Ri ndZddlZddlZddlmZddlmZejdZGddZ dZ y) znCode for chopping up (dicing) a structure. This module is used internally by the Bio.PDB.extract() function. N)BiopythonWarning)PDBIOz [123 ]*H.*c0eZdZdZddZdZdZdZdZy) ChainSelectorzOnly accepts residues with right chainid, between start and end. Remove hydrogens, waters and ligands. Only use model 0 by default. c<||_||_||_||_y)zInitialize the class.N)chain_idstartendmodel_id)selfrr r r s D/home/agent/.friday_env/lib/python3.12/site-packages/Bio/PDB/Dice.py__init__zChainSelector.__init__s     c@|j|jk(ryy)z+Verify if model match the model identifier.r)get_idr )r models r accept_modelzChainSelector.accept_model#s <<>T]] *rc@|j|jk(ryy)z'Verify if chain match chain identifier.rr)rr)r chains r accept_chainzChainSelector.accept_chain*s <<>T]] *rc|j\}}}|dk7ry|dk7r tjd|d|t|j|cxkr|j kryyy)zCVerify if a residue sequence is between the start and end sequence. rzWARNING: Icode z at position r)rwarningswarnrr r )r residue hetatm_flagresseqicodes r accept_residuezChainSelector.accept_residue0sj&-^^%5" VU #  C< MM!% fX>@P  :: +488 + ,rcP|j}tj|ryy)z!Verify if atoms are not Hydrogen.rr)r _hydrogenmatch)r atomnames r accept_atomzChainSelector.accept_atom?s!{{} ??4 rN)r) __name__ __module__ __qualname____doc__rrrr r&rr rrs  ! rrcxt|||}t}|j||j||y)z'Write out selected portion to filename.N)rr set_structuresave) structurerr r filenameselios r extractr3Is3 % -C BYGGHcr) r*rerBior Bio.PDB.PDBIOrcompiler"rr3r+rr r8s8    BJJ| $ 00fr