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All Samples(16)  |  Call(7)  |  Derive(0)  |  Import(9)

src/c/o/cogent-1.5.3/cogent/app/stride.py   cogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath
from cogent.app.parameters import FlagParameter, ValuedParameter
from cogent.format.pdb import PDBWriter
 
 
    def _input_as_multiline_string(self, data):
        """This allows to feed entities to stride."""
        dummy_file = StringIO()
        PDBWriter(dummy_file, data)
        dummy_file.seek(0)

src/p/y/pycogent-HEAD/cogent/app/stride.py   pycogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath
from cogent.app.parameters import FlagParameter, ValuedParameter
from cogent.format.pdb import PDBWriter
 
 
    def _input_as_multiline_string(self, data):
        """This allows to feed entities to stride."""
        dummy_file = StringIO()
        PDBWriter(dummy_file, data)
        dummy_file.seek(0)

src/e/e/eebprogramming-HEAD/lec10review/6structure.py   eebprogramming(Download)
#!/usr/bin/env python
# taken from http://pycogent.sourceforge.net/
from cogent.parse.pdb import PDBParser
from cogent.format.pdb import PDBWriter
import tempfile, os
os.close(open_handle)
new_pdb_file = open(file_name,'wb')
PDBWriter(new_pdb_file, new_structure)
print structure.id 
print structure.getId() 

src/c/o/cogent-1.5.3/cogent/format/structure.py   cogent(Download)
#!/usr/bin/env python
 
import os
from cogent.format.pdb import PDBWriter, PDBXWriter
from cogent.format.xyzrn import XYZRNWriter

src/p/y/pycogent-HEAD/cogent/format/structure.py   pycogent(Download)
#!/usr/bin/env python
 
import os
from cogent.format.pdb import PDBWriter, PDBXWriter
from cogent.format.xyzrn import XYZRNWriter

src/c/o/cogent-1.5.3/tests/test_struct/test_manipulation.py   cogent(Download)
    from cogent.util.unit_test import TestCase, main
    from cogent.parse.pdb import PDBParser
    from cogent.format.pdb import PDBWriter
    from cogent.struct.selection import einput
    from cogent.struct.manipulation import copy, clean_ical, \
    from zenpdb.cogent.util.unit_test import TestCase, main
    from zenpdb.cogent.parse.pdb import PDBParser
    from cogent.format.pdb import PDBWriter
    from zenpdb.cogent.struct.selection import einput
    from zenpdb.cogent.struct.manipulation import copy, clean_ical, \
        os.close(fd)
        fh = open(fn, 'w')
        PDBWriter(fh, mh, self.input_structure.raw_header)
        fh.close()
 
        self.assertTrue(len(a1), len(a2))
        self.assertRaises(AssertionError, self.assertFloatEqual, a1c, a2c)
        PDBWriter(fh, sh)
        fh.close()
        os.unlink(fn)

src/p/y/pycogent-HEAD/tests/test_struct/test_manipulation.py   pycogent(Download)
    from cogent.util.unit_test import TestCase, main
    from cogent.parse.pdb import PDBParser
    from cogent.format.pdb import PDBWriter
    from cogent.struct.selection import einput
    from cogent.struct.manipulation import copy, clean_ical, \
    from zenpdb.cogent.util.unit_test import TestCase, main
    from zenpdb.cogent.parse.pdb import PDBParser
    from cogent.format.pdb import PDBWriter
    from zenpdb.cogent.struct.selection import einput
    from zenpdb.cogent.struct.manipulation import copy, clean_ical, \
        os.close(fd)
        fh = open(fn, 'w')
        PDBWriter(fh, mh, self.input_structure.raw_header)
        fh.close()
 
        self.assertTrue(len(a1), len(a2))
        self.assertRaises(AssertionError, self.assertFloatEqual, a1c, a2c)
        PDBWriter(fh, sh)
        fh.close()
        os.unlink(fn)