| name | molclaw-pdbfixer |
| description | Repair a protein PDB file with PDBFixer: fix missing atoms/residues, add hydrogens, remove heterogens, etc. |
Repair Protein Structure File
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"]
⚠ Mandatory Output File Download (L3 Principle 14)
After calling this tool, you MUST download all output structure files from the MCP server to the local workspace using server_file_to_base64. A tool call is NOT considered complete until its output files have been downloaded and verified locally (ls -la <file> — size must be > 0).
import base64, os
response = await client.session.call_tool(
"server_file_to_base64",
arguments={"file_path": result["output_file"]}
)
dl = client.parse_result(response)
local_path = "stepNN_descriptive_name.ext"
with open(local_path, "wb") as f:
f.write(base64.b64decode(dl["base64_string"]))
assert os.path.getsize(local_path) > 0, f"Download failed: {local_path}"
Download policy: All structure output files are Category A (user-critical) — essential for user verification, downstream analysis, and reproducibility. When in doubt, download. Over-collection is always preferred over under-collection.
