pdbqc 0.1.3

Structure quality report and cleaning for PDB/mmCIF files

pdbqc

A Python tool for structure quality reporting and cleaning of PDB/mmCIF files. Detects and reports common structural pathologies — alternate locations, insertion codes, microheterogeneity, missing residues, and selenomethionine conversions — in a clean, colored terminal report.

Install

pip install pdbqc

Usage

Python

from pdbqc import clean_structure, format_report

# Basic usage
qc, structure = clean_structure("my_structure.cif")
format_report(qc)

# With CIF file for coverage and missing residue data
qc, structure = clean_structure("my_structure.pdb", cif_path="my_structure.cif")
format_report(qc)

# Keep ligands in cleaned structure
qc, structure = clean_structure("my_structure.pdb", keep_ligands=True)
format_report(qc)

CLI

pdbqc my_structure.pdb
pdbqc my_structure.pdb --cif my_structure.cif
pdbqc my_structure.pdb --keep-ligands

Output

╔══════════════════════════════════════╗ ║ Structure Quality Report ║ ╚══════════════════════════════════════╝ Atoms: 2671 Altlocs detected: none Insertion codes: none Microheterogeneity: none Chain Missing Residues Coverage ────────────────────────────────── A 15 90.5% B 13 91.8% C 0 100.0% D 0 100.0% MSE residues converted: none

What it checks

• Alternate locations — counts atoms with altlocs before filtering; keeps highest occupancy
• Insertion codes — detects and reports non-standard residue numbering
• Microheterogeneity — flags residues with conflicting identities across altlocs
• Missing residues — compares observed CA atoms to SEQRES (requires CIF)
• Coverage — per-chain percentage of observed vs expected residues
• MSE conversion — selenomethionine residues renamed to MET for standardized downstream use

Links

• PyPI
• GitHub