BioShell Examples - jython scripts

protein_dihedrals.py

Reads a PDB file and prints values of Phi, Psi dihedral angles, Chi side chain dihedral angles and some statistics for each residue.

ligand_neighborhood.py

Finds a ligand molecule (or a residue) identified by a three-letter code and prints all atoms that are in spatial contacts with it. The result is a PDB file that contains only the requested residue with its neighbors

detect_disulfides.py

Reads a PDB file and detects difulfide bonds based on geometric criteria.

contact_map.py

Reads a number of PDB files that may contain multiple models of the same protein and create a summary contact map.