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src/c/o/cogent-1.5.3/cogent/struct/contact.py   cogent(Download)
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
from cogent.maths.geometry import coords_to_symmetry, \
                                  coords_to_crystal
from _contact import cnt_loop
        # 1, 14, 63, 172, 365, 666, 1099, 1688, 2457, 3430, 4631, 6084, 7813 ...
        if symmetry_mode == 'table':
            lcoords = coords_to_crystal(lcoords, \
                                        sh['table_fmx'], \
                                        sh['table_omx'], \
                                        crystal_mode)
        elif symmetry_mode == 'uc':
            lcoords = coords_to_crystal(lcoords, \

src/p/y/pycogent-HEAD/cogent/struct/contact.py   pycogent(Download)
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
from cogent.maths.geometry import coords_to_symmetry, \
                                  coords_to_crystal
from _contact import cnt_loop
        # 1, 14, 63, 172, 365, 666, 1099, 1688, 2457, 3430, 4631, 6084, 7813 ...
        if symmetry_mode == 'table':
            lcoords = coords_to_crystal(lcoords, \
                                        sh['table_fmx'], \
                                        sh['table_omx'], \
                                        crystal_mode)
        elif symmetry_mode == 'uc':
            lcoords = coords_to_crystal(lcoords, \

src/c/o/cogent-1.5.3/cogent/struct/asa.py   cogent(Download)
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
from cogent.maths.geometry import sphere_points, coords_to_symmetry, \
                                  coords_to_crystal
from _asa import asa_loop
        # expand to crystal, real 4D
        if crystal_mode:
            coords = coords_to_crystal(coords, \
                                               sh[symmetry_mode + '_fmx'], \
                                               sh[symmetry_mode + '_omx'], \

src/p/y/pycogent-HEAD/cogent/struct/asa.py   pycogent(Download)
from cogent.struct.selection import einput
from cogent.struct.annotation import xtradata
from cogent.maths.geometry import sphere_points, coords_to_symmetry, \
                                  coords_to_crystal
from _asa import asa_loop
        # expand to crystal, real 4D
        if crystal_mode:
            coords = coords_to_crystal(coords, \
                                               sh[symmetry_mode + '_fmx'], \
                                               sh[symmetry_mode + '_omx'], \

src/c/o/cogent-1.5.3/cogent/struct/manipulation.py   cogent(Download)
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
 
    coords = array([atoms.getData('coords')]) # fake 3D
    # 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

src/p/y/pycogent-HEAD/cogent/struct/manipulation.py   pycogent(Download)
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
 
    coords = array([atoms.getData('coords')]) # fake 3D
    # 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