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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
    if symmetry_mode:
        if symmetry_mode == 'table':
            lcoords = coords_to_symmetry(lcoords, \
                                         sh['table_fmx'], \
                                         sh['table_omx'], \
                                         sh['table_mxs'], \
                                         symmetry_mode)
        elif symmetry_mode == 'uc':
            lcoords = coords_to_symmetry(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
    if symmetry_mode:
        if symmetry_mode == 'table':
            lcoords = coords_to_symmetry(lcoords, \
                                         sh['table_fmx'], \
                                         sh['table_omx'], \
                                         sh['table_mxs'], \
                                         symmetry_mode)
        elif symmetry_mode == 'uc':
            lcoords = coords_to_symmetry(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
                                                forgiving=False, method=True)))
        # expand to unit-cell, real 3D
        coords = coords_to_symmetry(coords, \
                                            sh[symmetry_mode + '_fmx'], \
                                            sh[symmetry_mode + '_omx'], \
                                              forgiving=False, method=True)))
            stop = start + mx_num
            coords = coords_to_symmetry(coords, \
                                               sh['uc_fmx'], \
                                               sh['uc_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
                                                forgiving=False, method=True)))
        # expand to unit-cell, real 3D
        coords = coords_to_symmetry(coords, \
                                            sh[symmetry_mode + '_fmx'], \
                                            sh[symmetry_mode + '_omx'], \
                                              forgiving=False, method=True)))
            stop = start + mx_num
            coords = coords_to_symmetry(coords, \
                                               sh['uc_fmx'], \
                                               sh['uc_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'))
    # expand the coordinates to symmetry
    all_coords = coords_to_symmetry(coords, fmx, omx, mxs, mode)
    models = ModelHolder(name)
 

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'))
    # expand the coordinates to symmetry
    all_coords = coords_to_symmetry(coords, fmx, omx, mxs, mode)
    models = ModelHolder(name)