:>"^ @ssdZddlZddlZddlmZddlmZejdZGddde Z 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@sUeZdZdZdddZddZddZd 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 1/tmp/pip-build-ww9dw3qa/biopython/Bio/PDB/Dice.py__init__s   zChainSelector.__init__cCs|j|jkrdSdS)z+Verify if model match the model identifier.r)get_idr)r modelr r r accept_model#szChainSelector.accept_modelcCs|j|jkrdSdS)z'Verify if chain match chain identifier.r r)rr)r chainr r r accept_chain*szChainSelector.accept_chaincCsu|j\}}}|dkr%dS|dkrKtjd||ft|j|koh|jknrqdSdS)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_residue0s  "zChainSelector.accept_residuecCs'|j}tj|rdSdSdS)z!Verify if atoms are not Hydrogen.rr N)r _hydrogenmatch)r Zatomnamer r r accept_atom?s zChainSelector.accept_atomN) __name__ __module__ __qualname____doc__r rrrrr r r r rs    rcCs<t|||}t}|j||j||dS)z'Write out selected portion to filename.N)rrZ set_structuresave)Z structurerrrfilenameselior r r extractIs  r#) rrerZ Bio.PDB.PDBIOrZBiorcompilerobjectrr#r r r r  s  3