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All Samples(8)  |  Call(4)  |  Derive(0)  |  Import(4)

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 = ModelHolder(name, all)
        elif higher_level == 'H':
            holder = StructureHolder(name, all)
    else:
        raise ValueError, "einput got no input entites."

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 = ModelHolder(name, all)
        elif higher_level == 'H':
            holder = StructureHolder(name, all)
    else:
        raise ValueError, "einput got no input entites."

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 crystal
    all_coords = coords_to_crystal(coords, fmx, omx, n)
    structures = StructureHolder(name)
    rng = range(-n, n + 1) # a range like -2, -1, 0, 1, 2
    vectors = [(x, y, z) for x in rng for y in rng for z in rng]

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 crystal
    all_coords = coords_to_crystal(coords, fmx, omx, n)
    structures = StructureHolder(name)
    rng = range(-n, n + 1) # a range like -2, -1, 0, 1, 2
    vectors = [(x, y, z) for x in rng for y in rng for z in rng]