def get_real_space_primitive_matrix(lattice, matrix, wd = None):
'''Get the primitive real space vectors for the unit cell and
lattice type. Note that the resulting matrix will need to be
scaled by a factor equal to the wavelength in Angstroms.'''
# parse the orientation matrix
cell, a, u = parse_matrix(matrix)
# generate other possibilities
o = _Othercell()
if wd:
o.set_working_directory(wd)
auto_logfiler(o)
o.set_cell(cell)
o.set_lattice(lattice)
o.generate()
# transform the possibly centred cell to the primitive setting
new_cell = o.get_cell('aP')
op = symop_to_mat(o.get_reindex_op('aP'))
primitive_a = matmul(invert(op), a)
# then convert to real space
real_a = invert(primitive_a)
return real_a[0:3], real_a[3:6], real_a[6:9]
def get_reciprocal_space_primitive_matrix(lattice, matrix, wd = None):
'''Get the primitive reciprocal space vectors for this matrix.'''
# parse the orientation matrix
cell, a, u = parse_matrix(matrix)
# generate other possibilities
o = _Othercell()
if wd:
o.set_working_directory(wd)
auto_logfiler(o)
o.set_cell(cell)
o.set_lattice(lattice)
o.generate()
# transform the possibly centred cell to the primitive setting
new_cell = o.get_cell('aP')
op = symop_to_mat(o.get_reindex_op('aP'))
primitive_a = matmul(invert(op), a)
return mat2vec(primitive_a)
def get_reciprocal_space_primitive_matrix(lattice, matrix, wd=None):
"""Get the primitive reciprocal space vectors for this matrix."""
# parse the orientation matrix
cell, a, u = parse_matrix(matrix)
# generate other possibilities
o = _Othercell()
if wd:
o.set_working_directory(wd)
auto_logfiler(o)
o.set_cell(cell)
o.set_lattice(lattice)
o.generate()
# transform the possibly centred cell to the primitive setting
op = symop_to_mat(o.get_reindex_op("aP"))
primitive_a = matmul(invert(op), a)
return mat2vec(primitive_a)
def get_real_space_primitive_matrix(lattice, matrix, wd=None):
"""Get the primitive real space vectors for the unit cell and
lattice type. Note that the resulting matrix will need to be
scaled by a factor equal to the wavelength in Angstroms."""
# parse the orientation matrix
cell, a, u = parse_matrix(matrix)
# generate other possibilities
o = _Othercell()
if wd:
o.set_working_directory(wd)
auto_logfiler(o)
o.set_cell(cell)
o.set_lattice(lattice)
o.generate()
# transform the possibly centred cell to the primitive setting
op = symop_to_mat(o.get_reindex_op("aP"))
primitive_a = matmul(invert(op), a)
# then convert to real space
real_a = invert(primitive_a)
return real_a[0:3], real_a[3:6], real_a[6:9]
def transmogrify_matrix(lattice, matrix, target_lattice,
wavelength, wd = None):
'''Transmogrify a matrix for lattice X into a matrix for lattice
Y. This should work find for Mosflm... Will also return the new
unit cell.'''
cell, a, u = parse_matrix(matrix)
o = _Othercell()
if wd:
o.set_working_directory(wd)
auto_logfiler(o)
o.set_cell(cell)
o.set_lattice(lattice)
o.generate()
new_cell = o.get_cell(target_lattice)
op = symop_to_mat(o.get_reindex_op(target_lattice))
# HACK! again - bug # 3193
if 'lattice_symmetry' in o.get_executable():
op = transpose(op)
# why is only one of the matrices inverted?!
a = matmul(invert(op), a)
u = matmul(op, u)
# in here test that the given unit cell corresponds to the
# one calculated from the A matrix.
anew = matscl(a, 1.0 / wavelength)
reala = transpose(invert(anew))
_a, _b, _c = mat2vec(reala)
la = math.sqrt(dot(_a, _a))
lb = math.sqrt(dot(_b, _b))
lc = math.sqrt(dot(_c, _c))
if math.fabs(la - new_cell[0]) / new_cell[0] > 0.01:
raise RuntimeError, 'cell check failed (wavelength != %f)' % \
wavelength
if math.fabs(lb - new_cell[1]) / new_cell[1] > 0.01:
raise RuntimeError, 'cell check failed (wavelength != %f)' % \
wavelength
if math.fabs(lc - new_cell[2]) / new_cell[2] > 0.01:
raise RuntimeError, 'cell check failed (wavelength != %f)' % \
wavelength
return format_matrix(new_cell, a, u)
def transmogrify_matrix(lattice, matrix, target_lattice, wavelength, wd=None):
"""Transmogrify a matrix for lattice X into a matrix for lattice
Y. This should work find for Mosflm... Will also return the new
unit cell."""
