Code
This page lists software projects and research codes that I maintain on GitHub. The repositories below are connected to my work on molecular distance geometry, protein structure data, and algorithms for distance-constraint problems.
You can also find my public repositories on my GitHub profile.
pdb-parser
pdb-parser is a lightweight Python toolkit for parsing Protein Data Bank (PDB) Nuclear Magnetic Resonance (NMR) structures and generating distance and torsion-angle constraints tailored for Distance Geometry Problem (DGP) workflows.
The package extracts structural information from PDB files and produces constraint sets that can be used in algorithms for protein structure determination.
Main features
- Generates distance-constraint lists from PDB/NMR structures.
- Generates backbone torsion-angle data.
- Extracts 3D coordinate data.
- Provides command-line tools for parsing instances and reordering generated outputs.
- Supports configurable workflows through text-based configuration files.
Technical details
- Language: Python
- Current release: v0.2.0
- Related topic: molecular distance geometry, PDB/NMR data, protein structure determination
- Citation: connected to the preprint An Angle-Based Algorithmic Framework for the Interval Discretizable Distance Geometry Problem
bpbm-3d-iddgp
bpbm-3d-iddgp implements Branch-and-Prune based methods for the 3D Interval Discretizable Distance Geometry Problem (iDDGP).
The code implements three algorithmic variants for embedding molecular structures from interval distance data and torsional constraints, producing feasible conformations under geometric rules.
Implemented methods
- iBP: interval Branch-and-Prune
- iABP: interval Angular Branch-and-Prune
- iTBP: interval Torsion-angle Branch-and-Prune
Technical details
- Language: C (C11)
- Current release: v1.0.0
- Dependencies: LAPACKE, LAPACK, BLAS, and the C math library
- Related topic: interval distance geometry, molecular conformation, Branch-and-Prune algorithms
- Citation: connected to the preprint An Angle-Based Algorithmic Framework for the Interval Discretizable Distance Geometry Problem
The benchmark datasets associated with this project are maintained separately in the benchmarks repository.