B b @sPdZddlZddlZddlmZddlmZedZGdddZ dd Z dS) znCode for chopping up (dicing) a structure. This module is used internally by the Bio.PDB.extract() function. N)PDBIO)BiopythonWarningz [123 ]*H.*c@s:eZdZdZdddZddZddZd d Zd d Zd S) ChainSelectorzOnly accepts residues with right chainid, between start and end. Remove hydrogens, waters and ligands. Only use model 0 by default. rcCs||_||_||_||_dS)zInitialize the class.N)chain_idstartendmodel_id)selfrrrrr +lib/python3.7/site-packages/Bio/PDB/Dice.py__init__szChainSelector.__init__cCs||jkrdSdS)z+Verify if model match the model identifier.r)get_idr)r Zmodelr r r accept_model#szChainSelector.accept_modelcCs||jkrdSdS)z'Verify if chain match chain identifier.r r)rr)r chainr r r accept_chain*szChainSelector.accept_chaincCsZ|\}}}|dkrdS|dkr6td||ft|j|krN|jkrVnndSdS)zCVerify if a residue sequence is between the start and end sequence. rz WARNING: Icode %s at position %sr )rwarningswarnrrr)r ZresidueZ hetatm_flagZresseqZicoder r r accept_residue0szChainSelector.accept_residuecCs|}t|rdSdSdS)z!Verify if atoms are not Hydrogen.rr N)r _hydrogenmatch)r Zatomnamer r r accept_atom?s zChainSelector.accept_atomN)r) __name__ __module__ __qualname____doc__r rrrrr r r r rs  rcCs,t|||}t}|||||dS)z'Write out selected portion to filename.N)rrZ set_structureZsave)Z structurerrrfilenameZselior r r extractIs  r ) rrerZ Bio.PDB.PDBIOrZBiorcompilerrr r r r r  s   3