cell, a, u = parse_matrix(matrix)
o = _Othercell()
if wd:
o.set_working_directory(wd)
auto_logfiler(o)
o.set_cell(cell)
o.set_lattice(lattice)
o.generate()
new_cell = o.get_cell(target_lattice)
op = symop_to_mat(o.get_reindex_op(target_lattice))
# HACK! again - bug # 3193
if "lattice_symmetry" in o.get_executable():
op = transpose(op)
# why is only one of the matrices inverted?!
a = matmul(invert(op), a)
u = matmul(op, u)
# in here test that the given unit cell corresponds to the
# one calculated from the A matrix.
anew = matscl(a, 1.0 / wavelength)
reala = transpose(invert(anew))
_a, _b, _c = mat2vec(reala)
la = math.sqrt(dot(_a, _a))
lb = math.sqrt(dot(_b, _b))
lc = math.sqrt(dot(_c, _c))
if (
math.fabs(la - new_cell[0]) / new_cell[0] > 0.01
or math.fabs(lb - new_cell[1]) / new_cell[1] > 0.01
or math.fabs(lc - new_cell[2]) / new_cell[2] > 0.01
):
raise RuntimeError("cell check failed (wavelength != %f)" % wavelength)
return format_matrix(new_cell, a, u)
def set_integrater_reindex_operator(self, reindex_operator,
compose=True,
reason=None):
'''Assign a symmetry operator to the reflections - note
that this is cumulative...'''
reindex_operator = reindex_operator.lower().strip()
# see if we really need to do anything
if reindex_operator == 'h,k,l' and \
self._intgr_reindex_operator == 'h,k,l':
return
# ok we need to do something - either just record the new
# operation or compose it with the existing operation
self.set_integrater_finish_done(False)
if reason:
Debug.write('Reindexing to %s (compose=%s) because %s' %
(reindex_operator, compose, reason))
if self._intgr_reindex_operator is None or not compose:
self._intgr_reindex_operator = reindex_operator
else:
old_operator = self._intgr_reindex_operator
self._intgr_reindex_operator = compose_symops(
reindex_operator, old_operator)
Debug.write('Composing %s and %s -> %s' % \
(old_operator, reindex_operator,
self._intgr_reindex_operator))
# convert this to a 3x3 matrix form for e.g. XDS CORRECT
self._intgr_reindex_matrix = symop_to_mat(
self._intgr_reindex_operator)
self._set_integrater_reindex_operator_callback()
return
def set_integrater_reindex_operator(self,
reindex_operator,
compose=True,
reason=None):
'''Assign a symmetry operator to the reflections - note
that this is cumulative...'''
reindex_operator = reindex_operator.lower().strip()
# see if we really need to do anything
if reindex_operator == 'h,k,l' and \
self._intgr_reindex_operator == 'h,k,l':
return
# ok we need to do something - either just record the new
# operation or compose it with the existing operation
self.set_integrater_finish_done(False)
if reason:
Debug.write('Reindexing to %s (compose=%s) because %s' %
(reindex_operator, compose, reason))
if self._intgr_reindex_operator is None or not compose:
self._intgr_reindex_operator = reindex_operator
else:
old_operator = self._intgr_reindex_operator
self._intgr_reindex_operator = compose_symops(
reindex_operator, old_operator)
Debug.write('Composing %s and %s -> %s' % \
(old_operator, reindex_operator,
self._intgr_reindex_operator))
# convert this to a 3x3 matrix form for e.g. XDS CORRECT
self._intgr_reindex_matrix = symop_to_mat(self._intgr_reindex_operator)
self._set_integrater_reindex_operator_callback()
def mosflm_a_matrix_to_real_space(wavelength, lattice, matrix):
'''Given a Mosflm A matrix and the associated spacegroup (think of this
Bravais lattice (which will be converted to a spacegroup for the benefit
of the CCTBX program lattice_symmetry) return the real space primative
crystal lattice vectors in the xia2 reference frame. This reference frame
corresponds to that defined for imgCIF.'''
