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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
 
 
        except ValueError:
            # Invalid model number (malformed file)
            raise PDBConstructionException("Invalid model number")
        try:
            aniso_u11=mmcif_dict["_atom_site.aniso_U[1][1]"]
                tempfactor=float(b_factor_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing B factor")
            try:
                occupancy=float(occupancy_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing occupancy")

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
 
 
        except ValueError:
            # Invalid model number (malformed file)
            raise PDBConstructionException("Invalid model number")
        try:
            aniso_u11=mmcif_dict["_atom_site.aniso_U[1][1]"]
                tempfactor=float(b_factor_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing B factor")
            try:
                occupancy=float(occupancy_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing occupancy")

src/b/i/biopython-1.63/Bio/PDB/Entity.py   biopython(Download)
from copy import copy
 
from Bio.PDB.PDBExceptions import PDBConstructionException
 
"""Base class for Residue, Chain, Model and Structure classes.
        if self.has_id(entity_id):
            raise PDBConstructionException(
                "%s defined twice" % str(entity_id))
        entity.set_parent(self)
        self.child_list.append(entity)
        if self.has_id(entity_id):
            raise PDBConstructionException(
                "%s defined twice" % str(entity_id))
        entity.set_parent(self)
        self.child_list[pos:pos] = [entity]

src/b/i/biopython-HEAD/Bio/PDB/Entity.py   biopython(Download)
from copy import copy
 
from Bio.PDB.PDBExceptions import PDBConstructionException
 
"""Base class for Residue, Chain, Model and Structure classes.
        if self.has_id(entity_id):
            raise PDBConstructionException(
                "%s defined twice" % str(entity_id))
        entity.set_parent(self)
        self.child_list.append(entity)
        if self.has_id(entity_id):
            raise PDBConstructionException(
                "%s defined twice" % str(entity_id))
        entity.set_parent(self)
        self.child_list[pos:pos] = [entity]

src/b/i/biopython-1.63/Bio/PDB/PDBParser.py   biopython(Download)
from Bio.File import as_handle
 
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.PDBExceptions import PDBConstructionWarning
 
                    # Should we allow parsing to continue in permissive mode?
                    # If so, what coordinates should we default to?  Easier to abort!
                    raise PDBConstructionException("Invalid or missing coordinate(s) at line %i."
                                                   % global_line_counter)
                coord = numpy.array((x, y, z), "f")
        else:
            # exceptions are fatal - raise again with new message (including line nr)
            raise PDBConstructionException(message)
 
 

src/b/i/biopython-HEAD/Bio/PDB/PDBParser.py   biopython(Download)
from Bio.File import as_handle
 
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.PDBExceptions import PDBConstructionWarning
 
                    # Should we allow parsing to continue in permissive mode?
                    # If so, what coordinates should we default to?  Easier to abort!
                    raise PDBConstructionException("Invalid or missing coordinate(s) at line %i."
                                                   % global_line_counter)
                coord = numpy.array((x, y, z), "f")
        else:
            # exceptions are fatal - raise again with new message (including line nr)
            raise PDBConstructionException(message)
 
 

src/b/i/biopython-1.63/Bio/PDB/StructureBuilder.py   biopython(Download)
from Bio.PDB.Atom import Atom, DisorderedAtom
 
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.PDBExceptions import PDBConstructionWarning
 
                        self.residue=None
                        raise PDBConstructionException(
                            "Blank altlocs in duplicate residue %s ('%s', %i, '%s')"
                            % (resname, field, resseq, icode))
                    self.chain.detach_child(res_id)

src/b/i/biopython-HEAD/Bio/PDB/StructureBuilder.py   biopython(Download)
from Bio.PDB.Atom import Atom, DisorderedAtom
 
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.PDBExceptions import PDBConstructionWarning
 
                        self.residue=None
                        raise PDBConstructionException(
                            "Blank altlocs in duplicate residue %s ('%s', %i, '%s')"
                            % (resname, field, resseq, icode))
                    self.chain.detach_child(res_id)

src/b/i/biopython-1.63/Bio/PDB/Residue.py   biopython(Download)
 
# My Stuff
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.Entity import Entity, DisorderedEntityWrapper
 
        if self.has_id(atom_id):
            raise PDBConstructionException(
                "Atom %s defined twice in residue %s" % (atom_id, self))
        Entity.add(self, atom)
 
            residue.add(atom)
            raise PDBConstructionException(
                "Blank altlocs in duplicate residue %s (%s, %i, %s)"
                % (resname, het, resseq, icode) )
        residue.add(atom)

src/b/i/biopython-HEAD/Bio/PDB/Residue.py   biopython(Download)
 
# My Stuff
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.Entity import Entity, DisorderedEntityWrapper
 
        if self.has_id(atom_id):
            raise PDBConstructionException(
                "Atom %s defined twice in residue %s" % (atom_id, self))
        Entity.add(self, atom)
 
            residue.add(atom)
            raise PDBConstructionException(
                "Blank altlocs in duplicate residue %s (%s, %i, %s)"
                % (resname, het, resseq, icode) )
        residue.add(atom)

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