dials.algorithms.indexing

Table of Contents

class dials.algorithms.indexing.indexer.Solution(**keyword_arguments)[source]

Bases: libtbx.group_args

class dials.algorithms.indexing.indexer.SolutionTrackerFilter(check_doubled_cell=True, likelihood_cutoff=0.8, volume_cutoff=1.25, n_indexed_cutoff=0.9)[source]

Bases: object

append(item)[source]
best_solution()[source]
filter_by_likelihood(solutions)[source]
filter_by_n_indexed(solutions, n_indexed_cutoff=None)[source]
filter_by_volume(solutions)[source]
update_analysis()[source]
class dials.algorithms.indexing.indexer.SolutionTrackerWeighted(power=2, volume_weight=1, n_indexed_weight=1, rmsd_weight=1)[source]

Bases: object

append(item)[source]
best_solution()[source]
score_by_fraction_indexed(reverse=False)[source]
score_by_rmsd_xy(reverse=False)[source]
score_by_rmsd_z(reverse=False)[source]
score_by_volume(reverse=False)[source]
solution_scores()[source]
dials.algorithms.indexing.indexer.apply_hkl_offset(indices, offset)[source]
class dials.algorithms.indexing.indexer.basis_vector_minimser(reciprocal_lattice_points, vector, lbfgs_termination_params=None, lbfgs_core_params=<scitbx.lbfgs.core_parameters object>)[source]

Bases: object

callback_after_step(minimizer)[source]
compute_functional_and_gradients()[source]
class dials.algorithms.indexing.indexer.basis_vector_target(reciprocal_lattice_points)[source]

Bases: object

compute_functional_and_gradients(vector)[source]
dials.algorithms.indexing.indexer.detect_non_primitive_basis(miller_indices, threshold=0.9)[source]
dials.algorithms.indexing.indexer.filter_doubled_cell(solutions)[source]
dials.algorithms.indexing.indexer.filter_reflections_by_scan_range(reflections, scan_range)[source]
dials.algorithms.indexing.indexer.find_max_cell(reflections, max_cell_multiplier, step_size, nearest_neighbor_percentile=None, histogram_binning='linear', nn_per_bin=5, max_height_fraction=0.25, filter_ice=True, filter_overlaps=True, overlaps_border=0)[source]
dials.algorithms.indexing.indexer.hist_outline(hist)[source]
class dials.algorithms.indexing.indexer.indexer_base(reflections, imagesets, params=None)[source]

Bases: object

apply_symmetry(crystal_model, target_space_group)[source]
static calculate_entering_flags(beam, goniometer)[source]
choose_best_orientation_matrix(candidate_orientation_matrices)[source]
correct_non_primitive_basis(experiments, reflections, threshold)[source]
debug_plot_candidate_basis_vectors()[source]
debug_show_candidate_basis_vectors()[source]
debug_write_ccp4_map(map_data, file_name)[source]
debug_write_reciprocal_lattice_points_as_pdb(file_name='reciprocal_lattice.pdb')[source]
export_as_json(experiments, file_name='experiments.json', compact=False)[source]
export_reflections(reflections, file_name='reflections.pickle')[source]
filter_reflections_by_scan_range()[source]
find_candidate_orientation_matrices(candidate_basis_vectors)[source]
find_lattices()[source]
find_max_cell()[source]
static from_parameters(imagesets, known_crystal_models=None, params=None)[source]
index()[source]
index_reflections(experiments, reflections)[source]
static map_centroids_to_reciprocal_space(detector, beam, goniometer, calculated=False)[source]

Map mm/radian spot centroids to reciprocal space.

Used to convert spot centroids provided in mm/radian units to reciprocal space as required for indexing. Adds the column ‘rlp’ to the reflection table, which contains a flex.vec3_double array of the reciprocal lattice vectors.

Parameters:
  • spots_mm (dials.array_family.flex.reflection_table) – a reflection table containing the column ‘xyzobs.mm.value’
  • detector (dxtbx.model.detector.Detector) – a dxtbx detector object
  • beam (dxtbx.model.beam.Beam) – a dxtbx beam object
  • goniometer (dxtbx.model.goniometer.Goniometer) – a dxtbx goniometer object. May be None, e.g. for a still image
static map_spots_pixel_to_mm_rad(detector, scan)[source]

Map spot centroids from pixel/image number to mm/radian.

Used to convert spot centroids coming from e.g. dials.find_spots which are in pixel/image number units to mm/radian units as required for indexing and refinement.

