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src/b/i/bioEuler-HEAD/src/parser.py   bioEuler(Download)
import os
import sys
 
from Bio.PDB import PDBParser, PPBuilder, Polypeptide
from numpy import array, matrix, linalg
    model = structure[0]
 
    ppb = PPBuilder()
    pp_list = ppb.build_peptides(model)
 

src/b/i/biopython-1.63/Tests/test_PDB.py   biopython(Download)
from Bio.Seq import Seq
from Bio.Alphabet import generic_protein
from Bio.PDB import PDBParser, PPBuilder, CaPPBuilder, PDBIO, Select
from Bio.PDB import HSExposureCA, HSExposureCB, ExposureCN
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
    def test_c_n(self):
        """Extract polypeptides using C-N."""
        ppbuild = PPBuilder()
        polypeptides = ppbuild.build_peptides(self.structure[1])
        self.assertEqual(len(polypeptides), 1)
        structure = parser.get_structure("example", "PDB/1A8O.pdb")
        self.assertEqual(len(structure), 1)
        for ppbuild in [PPBuilder(), CaPPBuilder()]:
            #==========================================================
            #First try allowing non-standard amino acids,

src/b/i/biopython-HEAD/Tests/test_PDB.py   biopython(Download)
from Bio.Seq import Seq
from Bio.Alphabet import generic_protein
from Bio.PDB import PDBParser, PPBuilder, CaPPBuilder, PDBIO, Select
from Bio.PDB import HSExposureCA, HSExposureCB, ExposureCN
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
    def test_c_n(self):
        """Extract polypeptides using C-N."""
        ppbuild = PPBuilder()
        polypeptides = ppbuild.build_peptides(self.structure[1])
        self.assertEqual(len(polypeptides), 1)
        structure = parser.get_structure("example", "PDB/1A8O.pdb")
        self.assertEqual(len(structure), 1)
        for ppbuild in [PPBuilder(), CaPPBuilder()]:
            #==========================================================
            #First try allowing non-standard amino acids,

src/b/i/biopython-HEAD/Tests/test_MMCIF.py   biopython(Download)
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
 
from Bio.PDB import PPBuilder, CaPPBuilder
from Bio.PDB.MMCIFParser import MMCIFParser
 
        structure = parser.get_structure("example", "PDB/1A8O.cif")
        self.assertEqual(len(structure), 1)
        for ppbuild in [PPBuilder(), CaPPBuilder()]:
            #==========================================================
            # Check that serial_num (model column) is stored properly
        structure = parser.get_structure("example", "PDB/1LCD.cif")
        self.assertEqual(len(structure), 3)
        for ppbuild in [PPBuilder(), CaPPBuilder()]:
                #==========================================================
                # Check that serial_num (model column) is stored properly

src/b/i/biopython-1.63/Tests/test_MMCIF.py   biopython(Download)
from Bio.PDB.PDBExceptions import PDBConstructionException, PDBConstructionWarning
 
from Bio.PDB import PPBuilder, CaPPBuilder
from Bio.PDB.MMCIFParser import MMCIFParser
 
        structure = parser.get_structure("example", "PDB/1A8O.cif")
        self.assertEqual(len(structure), 1)
        for ppbuild in [PPBuilder(), CaPPBuilder()]:
            #==========================================================
            # Check that serial_num (model column) is stored properly
        structure = parser.get_structure("example", "PDB/1LCD.cif")
        self.assertEqual(len(structure), 3)
        for ppbuild in [PPBuilder(), CaPPBuilder()]:
                #==========================================================
                # Check that serial_num (model column) is stored properly