:>"^ü*ã@s¨dZddlZddlmZddlmZddlmZddlm Z m Z ddl m Z m Z ddlmZdd lmZGd d „d eƒZdS) 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@sÓeZdZdZdd„Zdd„Zdd„Zdd „Zd d „Zd d d„Z dd„Z dd„Z dd„Z d d dd„Z dd„Zdd„Zdd„Zdd„Zdd „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©rú=/tmp/pip-build-ww9dw3qa/biopython/Bio/PDB/StructureBuilder.pyÚ__init__s zStructureBuilder.__init__cCs=|jƒ}x*|D]"}|jƒ}|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$s     z*StructureBuilder._is_completely_disorderedcCs ||_dS)z Set header.N)r )rr rrrÚ set_header/szStructureBuilder.set_headercCs ||_dS)zmTracks line in the PDB file that is being parsed. Arguments: - line_counter - int N)r )rr rrrÚset_line_counter3sz!StructureBuilder.set_line_countercCst|ƒ|_dS)zeInitialize a new Structure object with given id. Arguments: - id - string N)rÚ structure)rZ structure_idrrrÚinit_structure<szStructureBuilder.init_structureNcCs)t||ƒ|_|jj|jƒdS)zvCreate a new Model object with given id. Arguments: - id - int - serial_num - int N)rÚmodelrÚadd)rZmodel_idZ serial_numrrrÚ init_modelEszStructureBuilder.init_modelcCsh|jj|ƒrB|j||_tjd||jftƒn"t|ƒ|_|jj|jƒdS)zcCreate a new Chain object with given id. Arguments: - chain_id - string z.WARNING: Chain %s is discontinuous at line %i.N) rÚhas_idÚchainÚwarningsÚwarnr r rr)rZchain_idrrrÚ init_chainPs  zStructureBuilder.init_chaincCs ||_dS)zOFlag a change in segid. Arguments: - segid - string N)Úsegid)rr$rrrÚinit_segbszStructureBuilder.init_segc Csø|dkr"|dkr"d|}|||f}|dkrÉ|jj|ƒrÉtjd||||jftƒ|j|}|jƒdkrë|j|ƒr¹||_|j |ƒqÉt |||j ƒ}|j |ƒ||_dSnÞ||j kr-tjd|||||jftƒ||_dS|j|ƒsad|_td||||fƒ‚|jj|ƒt |||j ƒ}t|ƒ}|jj|ƒ|j |ƒ|j |ƒ||_dSt |||j ƒ|_|jj|jƒdS) 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*ÚfieldZresseqZicodeZres_idZduplicate_residueZ new_residueZdisordered_residuerrrÚ init_residueksR              zStructureBuilder.init_residuec Cs|j} | dkrdS| j|ƒrp| |} | jƒ} | |krp|}tjd| ||jftƒt||||||||ƒ|_|dkr{| j|ƒrE| |} | j ƒdkrÞ| j |jƒqx| j |ƒt |ƒ} | j | ƒ| j |jƒ| j | ƒ| jƒtjd|jtƒq‹t |ƒ} | j | ƒ| j |jƒ| jƒn| j |jƒdS)aÈCreate 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 Nz6Atom names %r and %r differ only in spaces at line %i.rr'zAWARNING: disordered atom found with blank altloc before line %i. )rrÚ get_fullnamer!r"r r rrr(r)r+rrZflag_disordered) rÚnameZcoordZb_factorZ occupancyrÚfullnameZ serial_numberÚelementrZduplicate_atomZduplicate_fullnameZdisordered_atomrrrÚ init_atom³sD     !           zStructureBuilder.init_atomcCs|jj|ƒdS)z)Set anisotropic B factor of current Atom.N)rÚ set_anisou)rZ anisou_arrayrrrr3szStructureBuilder.set_anisoucCs|jj|ƒdS)z?Set standard deviation of anisotropic B factor of current Atom.N)rÚ set_siguij)rZ siguij_arrayrrrr4 szStructureBuilder.set_siguijcCs|jj|ƒdS)z8Set standard deviation of atom position of current Atom.N)rÚ set_sigatm)rZ sigatm_arrayrrrr5szStructureBuilder.set_sigatmcCs|j|j_|jS)zReturn the structure.)r r)rrrrÚ get_structureszStructureBuilder.get_structurecCsdS)z Set symmetry.Nr)rZ spacegroupÚcellrrrÚ set_symmetryszStructureBuilder.set_symmetry)Ú__name__Ú __module__Ú __qualname__Ú__doc__rrrrrrr#r%r-r2r3r4r5r6r8rrrrr s"      PL    r )r<r!ZBio.PDB.StructurerZ Bio.PDB.ModelrZ Bio.PDB.ChainrZBio.PDB.ResiduerrZ Bio.PDB.AtomrrZBio.PDB.PDBExceptionsr r Úobjectr rrrrÚ s