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src/b/i/biopython-1.63/Bio/PDB/FragmentMapper.py   biopython(Download)
 
from Bio.PDB import Selection
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Polypeptide import PPBuilder
        """
        if self.counter>=self.length:
            raise PDBException("Fragment boundary exceeded.")
        self.resname_list.append(resname)
        self.coords_ca[self.counter]=ca_coord
                ca=residue["CA"]
            else:
                raise PDBException("CHAINBREAK")
            if ca.is_disordered():
                raise PDBException("CHAINBREAK")
            self.edge=3
        else:
            raise PDBException("Fragment length should be 5 or 7.")
        self.flength=flength
        self.lsize=lsize

src/b/i/biopython-HEAD/Bio/PDB/FragmentMapper.py   biopython(Download)
 
from Bio.PDB import Selection
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Polypeptide import PPBuilder
        """
        if self.counter>=self.length:
            raise PDBException("Fragment boundary exceeded.")
        self.resname_list.append(resname)
        self.coords_ca[self.counter]=ca_coord
                ca=residue["CA"]
            else:
                raise PDBException("CHAINBREAK")
            if ca.is_disordered():
                raise PDBException("CHAINBREAK")
            self.edge=3
        else:
            raise PDBException("Fragment length should be 5 or 7.")
        self.flength=flength
        self.lsize=lsize

src/b/i/biopython-1.63/Bio/PDB/Superimposer.py   biopython(Download)
 
from Bio.SVDSuperimposer import SVDSuperimposer
from Bio.PDB.PDBExceptions import PDBException
 
 
        """
        if not (len(fixed)==len(moving)):
            raise PDBException("Fixed and moving atom lists differ in size")
        l=len(fixed)
        fixed_coord=numpy.zeros((l, 3))
        """
        if self.rotran is None:
            raise PDBException("No transformation has been calculated yet")
        rot, tran=self.rotran
        rot=rot.astype('f')

src/b/i/biopython-1.63/Bio/PDB/Selection.py   biopython(Download)
from Bio.PDB.Atom import Atom
from Bio.PDB.Entity import Entity
from Bio.PDB.PDBExceptions import PDBException
 
 
    """
    if not target_level in entity_levels:
        raise PDBException("%s: Not an entity level." % target_level)
    if entity_list == []:
        return []
    level = entity_list[0].get_level()
    if not all(entity.get_level() == level for entity in entity_list):
        raise PDBException("Entity list is not homogeneous.")
 
    target_index = entity_levels.index(target_level)

src/b/i/biopython-HEAD/Bio/PDB/Superimposer.py   biopython(Download)
 
from Bio.SVDSuperimposer import SVDSuperimposer
from Bio.PDB.PDBExceptions import PDBException
 
 
        """
        if not (len(fixed)==len(moving)):
            raise PDBException("Fixed and moving atom lists differ in size")
        l=len(fixed)
        fixed_coord=numpy.zeros((l, 3))
        """
        if self.rotran is None:
            raise PDBException("No transformation has been calculated yet")
        rot, tran=self.rotran
        rot=rot.astype('f')

src/b/i/biopython-HEAD/Bio/PDB/Selection.py   biopython(Download)
from Bio.PDB.Atom import Atom
from Bio.PDB.Entity import Entity
from Bio.PDB.PDBExceptions import PDBException
 
 
    """
    if not target_level in entity_levels:
        raise PDBException("%s: Not an entity level." % target_level)
    if entity_list == []:
        return []
    level = entity_list[0].get_level()
    if not all(entity.get_level() == level for entity in entity_list):
        raise PDBException("Entity list is not homogeneous.")
 
    target_index = entity_levels.index(target_level)

src/b/i/biopython-1.63/Bio/PDB/NeighborSearch.py   biopython(Download)
from Bio.KDTree import KDTree
 
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.Selection import unfold_entities, entity_levels, uniqueify
 
        """
        if not level in entity_levels:
            raise PDBException("%s: Unknown level" % level)
        self.kdt.search(center, radius)
        indices=self.kdt.get_indices()
        """
        if not level in entity_levels:
            raise PDBException("%s: Unknown level" % level)
        self.kdt.all_search(radius)
        indices=self.kdt.all_get_indices()

src/b/i/biopython-HEAD/Bio/PDB/NeighborSearch.py   biopython(Download)
from Bio.KDTree import KDTree
 
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.Selection import unfold_entities, entity_levels, uniqueify
 
        """
        if not level in entity_levels:
            raise PDBException("%s: Unknown level" % level)
        self.kdt.search(center, radius)
        indices=self.kdt.get_indices()
        """
        if not level in entity_levels:
            raise PDBException("%s: Unknown level" % level)
        self.kdt.all_search(radius)
        indices=self.kdt.all_get_indices()

src/b/i/biopython-1.63/Bio/PDB/Polypeptide.py   biopython(Download)
from Bio.Data import SCOPData
from Bio.Seq import Seq
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.Vector import calc_dihedral, calc_angle
 
            chain_list=[entity]
        else:
            raise PDBException("Entity should be Structure, Model or Chain.")
        pp_list=[]
        for chain in chain_list:

src/b/i/biopython-1.63/Bio/PDB/DSSP.py   biopython(Download)
 
from Bio.PDB.AbstractPropertyMap import AbstractResiduePropertyMap
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.PDBParser import PDBParser
 
            # Take care of HETATM again
            if (resname != aa) and (res.id[0] == ' ' or aa != 'X'):
                raise PDBException("Structure/DSSP mismatch at %s" % res)
            dssp_map[key] = ((res, ss, acc, rel_acc, phi, psi))
            dssp_list.append((res, ss, acc, rel_acc, phi, psi))

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