Welcome to pdb_cpp’s documentation!
pdb_cpp is a structural bioinformatics toolkit with a C++ core and Python
API for fast PDB/mmCIF parsing, atom selection, sequence/structure alignment,
TM-score, and DockQ evaluation.
Getting Started
User Guide
- Functionality Guide
- 1. Reading and writing structures
- Interaction analysis
- 2. The
CoorandModelobjects - 3.1 SASA and interface SASA
- 3. Atom selection
- 4. Sequence extraction
- 5. Sequence alignment
- 6. Structural alignment (RMSD-based)
- 7. TM-align and TM-score
- 8. Secondary structure assignment
- 9. DockQ scoring
- 10. Hydrogen bond detection
- 11. Geometry utilities
- 12. Data cleaning utilities
- 13. Module summary
- 14. Data subpackage (
pdb_cpp.data)
Recipes
- Quick Recipes
- 1) Load a structure from local file or PDB ID
- 2) Force a specific file format
- 3) Load an asymmetric unit or biological assembly from RCSB
- 4) Inspect atom properties
- 5) Extract an interface selection between two chains
- 6) Select a receptor-ligand complex subset
- 7) Clean up: remove incomplete backbone residues
- 8) Sequence alignment (two chains)
- 9) Structural alignment (RMSD-based)
- 10) One-step sequence-based alignment
- 11) Chain-permutation alignment (unknown chain mapping)
- 12) TM-align and TM-score
- 13) DockQ with automatic chain-role inference
- 14) DockQ with explicit receptor/ligand chains
- 15) DockQ multimer from the command line
- 16) Secondary structure assignment
- 17) Geometry utilities: distance matrix
- 18) SASA and interface SASA
- 19) Estimate protein-protein shape complementarity
- 20) D/L amino acid and nucleic acid sequences
- 21) Hybrid-36 encoding/decoding
- 22) Multi-model: iterate and compute per-model RMSD
- 23) Bond topology (CONECT / _struct_conn)
- 24) Interaction analysis (H-bonds and salt bridges)
Development