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src/c/o/cogent-1.5.3/cogent/struct/selection.py   cogent(Download)
"""Contains functions to select and group structural entities."""
 
from cogent.core.entity import StructureHolder, ModelHolder, ChainHolder, \
                               ResidueHolder, AtomHolder, HIERARCHY
 
            holder = ChainHolder(name, all)
        elif higher_level == 'S':
            holder = ModelHolder(name, all)
        elif higher_level == 'H':
            holder = StructureHolder(name, all)

src/p/y/pycogent-HEAD/cogent/struct/selection.py   pycogent(Download)
"""Contains functions to select and group structural entities."""
 
from cogent.core.entity import StructureHolder, ModelHolder, ChainHolder, \
                               ResidueHolder, AtomHolder, HIERARCHY
 
            holder = ChainHolder(name, all)
        elif higher_level == 'S':
            holder = ModelHolder(name, all)
        elif higher_level == 'H':
            holder = StructureHolder(name, all)

src/c/o/cogent-1.5.3/cogent/struct/manipulation.py   cogent(Download)
from numpy import array
from itertools import izip
from cogent.core.entity import HIERARCHY, copy, StructureHolder, ModelHolder
from cogent.maths.geometry import coords_to_symmetry, coords_to_crystal
from cogent.struct.selection import einput
    # expand the coordinates to symmetry
    all_coords = coords_to_symmetry(coords, fmx, omx, mxs, mode)
    models = ModelHolder(name)
 
    for i in xrange(0, len(mxs)):

src/p/y/pycogent-HEAD/cogent/struct/manipulation.py   pycogent(Download)
from numpy import array
from itertools import izip
from cogent.core.entity import HIERARCHY, copy, StructureHolder, ModelHolder
from cogent.maths.geometry import coords_to_symmetry, coords_to_crystal
from cogent.struct.selection import einput
    # expand the coordinates to symmetry
    all_coords = coords_to_symmetry(coords, fmx, omx, mxs, mode)
    models = ModelHolder(name)
 
    for i in xrange(0, len(mxs)):