B ‰°b¼-ã@szdZddlZddlmZddlmZddlmZddlm Z m Z ddl m Z m Z ddlmZdd lmZGd d „d ƒZdS) zgConsumer class that builds a Structure object. This is used by the PDBParser and MMCIFparser classes. éN)Ú Structure)ÚModel)ÚChain)ÚResidueÚDisorderedResidue)ÚAtomÚDisorderedAtom)ÚPDBConstructionException)ÚPDBConstructionWarningc@sŒeZdZdZdd„Zdd„Zdd„Zdd „Zd d „Zd"d d„Z dd„Z dd„Z dd„Z d#dd„Z dd„Zdd„Zdd„Zdd„Zd d!„Zd S)$ÚStructureBuilderz¢Deals with constructing the Structure object. The StructureBuilder class is used by the PDBParser classes to translate a file to a Structure object. cCsd|_i|_dS)zInitialize the class.rN)Ú line_counterÚheader)Úself©rú7lib/python3.7/site-packages/Bio/PDB/StructureBuilder.pyÚ__init__szStructureBuilder.__init__cCs.| ¡}x |D]}| ¡}|dkrdSqWdS)zGReturn 1 if all atoms in the residue have a non blank altloc (PRIVATE).ú ré)Zget_unpacked_listZ get_altloc)rÚresidueZ atom_listÚatomÚaltlocrrrÚ_is_completely_disordered$s  z*StructureBuilder._is_completely_disorderedcCs ||_dS)z Set header.N)r )rr rrrÚ set_header/szStructureBuilder.set_headercCs ||_dS)zmTracks line in the PDB file that is being parsed. Arguments: - line_counter - int N)r )rr rrrÚset_line_counter3sz!StructureBuilder.set_line_countercCst|ƒ|_dS)zeInitialize a new Structure object with given id. Arguments: - id - string N)rÚ structure)rZ structure_idrrrÚinit_structure<szStructureBuilder.init_structureNcCst||ƒ|_|j |j¡dS)zvCreate a new Model object with given id. Arguments: - id - int - serial_num - int N)rÚmodelrÚadd)rZmodel_idZ serial_numrrrÚ init_modelEs zStructureBuilder.init_modelcCsL|j |¡r0|j||_t d||jft¡nt|ƒ|_|j |j¡dS)zcCreate a new Chain object with given id. Arguments: - chain_id - string z.WARNING: Chain %s is discontinuous at line %i.N) rÚhas_idÚchainÚwarningsÚwarnr r rr)rZchain_idrrrÚ init_chainPs    zStructureBuilder.init_chaincCs ||_dS)zOFlag a change in segid. Arguments: - segid - string N)Úsegid)rr$rrrÚinit_segbszStructureBuilder.init_segc Csl|dkr|dkrd|}|||f}|dkrJ|j |¡rJt d||||jft¡|j|}| ¡dkrª| |¡r†||_|  |¡n"t |||j ƒ}|  |¡||_dSn ||j krÚt d|||||jft¡||_dS| |¡sþd|_td||||fƒ‚|j |¡t |||j ƒ}t|ƒ}|j |¡|  |¡|  |¡||_dSt |||j ƒ|_|j |j¡dS) aCreate a new Residue object. Arguments: - resname - string, e.g. "ASN" - field - hetero flag, "W" for waters, "H" for hetero residues, otherwise blank. - resseq - int, sequence identifier - icode - string, insertion code rÚHZH_z7WARNING: Residue ('%s', %i, '%s') redefined at line %i.éNzVWARNING: Residue ('%s', %i, '%s','%s') already defined with the same name at line %i.z6Blank altlocs in duplicate residue %s ('%s', %i, '%s'))r rr!r"r r Ú is_disorderedZdisordered_has_idrZdisordered_selectrr$Údisordered_addÚresnamerr Ú detach_childrr) rr*ZfieldZresseqZicodeZres_idZduplicate_residueZ new_residueZdisordered_residuerrrÚ init_residueksR              zStructureBuilder.init_residueFc  CsL|j} | dkrdS|  |¡rP| |} |  ¡}||krP|}t d|||jft¡| snt||||||||ƒ|_n | rŽt||dd||||| | ƒ |_|dkr<|  |¡r| |} |   ¡dkrÆ|   |j¡nL|   |¡t |ƒ}|   |¡|  |j¡|  | ¡|  ¡t d|jt¡n&t |ƒ}|   |¡|  |j¡|  ¡n |   |j¡dS)a€Create a new Atom object. Arguments: - name - string, atom name, e.g. CA, spaces should be stripped - coord - Numeric array (Float0, size 3), atomic coordinates - b_factor - float, B factor - occupancy - float - altloc - string, alternative location specifier - fullname - string, atom name including spaces, e.g. " CA " - element - string, upper case, e.g. "HG" for mercury - pqr_charge - float, atom charge (PQR format) - radius - float, atom radius (PQR format) - is_pqr - boolean, flag to specify if a .pqr file is being parsed Nz6Atom names %r and %r differ only in spaces at line %i.rr'zAWARNING: disordered atom found with blank altloc before line %i. )rrZ get_fullnamer!r"r r rrr(r)r+rrZflag_disordered)rÚnameZcoordZb_factorZ occupancyrÚfullnameZ serial_numberÚelementZ pqr_chargeZradiusZis_pqrrZduplicate_atomZduplicate_fullnameZdisordered_atomrrrÚ init_atom³sl             zStructureBuilder.init_atomcCs|j |¡dS)z)Set anisotropic B factor of current Atom.N)rÚ set_anisou)rZ anisou_arrayrrrr1#szStructureBuilder.set_anisoucCs|j |¡dS)z?Set standard deviation of anisotropic B factor of current Atom.N)rÚ set_siguij)rZ siguij_arrayrrrr2'szStructureBuilder.set_siguijcCs|j |¡dS)z8Set standard deviation of atom position of current Atom.N)rÚ set_sigatm)rZ sigatm_arrayrrrr3+szStructureBuilder.set_sigatmcCs|j|j_|jS)zReturn the structure.)r r)rrrrÚ get_structure/s zStructureBuilder.get_structurecCsdS)z Set symmetry.Nr)rZ spacegroupZcellrrrÚ set_symmetry7szStructureBuilder.set_symmetry)N)NNNNF)Ú__name__Ú __module__Ú __qualname__Ú__doc__rrrrrrr#r%r,r0r1r2r3r4r5rrrrr s(    P dr )r9r!ZBio.PDB.StructurerZ Bio.PDB.ModelrZ Bio.PDB.ChainrZBio.PDB.ResiduerrZ Bio.PDB.AtomrrZBio.PDB.PDBExceptionsr r r rrrrÚ s