Bio.PDB.Dice module¶
Code for chopping up (dicing) a structure.
This module is used internally by the Bio.PDB.extract() function.
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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.
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__init__
(self, chain_id, start, end, model_id=0)¶ Initialize the class.
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accept_model
(self, model)¶ Verify if model match the model identifier.
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accept_chain
(self, chain)¶ Verify if chain match chain identifier.
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accept_residue
(self, residue)¶ Verify if a residue sequence is between the start and end sequence.
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accept_atom
(self, atom)¶ Verify if atoms are not Hydrogen.
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Bio.PDB.Dice.
extract
(structure, chain_id, start, end, filename)¶ Write out selected portion to filename.