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src/m/d/MDAnalysis-0.8.1/MDAnalysis/coordinates/pdb/extensions.py   MDAnalysis(Download)
class SloppyPDBIO(Bio.PDB.PDBIO):
    """PDBIO class that can deal with large pdb files as used in MD simulations.
 
    - resSeq simply wrap and are printed modulo 10,000.
    - atom numbers wrap at 99,999 and are printed modulo 100,000

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
        confirm_numbering(struct1)
        # Round trip: serialize and parse again
        io = PDBIO()
        io.set_structure(struct1)
        filenumber, filename = tempfile.mkstemp()
    def test_pdbio_write_structure(self):
        """Write a full structure using PDBIO"""
        io = PDBIO()
        struct1 = self.structure
        # Write full model to temp file
    def test_pdbio_write_residue(self):
        """Write a single residue using PDBIO"""
        io = PDBIO()
        struct1 = self.structure
        residue1 = list(struct1.get_residues())[0]
    def test_pdbio_write_custom_residue(self):
        """Write a chainless residue using PDBIO"""
        io = PDBIO()
 
        res = Residue.Residue((' ', 1, ' '), 'DUM', '')

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
        confirm_numbering(struct1)
        # Round trip: serialize and parse again
        io = PDBIO()
        io.set_structure(struct1)
        filenumber, filename = tempfile.mkstemp()
    def test_pdbio_write_structure(self):
        """Write a full structure using PDBIO"""
        io = PDBIO()
        struct1 = self.structure
        # Write full model to temp file
    def test_pdbio_write_residue(self):
        """Write a single residue using PDBIO"""
        io = PDBIO()
        struct1 = self.structure
        residue1 = list(struct1.get_residues())[0]
    def test_pdbio_write_custom_residue(self):
        """Write a chainless residue using PDBIO"""
        io = PDBIO()
 
        res = Residue.Residue((' ', 1, ' '), 'DUM', '')