def symexpcell(prefix='mate', object=None, a=0, b=0, c=0):
"""
DESCRIPTION
Creates all symmetry-related objects for the specified object that
occur with their bounding box center within the unit cell.
USAGE
symexpcell prefix, object, [a, b, c]
ARGUMENTS
prefix = string: prefix of new objects
object = string: object for which to create symmetry mates
a, b, c = integer: create neighboring cell {default: 0,0,0}
SEE ALSO
symexp, http://www.pymolwiki.org/index.php/SuperSym
"""
if object is None:
object = cmd.get_object_list()[0]
sym = cmd.get_symmetry(object)
cell_edges = sym[0:3]
cell_angles = sym[3:6]
spacegroup = sym[6]
basis = cellbasis(cell_angles, cell_edges)
basis = numpy.matrix(basis)
extent = cmd.get_extent(object)
center = sum(numpy.array(extent)) * 0.5
center = numpy.matrix(center.tolist() + [1.0]).T
center_cell = basis.I * center
extra_shift = [[float(i)] for i in (a,b,c)]
i = 0
matrices = xray.sg_sym_to_mat_list(spacegroup)
for mat in matrices:
i += 1
mat = numpy.matrix(mat)
shift = numpy.floor(mat * center_cell)
mat[0:3,3] -= shift[0:3,0]
mat[0:3,3] += extra_shift
mat = basis * mat * basis.I
mat_list = list(mat.flat)
name = '%s%d' % (prefix, i)
cmd.create(name, object)
cmd.transform_object(name, mat_list, 0)
cmd.color(i+1, name)
def symexpcell(prefix='mate', object=None, a=0, b=0, c=0):
'''
DESCRIPTION
Creates all symmetry-related objects for the specified object that
occur with their bounding box center within the unit cell.
USAGE
symexpcell prefix, object, [a, b, c]
ARGUMENTS
prefix = string: prefix of new objects
object = string: object for which to create symmetry mates
a, b, c = integer: create neighboring cell {default: 0,0,0}
SEE ALSO
symexp, http://www.pymolwiki.org/index.php/SuperSym
'''
if object is None:
object = cmd.get_object_list()[0]
sym = cmd.get_symmetry(object)
cell_edges = sym[0:3]
cell_angles = sym[3:6]
spacegroup = sym[6]
basis = cellbasis(cell_angles, cell_edges)
basis = numpy.matrix(basis)
extent = cmd.get_extent(object)
center = sum(numpy.array(extent)) * 0.5
center = numpy.matrix(center.tolist() + [1.0]).T
center_cell = basis.I * center
extra_shift = [[float(i)] for i in (a,b,c)]
i = 0
matrices = xray.sg_sym_to_mat_list(spacegroup)
for mat in matrices:
i += 1
mat = numpy.matrix(mat)
shift = numpy.floor(mat * center_cell)
mat[0:3,3] -= shift[0:3,0]
mat[0:3,3] += extra_shift
mat = basis * mat * basis.I
mat_list = list(mat.flat)
name = '%s%d' % (prefix, i)
cmd.create(name, object)
cmd.transform_object(name, mat_list)
cmd.color(i+1, name)
def symexpcell(prefix='mate', object=None, a=0, b=0, c=0,transformation=None,cutoff=None):
'''
DESCRIPTION
Creates all symmetry-related objects for the specified object that
occur with their bounding box center within the unit cell.
USAGE
symexpcell prefix, object, [a, b, c]
ARGUMENTS
prefix = string: prefix of new objects
object = string: object for which to create symmetry mates
a, b, c = integer: create neighboring cell {default: 0,0,0}
transformation = list: list of 16 floats giving the transformation matrix
to apply to the generated symmetry mates {default: identity matrix}
cutoff = int: restrict symmetry mates to within cutoff angstroms of the origin.