Parameters:
  • spots (dials.array_family.flex.reflection_table) – a reflection table containing the columns ‘xyzobs.px.value’, ‘xyzobs.px.variance’ and ‘panel’
  • detector (dxtbx.model.detector.Detector) – a dxtbx detector object
  • scan (dxtbx.model.scan.Scan) – a dxtbx scan object. May be None, e.g. for a still image
Returns:

A copy of the input reflection table containing the additional keys ‘xyzobs.mm.value’ and ‘xyzobs.mm.variance’

Return type:

dials.array_family.flex.reflection_table

refine(experiments, reflections)[source]
setup_indexing()[source]
show_experiments(experiments, reflections, d_min=None)[source]
dials.algorithms.indexing.indexer.is_approximate_integer_multiple(vec_a, vec_b, relative_tolerance=0.2, angular_tolerance=5.0)[source]
dials.algorithms.indexing.indexer.optimise_basis_vectors(reciprocal_lattice_points, vectors)[source]
dials.algorithms.indexing.indexer.plot_centroid_weights_histograms(reflections, n_slots=50)[source]
dials.algorithms.indexing.indexer.reject_weight_outliers_selection(reflections, sigma_cutoff=5)[source]
class dials.algorithms.indexing.indexer.vector_group[source]

Bases: object

append(vector, length, volume)[source]
compute_mean()[source]
mean()[source]
dials.algorithms.indexing.fft3d.clean_3d(dirty_beam, dirty_map, n_peaks, gamma=1)[source]
class dials.algorithms.indexing.fft3d.indexer_fft3d(reflections, imagesets, params)[source]

Bases: dials.algorithms.indexing.indexer.indexer_base

cluster_analysis_dbscan(vectors)[source]
cluster_analysis_hcluster(vectors)[source]
debug_plot_clusters(vectors, labels, min_cluster_size=1)[source]
fft()[source]
find_basis_vector_combinations_cluster_analysis()[source]
find_candidate_basis_vectors()[source]
find_lattices()[source]
find_peaks()[source]
find_peaks_clean()[source]
map_centroids_to_reciprocal_space_grid()[source]
optimise_peaks(peaks, reciprocal_lattice_points)[source]
dials.algorithms.indexing.fft3d.sampling_volume_map(data, angle_range, beam_vector, rotation_axis, rl_grid_spacing, d_min, b_iso)[source]
dials.algorithms.indexing.fft1d.candidate_basis_vectors_fft1d(reciprocal_lattice_vectors, params, max_cell=None)[source]
class dials.algorithms.indexing.fft1d.indexer_fft1d(reflections, imagesets, params)[source]

Bases: dials.algorithms.indexing.indexer.indexer_base

find_candidate_basis_vectors()[source]
find_lattices()[source]

Bases: dials.algorithms.indexing.indexer.indexer_base

find_lattices()[source]
dials.algorithms.indexing.compare_orientation_matrices.difference_rotation_matrix_axis_angle(crystal_a, crystal_b, target_angle=0)[source]
dials.algorithms.indexing.compare_orientation_matrices.show_rotation_matrix_differences(crystal_models, out=None, miller_indices=None, comparison='pairwise')[source]
class dials.algorithms.indexing.symmetry.bravais_setting(other)[source]

Bases: rstbx.symmetry.subgroup.MetricSubgroup

dials.algorithms.indexing.symmetry.dials_crystal_from_orientation(crystal_orientation, space_group)[source]
dials.algorithms.indexing.symmetry.find_matching_symmetry(unit_cell, target_space_group, max_delta=5)[source]
dials.algorithms.indexing.symmetry.identify_likely_solutions(all_solutions)[source]
dials.algorithms.indexing.symmetry.metric_supergroup(group)[source]
dials.algorithms.indexing.symmetry.refine_subgroup(args)[source]
dials.algorithms.indexing.symmetry.refined_settings_factory_from_refined_triclinic(params, experiments, reflections, i_setting=None, lepage_max_delta=5.0, nproc=1, refiner_verbosity=0)[source]
class dials.algorithms.indexing.symmetry.refined_settings_list[source]

Bases: list

as_dict()[source]
labelit_printout(out=None)[source]
supergroup()[source]
triclinic()[source]
dials.algorithms.indexing.refinement.debug_plot_residuals(refiner, inlier_sel=None)[source]
dials.algorithms.indexing.refinement.refine(params, reflections, experiments, verbosity=0, debug_plots=False)[source]