mmtbx.polygon
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/polygon/__init__.py

 
Package Contents
       
output
tst
tst_gui

 
Functions
       
apply_default_filter(database_dict, d_min, max_models_for_default_filter, key='high_resolution')
convert_to_histogram(data, n_slots)
convert_to_numeric(values)
filter_database(database_dict, key, value_min=None, value_max=None, target_value=None)
filter_histogram_of_key_value(database_dict, key, max_reject_fraction, edge_tolerance_small=0.0001, n_slots=3)
get_statistics_percentiles(d_min, stats)
For a given set of statistics, determine their percentile ranking compared
to other crystal structures at similar resolution.
leave_all_available_entries(database_dict, keys)
load_db(file_name=None)
order_by_value(database_dict, key, reverse=False)
polygon(params=<libtbx.phil.scope_extract object>, d_min=None, show_histograms=True, extract_gui_data=False)
select_database_dict_by_keys(select_keys, database_dict)
select_dict(database_dict, selection)
show_histogram(data, n_slots, smooth=True)

 
Data
        captions_str = 'R-work R-free R-work_(PDB) R-free_(PDB) R-work_(...Ramachandran_outliers Rotamer_outliers Clashscore'
default_keys = ['r_work', 'r_free', 'adp_mean_all', 'bond_rmsd', 'angle_rmsd', 'clashscore']
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
key_captions = ['R-work', 'R-free', 'R-work (PDB)', 'R-free (PDB)', 'R-work (after cutoff)', 'R-free (after cutoff)', 'Completeness in range', 'Completeness', 'Completeness to 6A', 'Average B', 'Minimum B', 'Maximum B', 'Wilson B', 'Solvent content', 'RMSD(bonds)', 'Bonds max.', 'RMSD(angles)', 'Angles max.', 'RMSD(dihedrals)', 'Dihedrals max.', ...]
key_name = 'clashscore'
key_params_str = '*r_work *r_free pdb_header_r_work pdb_header_r_f...llowed rama_outliers rotamer_outliers *clashscore'
keys_to_show = ['r_work', 'r_free', 'pdb_header_r_work', 'pdb_header_r_free', 'r_work_cutoffs', 'r_free_cutoffs', 'completeness_in_range', 'completeness_d_min_inf', 'completeness_6A_inf', 'adp_mean_all', 'adp_min_all', 'adp_max_all', 'wilson_b', 'solvent_content_via_mask', 'bond_rmsd', 'bond_max_deviation', 'angle_rmsd', 'angle_max_deviation', 'dihedral_rmsd', 'dihedral_max_deviation', ...]
master_params = <libtbx.phil.scope object>
other_captions = ['High resolution', 'Low resolution', 'Min. backbone ADP', 'Min. sidechain ADP', 'Min. solvent ADP', 'Max. backbone ADP', 'Max. sidechain ADP', 'Max. solvent ADP', 'Mean backbone ADP', 'Mean sidechain ADP', 'Mean solvent ADP', 'Unit cell volume']
other_numerical_keys = ['high_resolution', 'low_resolution', 'adp_min_backbone', 'adp_min_sidechain', 'adp_min_solvent', 'adp_max_backbone', 'adp_max_sidechain', 'adp_max_solvent', 'adp_mean_backbone', 'adp_mean_sidechain', 'adp_mean_solvent', 'unit_cell_volume']
polygon_params_str = ' database_file_name = None\n .type = str\n ...pe = str\n .short_caption = Target value\n }\n'
txt = 'Clashscore'