dxtbx.model.crystal

class dxtbx.model.Crystal

Bases: dxtbx_model_ext.CrystalBase

static from_dict(d)

Convert the dictionary to a crystal model

Params:
d The dictionary of parameters
Returns:The crystal model
get_crystal_symmetry(assert_is_compatible_unit_cell=True)
show(show_scan_varying=False, out=None)
to_dict()
class dxtbx.model.MosaicCrystalKabsch2010

Bases: dxtbx_model_ext.Crystal

static from_dict(d)

Convert the dictionary to a crystal model

Params:
d The dictionary of parameters
Returns:The crystal model
get_mosaicity((MosaicCrystalKabsch2010)arg1[, (bool)deg=True]) → float :
C++ signature :
double get_mosaicity(dxtbx::model::MosaicCrystalKabsch2010 {lvalue} [,bool=True])
is_similar_to((MosaicCrystalKabsch2010)arg1, (CrystalBase)other[, (float)angle_tolerance=0.01[, (float)uc_rel_length_tolerance=0.01[, (float)uc_abs_angle_tolerance=1.0[, (float)mosaicity_tolerance=0.8]]]]) → bool :
C++ signature :
bool is_similar_to(dxtbx::model::MosaicCrystalKabsch2010 {lvalue},dxtbx::model::CrystalBase [,double=0.01 [,double=0.01 [,double=1.0 [,double=0.8]]]])
set_mosaicity((MosaicCrystalKabsch2010)arg1, (float)mosaicity[, (bool)deg=True]) → None :
C++ signature :
void set_mosaicity(dxtbx::model::MosaicCrystalKabsch2010 {lvalue},double [,bool=True])
show(show_scan_varying=False, out=None)
to_dict()

Convert the crystal model to a dictionary

Params:
crystal The crystal model
Returns:A dictionary of the parameters
class dxtbx.model.MosaicCrystalSauter2014

Bases: dxtbx_model_ext.Crystal

static from_dict(d)

Convert the dictionary to a crystal model

Params:
d The dictionary of parameters
Returns:The crystal model
get_A_as_sqr()
get_A_inverse_as_sqr()
get_domain_size_ang((MosaicCrystalSauter2014)arg1) → float :
C++ signature :
double get_domain_size_ang(dxtbx::model::MosaicCrystalSauter2014 {lvalue})
get_half_mosaicity_deg((MosaicCrystalSauter2014)arg1) → float :
C++ signature :
double get_half_mosaicity_deg(dxtbx::model::MosaicCrystalSauter2014 {lvalue})
is_similar_to((MosaicCrystalSauter2014)arg1, (CrystalBase)other[, (float)angle_tolerance=0.01[, (float)uc_rel_length_tolerance=0.01[, (float)uc_abs_angle_tolerance=1.0[, (float)half_mosaicity_tolerance=0.4[, (float)domain_size_tolerance=1.0]]]]]) → bool :
C++ signature :
bool is_similar_to(dxtbx::model::MosaicCrystalSauter2014 {lvalue},dxtbx::model::CrystalBase [,double=0.01 [,double=0.01 [,double=1.0 [,double=0.4 [,double=1.0]]]]])
set_domain_size_ang((MosaicCrystalSauter2014)arg1, (float)domain_size_ang) → None :
C++ signature :
void set_domain_size_ang(dxtbx::model::MosaicCrystalSauter2014 {lvalue},double)
set_half_mosaicity_deg((MosaicCrystalSauter2014)arg1, (float)half_mosaicity_deg) → None :
C++ signature :
void set_half_mosaicity_deg(dxtbx::model::MosaicCrystalSauter2014 {lvalue},double)
show(show_scan_varying=False, out=None)
to_dict()

Convert the crystal model to a dictionary

Params:
crystal The crystal model
Returns:A dictionary of the parameters
class dxtbx.model.crystal.CrystalFactory[source]

Bases: object

static from_dict(d, t=None)[source]

Convert the dictionary to a crystal model

Params:
d The dictionary of parameters t The template dictionary to use
Returns:The crystal model
static from_mosflm_matrix(mosflm_A_matrix, unit_cell=None, wavelength=None, space_group=None)[source]

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.

Parameters:
  • mosflm_A_matrix (tuple of floats) – The A matrix in Mosflm convention.
  • unit_cell (cctbx.uctbx.unit_cell) – The unit cell parameters which are used to determine the wavelength from the Mosflm A matrix.
  • wavelength (float) – The wavelength to scale the A matrix
  • space_group (cctbx.sgtbx.space_group) – If the space group is None then the space_group will be assigned as P1
Returns:

A crystal model derived from the given Mosflm A matrix

Return type:

crystal_model