BiopLib

BiopLib provides a C library for parsing and manipulating protein structures (PDB and PDBML) and for computing solvent accessibility and renumbering atoms and residues.

Key Features:

• Protein Structure Handling: PDB parser that manages alternate occupancies and supports compressed PDB files and PDBML (XML) formats.
• Flexible Data Management: Represents PDB data either as a simple list of atoms or as a hierarchical model with chains, residues, and atoms.
• General Programming Utilities: Includes general-purpose programming and mathematical functions and routines for handling protein sequences.
• Command-Line Tools (BiopTools): BiopTools supplies command-line filter utilities that process PDB and PDBML files to renumber atoms and residues and to calculate solvent accessibility.

Scientific Applications:

• Structural Analysis and Visualization: Analysis and visualization of protein models using parsed PDB/PDBML data.
• Computational Studies: Studies of solvent accessibility and residue/atom renumbering.
• Tool Development: Development of custom bioinformatics tools that manipulate PDB and PDBML data and protein sequences.

Methodology:

Parsing of PDB and PDBML (including compressed files) with handling of alternate occupancies; representation of structures as atom lists or chain/residue/atom hierarchies; provision of general programming and mathematical routines; and command-line filtering operations for renumbering and solvent accessibility calculation.