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Source code for dxtbx.model.crystal
from __future__ import absolute_import, division, print_function
from cctbx.sgtbx import space_group as SG
from scitbx import matrix
from dxtbx_model_ext import Crystal, MosaicCrystalKabsch2010, MosaicCrystalSauter2014
[docs]class CrystalFactory(object):
[docs] @staticmethod
def from_dict(d, t=None):
"""Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The crystal model
"""
if d is None and t is None:
return None
joint = t.copy() if t else {}
joint.update(d)
# Create the model from the dictionary
if "ML_half_mosaicity_deg" in joint:
assert "ML_domain_size_ang" in joint
if (
joint["ML_half_mosaicity_deg"] is None
or joint["ML_domain_size_ang"] is None
):
assert (
joint["ML_half_mosaicity_deg"] is None
and joint["ML_domain_size_ang"] is None
)
else:
if joint.get("mosaicity", 0) > 0:
print(
"Warning, two kinds of mosaicity found. Using Sauter2014 model"
)
return MosaicCrystalSauter2014.from_dict(joint)
if "mosaicity" in joint:
return MosaicCrystalKabsch2010.from_dict(joint)
else:
return Crystal.from_dict(joint)
[docs] @staticmethod
def from_mosflm_matrix(
mosflm_A_matrix, unit_cell=None, wavelength=None, space_group=None
):
"""
Create a crystal_model from a Mosflm A matrix (a*, b*, c*); N.B. assumes
the mosflm coordinate frame::
/!
Y-axis / !
^ / !
! / !
! / !
! / / Xd !
! / / * ^ !
! / ! 3 ! !
!/ X-ray beam ! ! !
/------------------------/--!---->X-axis
/ ! / *1!
<-/- ! / !
/ \\+ve phi ! Yd /
/ / ! 2 /
/ ! * /
Z-axis Ys ^ _/
Rotation ! /| Xs
axis !/
O
Also assume that the mosaic spread is 0.
:param mosflm_A_matrix: The A matrix in Mosflm convention.
:type mosflm_A_matrix: tuple of floats
:param unit_cell: The unit cell parameters which are used to determine the
wavelength from the Mosflm A matrix.
:type unit_cell: cctbx.uctbx.unit_cell
:param wavelength: The wavelength to scale the A matrix
:type wavelength: float
:param space_group: If the space group is None then the space_group will
be assigned as P1
:type space_group: cctbx.sgtbx.space_group
:returns: A crystal model derived from the given Mosflm A matrix
:rtype: :py:class:`crystal_model`
"""
if not space_group:
space_group = SG("P1")
A_star = matrix.sqr(mosflm_A_matrix)
A = A_star.inverse()
if unit_cell:
unit_cell_constants = unit_cell.parameters()
a = matrix.col(A.elems[0:3])
wavelength = unit_cell_constants[0] / a.length()
A *= wavelength
elif wavelength:
A *= wavelength
else:
# assume user has pre-scaled
pass
a = A.elems[0:3]
b = A.elems[3:6]
c = A.elems[6:9]
rotate_mosflm_to_imgCIF = matrix.sqr((0, 0, 1, 0, 1, 0, -1, 0, 0))
_a = rotate_mosflm_to_imgCIF * a
_b = rotate_mosflm_to_imgCIF * b
_c = rotate_mosflm_to_imgCIF * c
return Crystal(_a, _b, _c, space_group=space_group)