Use 0 to generate all symmetry mates. {default: 0}
SEE ALSO
symexp, http://www.pymolwiki.org/index.php/SuperSym
'''
#print "symexpcell %s,%s,%d,%d,%d,%s"%(prefix,object,int(a),int(b),int(c),transformation)
if object is None:
object = cmd.get_object_list()[0]
if cutoff is not None:
cutoff = int(cutoff)
if cutoff <= 0: cutoff = None
sym = cmd.get_symmetry(object)
cell_edges = sym[0:3]
cell_angles = sym[3:6]
spacegroup = sym[6]
basis = cellbasis(cell_angles, cell_edges)
extent = cmd.get_extent(object)
center = sum(numpy.array(extent)) * 0.5
center = numpy.append(center,1.0).reshape(4,1)
center_cell = numpy.linalg.inv(basis) * center
extra_shift = numpy.array([[float(i)] for i in (a,b,c)])
origin = numpy.array([[0,0,0,1]]).T
if transformation is not None:
transmat = transformation_to_numpy(transformation)
#print "%s\n*\n%s\n=\n%s\n" % (origin,transmat,
# numpy.dot(numpy.linalg.inv(transmat),origin) )
origin = numpy.dot(numpy.linalg.inv(transmat),origin)
i = 0
matrices = xray.sg_sym_to_mat_list(spacegroup)
for mat in matrices:
i += 1
mat = numpy.array(mat)
shift = numpy.floor(numpy.dot(mat, center_cell))
mat[0:3,3] -= shift[0:3,0]
mat[0:3,3] += extra_shift[0:3,0]
mat = numpy.dot(numpy.dot(basis, mat), numpy.linalg.inv(basis) )
mat_list = list(mat.flat)
new_center = numpy.dot(mat,center)
#print "%s\n* (%d)\n%s\n=\n%s\n" % (center,i,mat, new_center)
if cutoff is not None:
dist = new_center - origin
dist = numpy.dot(dist.T,dist)
if dist > cutoff**2:
#print "Skipping %d%d%d_%d at distance %f" % (a,b,c,i,sqrt(dist))
continue
name = '%s%d' % (prefix, i)
cmd.create(name, object)
cmd.transform_object(name, mat_list)
# Apply extra transformation afterwards
if transformation is not None:
cmd.transform_object(name, transformation)
cmd.color(i+1, name)
def symexpcell(prefix='mate', object=None, a=0, b=0, c=0, *, _self=cmd):
'''
DESCRIPTION
Creates all symmetry-related objects for the specified object that
occur with their bounding box center within the unit cell.
USAGE
symexpcell prefix, object, [a, b, c]
ARGUMENTS
prefix = string: prefix of new objects
object = string: object for which to create symmetry mates
a, b, c = integer: create neighboring cell {default: 0,0,0}
SEE ALSO
symexp
'''
import numpy
from pymol import xray
if object is None:
object = _self.get_object_list()[0]
sym = _self.get_symmetry(object)
cell_edges = sym[0:3]
cell_angles = sym[3:6]
spacegroup = sym[6]
basis = cellbasis(cell_angles, cell_edges)
basis = numpy.matrix(basis)
extent = _self.get_extent(object)
center = sum(numpy.array(extent)) * 0.5
center = numpy.matrix(center.tolist() + [1.0]).T
center_cell = basis.I * center
spacegroup = xray.space_group_map.get(spacegroup, spacegroup)
i = 0
matrices = xray.sg_sym_to_mat_list(spacegroup)
for mat in matrices:
i += 1
mat = numpy.matrix(mat)
shift = -numpy.floor(numpy.array(mat * center_cell)[0:3, 0])
shift = shift.flatten().astype(int)
shift += [a, b, c]
mat[0:3, 3] += shift.reshape((3, 1))
mat = basis * mat * basis.I
mat_list = list(mat.flat)
name = '%s%d' % (prefix, i)
_self.create(name, object)
_self.transform_object(name, mat_list, 0)
_self.set_title(name, 1, "{}_{}{}{}".format(i, *(shift + 5).tolist()))
if len(matrices) > 1:
_self.color(i + 1, name)
