterparts (default: False)
keep_chains (List[str] | None): If provided, only retain the listed chain IDs (default: None)
add_missing_residues (bool): Attempt to model missing residues before filling atoms (default: False)
dry_run (bool): Validate and simulate repairs without writing output file (default: False)
Return:
status (str): 'success' or 'error'
msg (str): Human-readable summary of the result
output_dir (str | None): Run-specific folder under tool_result/pdbfixer_result
output_file (str | None): Path to the repaired PDB file (None during dry_run or on error)
atom_count (int | None): Total atoms in the repaired topology
residue_count (int | None): Total residues in the repaired topology
chain_count (int | None): Total chains in the repaired topology
Tool usage:
response = await client.session.call_tool(
"fix_pdb",
arguments={
"input_path": pdb_path,
"add_hydrogens": add_hydrogens,
"ph": ph,
"remove_water": remove_water,
"replace_nonstandard": replace_nonstandard,
"remove_heterogens": remove_heterogens,
"add_missing_residues": add_missing_residues
}
)
result = client.parse_result(response)
fixed_pdb_path = result["output_file"]
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