structure-analysis

Handles protein structure files and geometric criteria so that residue counts, contacts, hydrogen bonds and interfaces are reproducible, covering PDB versus mmCIF, author versus label chains and numbering, HETATM, water and ligand policy, alternate locations, insertion codes, biological assemblies versus the asymmetric unit, hydrogen-bond distance and angle cutoffs, interface definitions by distance or buried surface area, and the Biopython, MDAnalysis, gemmi, PyMOL and ChimeraX calls that implement them. Use whenever a task reads a structure file and reports anything derived from atom coordinates; use biopython for sequence work and molecular-docking or structure-prediction skills for generating structures.