Bio.PDB.Dice module

Code for chopping up (dicing) a structure.

This module is used internally by the Bio.PDB.extract() function.

class Bio.PDB.Dice.ChainSelector(chain_id, start, end, model_id=0)

Bases: object

Only accepts residues with right chainid, between start and end.

Remove hydrogens, waters and ligands. Only use model 0 by default.

__init__(self, chain_id, start, end, model_id=0)

Initialize the class.

accept_model(self, model)

Verify if model match the model identifier.

accept_chain(self, chain)

Verify if chain match chain identifier.

accept_residue(self, residue)

Verify if a residue sequence is between the start and end sequence.

accept_atom(self, atom)

Verify if atoms are not Hydrogen.

Bio.PDB.Dice.extract(structure, chain_id, start, end, filename)

Write out selected portion to filename.