mmtbx.validation.molprobity package

Submodules

mmtbx.validation.molprobity.mp_geo module

mmtbx.validation.molprobity.mp_geo.get_altloc(atoms_info)

mmtbx.validation.molprobity.mp_geo.get_atoms_str(atoms_info)

mmtbx.validation.molprobity.mp_geo.get_bond_and_angle_outliers(pdb_hierarchy, xray_structure, geometry_restraints_manager, use_segids, outliers_only=False, type=None)

mmtbx.validation.molprobity.mp_geo.get_master_phil()

mmtbx.validation.molprobity.mp_geo.run(args)

I suggest adding here: cctbx_project/mmtbx/validation/regression/tst_mp_geo.py test cases with just .pdb, without arguments, etc.

mmtbx.validation.molprobity.nqh_minimize module

Module contents

Classes for MolProbity validation, combining all other analyses in mmtbx.validation, which use the same APIs for storing and displaying results.

class mmtbx.validation.molprobity.MolProbityParser(program_class, custom_process_arguments=None, unused_phil_raises_sorry=True, logger=None, *args, **kwargs)

Bases: CCTBXParser

add_default_options()

class mmtbx.validation.molprobity.MolProbityTemplate(data_manager, params, master_phil=None, logger=None)

Bases: ProgramTemplate

get_results_as_PDB_JSON()

class mmtbx.validation.molprobity.molprobity(model, fmodel=None, fmodel_neutron=None, sequences=None, flags=None, header_info=None, raw_data=None, unmerged_data=None, keep_hydrogens=True, nuclear=False, save_probe_unformatted_file=None, show_hydrogen_outliers=False, min_cc_two_fofc=0.8, n_bins_data=10, count_anomalous_pairs_separately=False, use_internal_variance=True, outliers_only=True, use_pdb_header_resolution_cutoffs=False, file_name=None, ligand_selection=None, rotamer_library='8000', map_params=None)

Bases: slots_getstate_setstate

Comprehensive validation. At a minimum this performs the standard MolProbity analyses (ramalyze, rotalyze, cbetadev, clashscore). If a geometry restraints manager is available, the deviations from standard covalent geometry will also be displayed. Passing an fmodel object enables the re-calculation of R-factors and real-space correlation.

Parameters:

• model – model object (required)

• fmodel – mmtbx.f_model.manager object, after bulk solvent/scaling

• fmodel_neutron – separate Fmodel manager for neutron data (used in phenix.refine for join X/N refinement)

• sequences – parsed sequence objects (from iotbx.bioinformatics)

• flags – object containing boolean flags for analyses to perform

• header_info – extracted statistics from PDB file header

• raw_data – input data before French-Wilson treatment, etc.

• unmerged_data – separate unmerged intensities for merging statistics

• all_chain_proxies – object containing restraints information and advanced selections from mmtbx.monomer_library.pdb_interpretation

• keep_hydrogens – don’t discard and replace existing hydrogens for clashscore calculation

• nuclear – use nuclear hydrogen distances (for neutron experiments)

• save_probe_unformatted_file – file name for Probe output suitable for display in Coot

• show_hydrogen_outliers – show geometry outliers for hydrogen atoms

• min_cc_two_fofc – Fo-Fc map cutoff for real-space outliers

• n_bins_data – Number of resolution bins for data statistics

• count_anomalous_pairs_separately – count F+ and F- as separate reflections (default=False)

• outliers_only – only display validation outliers

• use_pdb_header_resolution_cutoffs – use resolution cutoff(s) specified in PDB header for data statistics

adp_stats

as_mmcif_records()

as_multi_criterion_view()

atoms_to_observations_ratio(assume_riding_hydrogens=True)

b_iso_mean()

cbeta_outliers()

cbetadev

clashes

clashscore()

crystal_symmetry

d_max_min(outer_shell=False)

d_min()

data_stats

display_wx_plots()

file_name

find_missing_atoms(out=None)

Function for finding missing protein atoms Derived from run_find_missing function in phenix/validation/__init__.py

fmodel_statistics_by_resolution()

Returns the resolution bins containing F(model) statistics; see mmtbx.f_model.f_model_info for details.

fmodel_statistics_graph_data()

Wrapper for fmodel_statistics_by_resolution(), returns object suitable for routines in wxtbx.plots.

