o Rŀgg/@sdZddlZddlmZddlZddlmZddlmZddl m Z ddl m Z ddl mZdd l mZdd lmZdd lmZdd lmZd edefddZGdddZdS)zgConsumer class that builds a Structure object. This is used by the PDBParser and MMCIFparser classes. N)Optional)Atom)DisorderedAtom)Chain)Model)PDBConstructionException)PDBConstructionWarning)DisorderedResidue)Residue) StructureresiduereturncCs,|}|D] }|}|dkrdSqdS)zJReturn whether all atoms in the residue have a non-blank altloc (PRIVATE). FT)get_unpacked_list get_altloc)r atom_listatomaltlocrL/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/StructureBuilder.py_is_completely_disorderedsrc@seZdZdZddZddZdefddZd efd d Z d4d ede efddZ defddZ defddZ dedededefddZ d5dedejd ed!ed"ed#ed$e ed%e ed&e ed'efd(d)Zd*d+Zd,d-Zd.d/Zd0d1Zd2d3Zd S)6StructureBuilderzDeals with constructing the Structure object. The StructureBuilder class is used by the PDBParser classes to translate a file to a Structure object. cCs4d|_d|_i|_d|_d|_d|_d|_d|_dS)zInitialize this instance.Nr)rchainheader line_countermodelr segid structureselfrrr__init__0s zStructureBuilder.__init__cC ||_dS)z Set header.N)r)rrrrr set_header=s zStructureBuilder.set_headerrcCr!)zmTracks line in the PDB file that is being parsed. Arguments: - line_counter - int N)r)rrrrrset_line_counterAs z!StructureBuilder.set_line_counter structure_idcCst||_dS)znInitialize a new Structure object with given id. Arguments: - structure_id - string N)r r)rr$rrrinit_structureJszStructureBuilder.init_structureNmodel_id serial_numcCst|||_|j|jdS)zuCreate a new Model object with given id. Arguments: - id - int - serial_num - int N)rrradd)rr&r'rrr init_modelRs zStructureBuilder.init_modelchain_idcCsN|j|r|j||_td||jftdSt||_|j|jdS)zbCreate a new Chain object with given id. Arguments: - chain_id - string z.WARNING: Chain %s is discontinuous at line %i.N) rhas_idrwarningswarnrrrr()rr*rrr init_chain\s   zStructureBuilder.init_chainrcCr!)zNFlag a change in segid. Arguments: - segid - string N)r)rrrrrinit_segms zStructureBuilder.init_segresnamefieldresseqicodec Csj|dkr |dkr d|}|||f}|dkr|j|rtd||||jft|j|}|dkrR||rA||_| |nct |||j }| |||_dS||j krjtd|||||jft||_dSt|s~d|_td|||||jjf|j|t |||j }t|}|j|| || |||_dSt |||j |_|j|jdS) 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 rHH_z7WARNING: Residue ('%s', %i, '%s') redefined at line %i.NzVWARNING: Residue ('%s', %i, '%s','%s') already defined with the same name at line %i.zDBlank altlocs in duplicate residue %s ('%s', %i, '%s') of chain '%s')rr+r,r-rr is_disordereddisordered_has_idr disordered_selectr rdisordered_addr0rrid detach_childr r() rr0r1r2r3res_idduplicate_residue new_residuedisordered_residuerrr init_residueus^              zStructureBuilder.init_residueFnamecoordb_factor occupancyrfullnameelement pqr_chargeradiusis_pqrc  CsJ|j} | dur dS| |r(| |} | }||kr(|}td|||jft| r9t||dd||||| | |_n t|||||||||_|dkr| |r| |} | dkr`| |jdS| |t |}| || |j| | | td|jtdSt |}| || |j| dS| |jdS)aCreate a new Atom object. Arguments: - name - string, atom name, e.g. CA, spaces should be stripped - coord - NumPy array (Float0, length 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.rr6zAWARNING: disordered atom found with blank altloc before line %i. )r r+ get_fullnamer,r-rrrrr7r:r<rr(flag_disordered)rrBrCrDrErrF serial_numberrGrHrIrJr duplicate_atomduplicate_fullnamedisordered_atomrrr init_atomsv            zStructureBuilder.init_atomcC|j|dS)z)Set anisotropic B factor of current Atom.N)r set_anisou)r anisou_arrayrrrrS,zStructureBuilder.set_anisoucCrR)z?Set standard deviation of anisotropic B factor of current Atom.N)r set_siguij)r siguij_arrayrrrrV0rUzStructureBuilder.set_siguijcCrR)z8Set standard deviation of atom position of current Atom.N)r set_sigatm)r sigatm_arrayrrrrX4rUzStructureBuilder.set_sigatmcCs|j|j_|jS)zReturn the structure.)rrrrrr get_structure8s zStructureBuilder.get_structurecCsdS)z Set symmetry.Nr)r spacegroupcellrrr set_symmetry@szStructureBuilder.set_symmetry)N)NNNNF)__name__ __module__ __qualname____doc__r r"intr#strr%rr)r.r/rAnpndarrayfloatboolrQrSrVrXrZr]rrrrr)sR   P    o r)rar,typingrnumpyrd Bio.PDB.Atomrr Bio.PDB.Chainr Bio.PDB.ModelrBio.PDB.PDBExceptionsrrBio.PDB.Residuer r Bio.PDB.Structurer rgrrrrrrs