# convert the lattice to a spacegroup - not needed, see below
# spacegroup_number = lattice_to_spacegroup(lattice)
# spacegroup = Syminfo.spacegroup_name_to_number(spacegroup_number)
# get the a, u, matrices and the unit cell
cell, a, u = parse_matrix(matrix)
# use iotbx.latice_symmetry to obtain the reindexing operator to
# a primative triclinic lattice - this should not be specific to
# using iotbx - othercell should be optionally supported too...
ls = _Othercell()
ls.set_cell(cell)
ls.set_lattice(lattice)
# ls.set_spacegroup(spacegroup)
# cell, reindex = ls.generate_primative_reindex()
ls.generate()
cell = ls.get_cell('aP')
reindex = ls.get_reindex_op('aP')
reindex_matrix = symop_to_mat(reindex)
# grim hack warning! - this is because for some reason (probably to
# do with LS getting the inverse operation) othercell is returning
# the transpose of the operator or something... FIXME bug # 3193
if 'othercell' in ls.get_executable():
reindex_matrix = transpose(reindex_matrix)
# scale the a matrix
a = matscl(a, 1.0 / wavelength)
# convert to real space (invert) and apply this reindex operator to the a
# matrix to get the primative real space triclinic cell axes
real_a = matmul(reindex_matrix, transpose(invert(a)))
# convert these to the xia2 reference frame
a, b, c = mat2vec(real_a)
ax = mosflm_to_xia2(a)
bx = mosflm_to_xia2(b)
cx = mosflm_to_xia2(c)
# FIXME in here add check that the unit cell lengths are within 1% of
# the correct value - if they are not, raise an exception as the wavelength
# provided is probably wrong...
la = math.sqrt(dot(ax, ax))
lb = math.sqrt(dot(bx, bx))
lc = math.sqrt(dot(cx, cx))
# print out values - the cell may have been reindexed.
Debug.write('Reindexed cell lengths: %.3f %.3f %.3f' % \
(cell[0], cell[1], cell[2]))
Debug.write('Calculated from matrix: %.3f %.3f %.3f' % \
(la, lb, lc))
if math.fabs(la - cell[0]) / cell[0] > 0.01:
raise RuntimeError, 'cell check failed (wavelength != %f)' % \
wavelength
if math.fabs(lb - cell[1]) / cell[1] > 0.01:
raise RuntimeError, 'cell check failed (wavelength != %f)' % \
wavelength
if math.fabs(lc - cell[2]) / cell[2] > 0.01:
raise RuntimeError, 'cell check failed (wavelength != %f)' % \
wavelength
# return these vectors
return ax, bx, cx
def mosflm_a_matrix_to_real_space(wavelength, lattice, matrix):
"""Given a Mosflm A matrix and the associated spacegroup (think of this
Bravais lattice (which will be converted to a spacegroup for the benefit
of the CCTBX program lattice_symmetry) return the real space primative
crystal lattice vectors in the xia2 reference frame. This reference frame
corresponds to that defined for imgCIF."""
# get the a, u, matrices and the unit cell
cell, a, u = parse_matrix(matrix)
# use iotbx.latice_symmetry to obtain the reindexing operator to
# a primative triclinic lattice - this should not be specific to
# using iotbx - othercell should be optionally supported too...
ls = _Othercell()
ls.set_cell(cell)
ls.set_lattice(lattice)
ls.generate()
cell = ls.get_cell("aP")
reindex = ls.get_reindex_op("aP")
reindex_matrix = symop_to_mat(reindex)
# grim hack warning! - this is because for some reason (probably to
# do with LS getting the inverse operation) othercell is returning
# the transpose of the operator or something... FIXME bug # 3193
if "othercell" in ls.get_executable():
reindex_matrix = transpose(reindex_matrix)
# scale the a matrix
a = matscl(a, 1.0 / wavelength)
# convert to real space (invert) and apply this reindex operator to the a
# matrix to get the primative real space triclinic cell axes
real_a = matmul(reindex_matrix, transpose(invert(a)))
# convert these to the xia2 reference frame
a, b, c = mat2vec(real_a)
ax = mosflm_to_xia2(a)
bx = mosflm_to_xia2(b)
cx = mosflm_to_xia2(c)
# FIXME in here add check that the unit cell lengths are within 1% of
# the correct value - if they are not, raise an exception as the wavelength
# provided is probably wrong...
la = math.sqrt(dot(ax, ax))
lb = math.sqrt(dot(bx, bx))
lc = math.sqrt(dot(cx, cx))
# print out values - the cell may have been reindexed.
Debug.write("Reindexed cell lengths: %.3f %.3f %.3f" % (cell[0], cell[1], cell[2]))
Debug.write("Calculated from matrix: %.3f %.3f %.3f" % (la, lb, lc))
if (
math.fabs(la - cell[0]) / cell[0] > 0.01
or math.fabs(lb - cell[1]) / cell[1] > 0.01
or math.fabs(lc - cell[2]) / cell[2] > 0.01
):
raise RuntimeError("cell check failed (wavelength != %f)" % wavelength)
# return these vectors
return ax, bx, cx
