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src/b/i/biopython-1.63/Bio/PDB/MMCIFParser.py   biopython(Download)
 
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
from Bio.PDB.StructureBuilder import StructureBuilder
from Bio.PDB.PDBExceptions import PDBConstructionException
 
 
class MMCIFParser(object):
    def get_structure(self, structure_id, filename):
        self._mmcif_dict=MMCIF2Dict(filename)
        self._structure_builder=StructureBuilder()

src/b/i/biopython-HEAD/Bio/PDB/MMCIFParser.py   biopython(Download)
 
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
from Bio.PDB.StructureBuilder import StructureBuilder
from Bio.PDB.PDBExceptions import PDBConstructionException
 
 
class MMCIFParser(object):
    def get_structure(self, structure_id, filename):
        self._mmcif_dict=MMCIF2Dict(filename)
        self._structure_builder=StructureBuilder()

src/b/i/biopython-1.63/Bio/PDB/PDBParser.py   biopython(Download)
from Bio.PDB.PDBExceptions import PDBConstructionWarning
 
from Bio.PDB.StructureBuilder import StructureBuilder
from Bio.PDB.parse_pdb_header import _parse_pdb_header_list
 
            self.structure_builder = structure_builder
        else:
            self.structure_builder = StructureBuilder()
        self.header = None
        self.trailer = None

src/b/i/biopython-1.63/Bio/PDB/PDBIO.py   biopython(Download)
from Bio._py3k import basestring
 
from Bio.PDB.StructureBuilder import StructureBuilder # To allow saving of chains, residues, etc..
from Bio.Data.IUPACData import atom_weights # Allowed Elements
 
            structure = pdb_object
        else:
            sb = StructureBuilder()
            sb.init_structure('pdb')
            sb.init_seg(' ')

src/b/i/biopython-HEAD/Bio/PDB/PDBParser.py   biopython(Download)
from Bio.PDB.PDBExceptions import PDBConstructionWarning
 
from Bio.PDB.StructureBuilder import StructureBuilder
from Bio.PDB.parse_pdb_header import _parse_pdb_header_list
 
            self.structure_builder = structure_builder
        else:
            self.structure_builder = StructureBuilder()
        self.header = None
        self.trailer = None

src/b/i/biopython-HEAD/Bio/PDB/PDBIO.py   biopython(Download)
from Bio._py3k import basestring
 
from Bio.PDB.StructureBuilder import StructureBuilder # To allow saving of chains, residues, etc..
from Bio.Data.IUPACData import atom_weights # Allowed Elements
 
            structure = pdb_object
        else:
            sb = StructureBuilder()
            sb.init_structure('pdb')
            sb.init_seg(' ')

src/m/d/MDAnalysis-0.8.1/MDAnalysis/coordinates/pdb/extensions.py   MDAnalysis(Download)
class SloppyStructureBuilder(Bio.PDB.StructureBuilder.StructureBuilder):
    """Cope with resSeq < 10,000 limitation by just incrementing internally.
 
    Solves the follwing problem with :class:`Bio.PDB.StructureBuilder.StructureBuilder`: