ó "˜ÎIc@s•ddlZdZddlmZddlmZddlmZddlmZmZddlmZmZddl m Z d d d „ƒYZ dS( iÿÿÿÿNsh Consumer class that builds a Structure object. This is used by the PDBParser and MMCIFparser classes. (t Structure(tModel(tChain(tResiduetDisorderedResidue(tAtomtDisorderedAtom(tPDBConstructionExceptiontStructureBuildercBs˜eZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z dd „Z d „Zd „Zd „Zd„Zd„ZRS(s¡ Deals with contructing the Structure object. The StructureBuilder class is used by the PDBParser classes to translate a file to a Structure object. cCsd|_i|_dS(Ni(t line_countertheader(tself((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt__init__s cCs=|jƒ}x*|D]"}|jƒ}|dkrdSqWdS(s=Return 1 if all atoms in the residue have a non blank altloc.t ii(tget_unpacked_listt get_altloc(R tresiduet atom_listtatomtaltloc((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt_is_completely_disordered#s     cCs ||_dS(N(R (R R ((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt set_header.scCs ||_dS(s¢ The line counter keeps track of the line in the PDB file that is being parsed. Arguments: o line_counter - int N(R (R R ((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pytset_line_counter1scCst|ƒ|_dS(saInitiate a new Structure object with given id. Arguments: o id - string N(Rt structure(R t structure_id((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pytinit_structure;scCs&t|ƒ|_|jj|jƒdS(sbInitiate a new Model object with given id. Arguments: o id - int N(RtmodelRtadd(R tmodel_id((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt init_modelCscCsh|jj|ƒrB|j||_tjjd||jfƒn"t|ƒ|_|jj|jƒdS(scInitiate a new Chain object with given id. Arguments: o chain_id - string s/WARNING: Chain %s is discontinuous at line %i. N( Rthas_idtchaintsyststderrtwriteR RR(R tchain_id((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt init_chainLs  cCs ||_dS(sUFlag a change in segid. Arguments: o segid - string N(tsegid(R R%((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pytinit_seg[sc CsÈ|dkr(|dkr(d|}q(n|||f}|dkr–|jj|ƒr–tjjd||||jfƒ|j|}|jƒdkrñ|j|ƒr¿||_|j |ƒqt |||j ƒ}|j |ƒ||_dSq“|j |ƒs(d|_td||||fƒ‚n|jj|ƒt |||j ƒ}t|ƒ}|jj|ƒ|j |ƒ|j |ƒ||_dSq–nt |||j ƒ} |jj| ƒ| |_dS(s& Initiate a new Residue object. Arguments: o resname - string, e.g. "ASN" o field - hetero flag, "W" for waters, "H" for hetero residues, otherwise blank. o resseq - int, sequence identifier o icode - string, insertion code R tHtH_s8WARNING: Residue ('%s', %i, '%s') redefined at line %i. iNs6Blank altlocs in duplicate residue %s ('%s', %i, '%s')(RRR R!R"R t is_disorderedtdisordered_has_idRtdisordered_selectRR%tdisordered_addRtNoneRt detach_childRR( R tresnametfieldtresseqticodetres_idtduplicate_residuet new_residuetdisordered_residueR((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt init_residuecsB              c CsŠ|j}|dkrdS|j|ƒrv||} | jƒ} | |krv|}tjjd| ||jfƒqvnt|||||||ƒ} |_ |dkry|j|ƒrF||} | j ƒdkrâ| j | ƒqv|j |ƒt |ƒ} |j| ƒ| j | ƒ| j | ƒ|jƒtjjd|jƒq†t |ƒ} |j| ƒ| j | ƒ|jƒn |j| ƒdS(s Initiate a new Atom object. Arguments: o name - string, atom name, e.g. CA, spaces should be stripped o coord - Numeric array (Float0, size 3), atomic coordinates o b_factor - float, B factor o occupancy - float o altloc - string, alternative location specifier o fullname - string, atom name including spaces, e.g. " CA " Ns@WARNING: atom names %s and %s differ only in spaces at line %i. R isAWARNING: disordered atom found with blank altloc before line %i. (RR-Rt get_fullnameR R!R"R RRR)R,R.RRtflag_disordered( R tnametcoordtb_factort occupancyRtfullnamet serial_numberRtduplicate_atomtduplicate_fullnameRtdisordered_atom((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt init_atom s:      %             cCs|jj|ƒdS(s)Set anisotropic B factor of current Atom.N(Rt set_anisou(R t anisou_array((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyRDäscCs|jj|ƒdS(s?Set standard deviation of anisotropic B factor of current Atom.N(Rt set_siguij(R t siguij_array((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyRFèscCs|jj|ƒdS(s8Set standard deviation of atom position of current Atom.N(Rt set_sigatm(R t sigatm_array((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyRHìscCs|j|j_|jS(sReturn the structure.(R R(R ((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt get_structureðscCsdS(N((R t spacegrouptcell((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyt set_symmetryøsN(t__name__t __module__t__doc__R RRRRRR$R&R7R-RCRDRFRHRJRM(((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyRs       = D    (( R RPRRRRRRRt PDBExceptionsRR(((s‹/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.pyts