o Rŀg!C@sbdZddlZddlZddlmZddlmZddlm Z ddlm Z ddl m Z Gdd d Z dS) zParser for PDB files.N) as_handle)_parse_pdb_header_list)PDBConstructionException)PDBConstructionWarning)StructureBuilderc@s\eZdZdZ     dddZddZd d Zd d Zd dZddZ ddZ ddZ dS) PDBParserz/Parse a PDB file and return a Structure object.TFNcCsL|dur||_nt|_d|_d|_d|_t||_t||_t||_dS)aCreate a PDBParser object. The PDB parser call a number of standard methods in an aggregated StructureBuilder object. Normally this object is instantiated by the PDBParser object itself, but if the user provides his/her own StructureBuilder object, the latter is used instead. Arguments: - PERMISSIVE - Evaluated as a Boolean. If false, exceptions in constructing the SMCRA data structure are fatal. If true (DEFAULT), the exceptions are caught, but some residues or atoms will be missing. THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!. - get_header - unused argument kept for historical compatibility. - structure_builder - an optional user implemented StructureBuilder class. - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing the SMCRA data will be suppressed. If false (DEFAULT), they will be shown. These warnings might be indicative of problems in the PDB file! - is_pqr - Evaluated as a Boolean. Specifies the type of file to be parsed. If false (DEFAULT) a .pdb file format is assumed. Set it to true if you want to parse a .pqr file instead. Nr) structure_builderrheadertrailer line_counterbool PERMISSIVEQUIETis_pqr)selfr get_headerrrrrE/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/PDBParser.py__init__s  zPDBParser.__init__c CstN|jrtjdtdd|_d|_|j|t |}| }|s*t d| |Wdn1s9wY|j |j|j}Wd|S1sUwY|S)zReturn the structure. Arguments: - id - string, the id that will be used for the structure - file - name of the PDB file OR an open filehandle ignore)categoryNz Empty file.)warningscatch_warningsrfilterwarningsrr r rinit_structurer readlines ValueError_parse set_header get_structure)ridfilehandlelines structurerrrrDs$      zPDBParser.get_structurecC|jS)zReturn the header.)r rrrrrazPDBParser.get_headercCr%)zReturn the trailer.)r r&rrr get_trailerer'zPDBParser.get_trailercCs ||\|_}|||_dS)zParse the PDB file (PRIVATE).N) _get_headerr _parse_coordinatesr )rheader_coords_trailercoords_trailerrrrrkszPDBParser._parsec Csx|j}d}tt|D]}||d||}|dd}|dvr$nq |d|}||_||d}t|}||fS)z:Get the header of the PDB file, return the rest (PRIVATE).r)ATOM HETATMMODEL N)rrangelenset_line_counterr r) rr+riline record_typer r, header_dictrrrr)rs   zPDBParser._get_headerc,Cshd}d}|j}d}d}d}d}d} d} tt|D]f} || d} | dd} |j|d}||| skrmd?d,| dd| dd| dd| dd| ddfD}*t |*d}+||+n| |vr~td@| dA|t|d7}q|j||_gS)Bz0Parse the atomic data in the PDB file (PRIVATE).> TER ANISOUENDMDLr0MASTERSIGATMSIGUIJr/r1rN r.r-r/r0  HOHWATWH &.6z,Invalid or missing coordinate(s) at line %i.f<zInvalid or missing occupancyz'Negative occupancy in one or more atomsBzInvalid or missing B factorg>zInvalid or missing chargeFzInvalid or missing radiuszNegative atom radiusHLNr:cSg|]}t|qSrfloat.0xrrr >z0PDBParser._parse_coordinates..#*+18?g@r1 z&Invalid or missing model serial numberzEND CONECTr;r>cSrYrrZr\rrrr_cr`r=cSrYrrZr\rrrr_sr`zIgnoring unrecognized record 'z ' at line )rr2r3rstripr r4strip init_modelsplitint Exceptionr[rnparrayr_handle_PDB_exceptionrwarnrupperinit_seg init_chain init_residue init_atomastype set_anisou set_siguij set_sigatm),rr,allowed_recordslocal_line_counterrcurrent_model_id model_opencurrent_chain_id current_segidcurrent_residue_idcurrent_resnamer5r6r7global_line_counterfullname split_listnamealtlocresnamechainid serial_numberresseqicode hetero_flag residue_idr^yzcoord occupancybfactor pqr_chargeradiusmessagesegidelementanisou anisou_array serial_numsiguij siguij_arraysigatm sigatm_arrayrrrr*s                                               zPDBParser._parse_coordinatescCs0d||f}|jrtd|tdSt|d)zHandle exception (PRIVATE). This method catches an exception that occurs in the StructureBuilder object (if PERMISSIVE), or raises it again, this time adding the PDB line number to the error message. z%s at line %i.zlPDBConstructionException: %s Exception ignored. Some atoms or residues may be missing in the data structure.N)r rrtrr)rrr rrrrss  zPDBParser._handle_PDB_exception)TFNFF) __name__ __module__ __qualname____doc__rrrr(rr)r*rsrrrrrs" , r)rrnumpyrqBio.FilerBio.PDB.parse_pdb_headerrBio.PDB.PDBExceptionsrrBio.PDB.StructureBuilderrrrrrrs