o Rŀg @sPdZddlZddlZddlmZddlmZedZGdddZ dd Z dS) znCode for chopping up (dicing) a structure. This module is used internally by the Bio.PDB.extract() function. N)BiopythonWarning)PDBIOz [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 @/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/Dice.py__init__s zChainSelector.__init__cC||jkr dSdS)z+Verify if model match the model identifier.r)get_idr)r modelr r r accept_model#szChainSelector.accept_modelcCr )z'Verify if chain match chain identifier.rr)rr)r chainr r r accept_chain*szChainSelector.accept_chaincCs^|\}}}|dkr dS|dkrtd|d|t|j|kr*|jkr-dSdSdS)zCVerify if a residue sequence is between the start and end sequence. rzWARNING: Icode z at position r)rwarningswarnrrr)r residue hetatm_flagresseqicoder r r accept_residue0szChainSelector.accept_residuecCs|}t|r dSdS)z!Verify if atoms are not Hydrogen.rr)r _hydrogenmatch)r atomnamer r r accept_atom?s zChainSelector.accept_atomN)r) __name__ __module__ __qualname____doc__r rrrr r r r r rs  rcCs,t|||}t}|||||dS)z'Write out selected portion to filename.N)rr set_structuresave) structurerrrfilenameselior r r extractIs  r+) r$rerBior Bio.PDB.PDBIOrcompilerrr+r r r r s    3