get_polygon_statistics(stat_names)

get_statistics_for_phenix_gui()

header_info

hydrogens

kinemage_file

merging

missing_atoms

model

model_statistics_geometry

model_statistics_geometry_result

model_stats

model_stats_new

molprobity_score()

molprobity_version_number = (4, 1)

neutron_stats

nqh_flips

omegalyze

pdb_hierarchy

polygon_stats

r_free(outer_shell=False)

r_work(outer_shell=False)

rama_allowed()

rama_favored()

rama_outliers()

ramalyze

real_space

restraints

rms_angles()

rms_bonds()

rna

rota_outliers()

rotalyze

sequence

show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, outliers_only=True, suppress_summary=False, show_percentiles=False)

Comprehensive output with individual outlier lists, plus summary.

show_summary(*args, **kwds)

Print summary of outliers or scores for each analysis.

space_group()

space_group_info()

summarize()

Condense results into a compact object - for compatibility with (now obsolete) mmtbx.validation_summary, and use in high-throughput analyses

twin_law()

unit_cell()

waters

wilson_b

write_coot_script(file_name)

Write a Python script for displaying outlier lists with click-to-recenter enabled.

xtriage

mmtbx.validation.molprobity.molprobity_flags()

Default flags for analyses to perform (all True).

class mmtbx.validation.molprobity.multi_criterion_view(pdb_hierarchy, include_all=False)

Bases: slots_getstate_setstate

Container for generating multi-criterion plots and tables from separate lists of outliers.

binned_data()

data()

display_wx_plots(parent=None)

get_residue_group_data(residue_group)

get_y_limits()

is_populated

process_outliers(outliers, log=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'>)

residues

class mmtbx.validation.molprobity.pdb_header_info(pdb_file, pdb_hierarchy=None)

Bases: slots_getstate_setstate

Container for information extracted from the PDB header (if available).

d_max

d_min

is_phenix_refinement()

n_tls_groups

r_free

r_work

refinement_program

rms_angles

rms_bonds

show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='', include_r_factors=True, include_rms_geom=True)

class mmtbx.validation.molprobity.residue_multi_criterion(**kwds)

Bases: residue

Container for multiple outliers associated with a single residue. If data are used, this may include real-space statistics regardless of whether the residue is technically an outlier or not.

add_outlier(outlier)

altloc

atom_selection

chain_id

get_outlier_plot_values(use_numpy_NaN=True)

get_real_space_plot_values(use_numpy_NaN=True)

i_seq

icode

is_cbeta_outlier()

is_clash_outlier()

is_geometry_outlier()

is_map_outlier(cc_min=0.8)

is_ramachandran_outlier()

is_rotamer_outlier()

n_confs

occupancy

outlier

outliers

resname

resseq

score

segid

xyz

mmtbx.validation.molprobity.run_molprobity_program(program_class=None, custom_process_arguments=None, args=None, logger=None)

Function for running programs using CCTBXParser and the program template

Parameters:

• program_class – ProgramTemplate type (required)

• custom_process_arguments – Custom function to parse unknown arguments (optional)

• args – list of command-line arguments (optional)

• logger – logger (e.g. multi_out) for output (optional)

Return type:

whatever is returned from program_class.get_results()

class mmtbx.validation.molprobity.summary(**kwds)

Bases: slots_getstate_setstate_default_initializer

Simplified container for overall statistics; replaces class of the same name in mmtbx.command_line.validation_summary. The more complete molprobity class is prefered when analyzing a single structure, but it is considerably larger.

angle_rmsd

bond_rmsd

c_beta_deviations

clashscore

d_min

formats = ['%6.2f', '%6.2f', '%6.2f', '%5d', '%6.2f', '%8.4f', '%6.2f', '%6.2f', '%6.2f', '%8.4f', '%8.4f', '%s']

iter_molprobity_gui_fields()

labels = ['Ramachandran outliers', '              favored', 'Rotamer outliers', 'C-beta deviations', 'Clashscore', 'RMS(bonds)', 'RMS(angles)', 'MolProbity score', 'Resolution', 'R-work', 'R-free', 'Refinement program']

mpscore

program

r_free

r_work

rama_favored

rama_outliers

rotamer_outliers

show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, prefix='  ', show_percentiles=False)