o Rŀg @sdZddlmZddlmZddlmZddlmZddlm Z ddl Z ddl m Z dd lmZd ed eeefd eedffd dZd ed eeefd eeeeefffddZde d eeeffddZde d eeefd eeeeffddZGdddZdS)zThis module contains a parser for PDBML (PDB XML) files. PDBML is a representation of PDB data in XML format. See https://pdbml.wwpdb.org/. )PathLike)TextIO)Union) ElementTree)ElementN) Structure)StructureBuildertree namespacesreturncCs4dD]}|||}|r|j}|rt|SqdS)N)z2PDBx:refineCategory/PDBx:refine/PDBx:ls_d_res_highz9PDBx:refine_histCategory/PDBx:refine_hist/PDBx:d_res_highzKPDBx:em_3d_reconstructionCategory/PDBx:em_3d_reconstruction/PDBx:resolution)findtextfloat)r r candidateelementr rG/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/PDBMLParser.py_parse_resolution_froms  rcCsR|d|j|d|j|d|jd|d|j|d|jdt||dS) Nz*PDBx:structCategory/PDBx:struct/PDBx:titlez;PDBx:struct_keywordsCategory/PDBx:struct_keywords/PDBx:textzPDBx:entryCategory/PDBx:entryidz^PDBx:pdbx_database_statusCategory/PDBx:pdbx_database_status/PDBx:recvd_initial_deposition_datezPDBx:exptlCategory/PDBx:exptlmethod)nameheadidcodedeposition_datestructure_method resolution)r r attribr)r r rrr_parse_header_from(s4rrc Cs|d|j}t|d|j}t|d|j}t|d|j}|t|||ftt|d|jt|d|j|d|jpCd|t|jd |d |jd S) NzPDBx:label_atom_idz PDBx:Cartn_xz PDBx:Cartn_yz PDBx:Cartn_zzPDBx:B_iso_or_equivzPDBx:occupancyzPDBx:label_alt_id rzPDBx:type_symbol)rcoordb_factor occupancyaltlocfullname serial_numberr)r r rnparrayintr)rr rxyzrrr_parse_atom_fromAs  r+cCs|jd|ddks J|d|j}|d|j}|d|}|dkr3|dks-|d kr0d }nd }nd }t|d |j}|durE|jnd }|||fS)N{PDBxz }atom_sitezPDBx:group_PDBPDBx:label_comp_idzPDBx:pdbx_PDB_ins_codeHETATMHOHWATWHrzPDBx:auth_seq_id)tagr r r')rr atom_group component_idins_code_element hetero_field sequence_idinsertion_coderrr_parse_residue_id_fromSs  r;c@s8eZdZdZddZdeeeee e fde fddZ dS) PDBMLParsera,A parser for PDBML (PDB XML) files. See https://pdbml.wwpdb.org/. This parser is based on the mmCIF parser also provided in the PDB package in the sense that the structure object returned by this parser is equal to the structure returned by the mmCIF parser for any given PDB structure. cCs t|_dS)zInitialize a PDBML parser.N)rstructure_builder)selfrrr__init__os zPDBMLParser.__init__sourcer cCs`tddt|dgD}t|dr|dt|}t||}|jj|dd|j || d|}d}d }d }d } d } |D]g} t | d |j } | d |j } | d |j }t | |}|rg| |krx|j|| |d 7}| }d }d } |r~| |kr|j| | }d } || ks|| kr|jj|g|R|} |} |jjdit| |qC|jS)zParse and return the PDB structure from XML source. :param Union[int, str, bytes, PathLike, TextIO] source: The XML representation of the PDB structure :return: the PDB structure :rtype: Bio.PDB.Structure.Structure cSsg|]\}}|qSrr).0_noderrr }sz-PDBMLParser.get_structure..zstart-nsseekrr) structure_idzPDBx:atom_siteCategoryNzPDBx:pdbx_PDB_model_numzPDBx:auth_asym_idr.r)dictr iterparsehasattrrEparserr=init_structure set_headerr r'r r; init_model init_chain init_residue init_atomr+ get_structure)r>r@r r header atom_elementsbuilder_model_countbuilder_model_numberbuilder_chain_idbuilder_residue_idbuilder_component_idr model_numberchain_idr6 residue_idrrrrRssH            zPDBMLParser.get_structureN) __name__ __module__ __qualname____doc__r?rr'strbytesrrrrRrrrrr<hsr<)r`osrtypingrr xml.etreerxml.etree.ElementTreernumpyr%Bio.PDB.StructurerBio.PDB.StructureBuilderrrHrarrrr+tupler'r;r<rrrrs@