Index

_

__init__() (restraintmaker.algorithm.Filter.ElementFilter method) (restraintmaker.algorithm.Filter.PropertyFilter method) (restraintmaker.algorithm.Filter.RingFilter method) (restraintmaker.algorithm.Optimizer.BruteForceRingOptimzer method) (restraintmaker.algorithm.Optimizer.GreedyGraphOptimizer method) (restraintmaker.algorithm.Optimizer.MetaMoleculeRingOptimizer method) (restraintmaker.algorithm.Selection.AllSelection method) (restraintmaker.algorithm.Selection.LimitedSelection method) (restraintmaker.algorithm.Selection.MCSSelection method) (restraintmaker.algorithm.Selection.PaintSelection method) (restraintmaker.algorithm.Selection.PairSelection method) (restraintmaker.algorithm.Selection.SingleAtomSelection method) (restraintmaker.algorithm.Selection.SphericalSelection method) (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) (restraintmaker.io.Exporter._Exporter method) (restraintmaker.io.Files.Gromos_blocks.atom_pair_distanceRes method) (restraintmaker.io.Files.Gromos_blocks.atom_pos_block method) (restraintmaker.io.Files.Gromos_blocks.atom_ref_pos_block method) (restraintmaker.io.Files.Gromos_blocks.atom_vel_block method) (restraintmaker.io.Files.Gromos_blocks.atomP method) (restraintmaker.io.Files.Gromos_blocks.atomV method) (restraintmaker.io.Files.Gromos_blocks.distance_res_spec_block method) (restraintmaker.io.Files.Gromos_blocks.genbox_block method) (restraintmaker.io.Files.Gromos_blocks.lattice_shift method) (restraintmaker.io.Files.Gromos_blocks.lattice_shifts_block method) (restraintmaker.io.Files.Gromos_blocks.timestep_block method) (restraintmaker.io.Files.Gromos_blocks.title_block method) (restraintmaker.io.Files.Gromos_files.disres method) (restraintmaker.io.Files.Gromos_files.general_gromos_file method) _action_button_pressed() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) _atom_list_to_pymol_selection() (in module restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities) _calc_pca_without_scaling() (in module restraintmaker.tools_Rdkit.Rdkit_Functions)

_calculate_value_convex_hull() (in module restraintmaker.algorithm.Optimizer) _calculate_value_scaled_pca_2d() (in module restraintmaker.algorithm.Optimizer) _calculate_value_unscaled_pca_2d() (in module restraintmaker.algorithm.Optimizer) _check_importing_packages() (in module restraintmaker.restraintMaker) _check_optimzer_results_pairwise_5() (in module restraintmaker.test.test_restraintMaker_PyMol) _check_optimzer_results_pairwise_6() (in module restraintmaker.test.test_restraintMaker_PyMol) _check_selection_status() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) _convert_molecules_to_pdb() (in module restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities) _Exporter (class in restraintmaker.io.Exporter) _optimzer_show_next_molecule_pair_2() (in module restraintmaker.test.test_restraintMaker_PyMol) _optimzer_show_next_molecule_pair_3() (in module restraintmaker.test.test_restraintMaker_PyMol) _read_gromos_block() (restraintmaker.io.Files.Gromos_files.general_gromos_file method) _set_exporter_type() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) _set_filter_type() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) _set_importer_type() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) _set_optimizer_type() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) _set_restraint_type() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) _set_selection_type() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) _test_optimizer_1() (in module restraintmaker.test.test_restraintMaker_PyMol) _test_optimizer_3() (in module restraintmaker.test.test_restraintMaker_PyMol) _toggle_button_pressed() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) _update_confirm() (restraintmaker.algorithm.Selection.AllSelection method) (restraintmaker.algorithm.Selection.MCSSelection method) (restraintmaker.algorithm.Selection.SphericalSelection method) _update_move() (restraintmaker.algorithm.Selection.AllSelection method) (restraintmaker.algorithm.Selection.MCSSelection method) (restraintmaker.algorithm.Selection.SphericalSelection method) _update_select() (restraintmaker.algorithm.Selection.AllSelection method) (restraintmaker.algorithm.Selection.LimitedSelection method) (restraintmaker.algorithm.Selection.MCSSelection method) _update_size() (restraintmaker.algorithm.Selection.AllSelection method) (restraintmaker.algorithm.Selection.MCSSelection method) (restraintmaker.algorithm.Selection.SphericalSelection method)

A

ActionState (class in restraintmaker.interface_Pymol.pymol_utilities.program_states) add_block() (restraintmaker.io.Files.Gromos_files.general_gromos_file method) additional_ring_interconnections() (in module restraintmaker.algorithm.Optimizer) AllSelection (class in restraintmaker.algorithm.Selection) alt (restraintmaker.utils.Utilities.Atom attribute) ALWAYS_DISABLED (restraintmaker.interface_Pymol.pymol_utilities.program_states.ActionState attribute) ALWAYS_ENABLED (restraintmaker.interface_Pymol.pymol_utilities.program_states.ActionState attribute)

Atom (class in restraintmaker.utils.Utilities) atom_pair_distanceRes (class in restraintmaker.io.Files.Gromos_blocks) atom_pos_block (class in restraintmaker.io.Files.Gromos_blocks) atom_ref_pos_block (class in restraintmaker.io.Files.Gromos_blocks) atom_vel_block (class in restraintmaker.io.Files.Gromos_blocks) atom_within_sphere() (restraintmaker.algorithm.Selection.SphericalSelection method) atomP (class in restraintmaker.io.Files.Gromos_blocks) atomV (class in restraintmaker.io.Files.Gromos_blocks)

B

b (restraintmaker.utils.Utilities.Atom attribute) BadArgumentException block_name (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file attribute) (restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file attribute) block_to_string() (restraintmaker.io.Files.Gromos_blocks.atom_pos_block method) (restraintmaker.io.Files.Gromos_blocks.atom_ref_pos_block method) (restraintmaker.io.Files.Gromos_blocks.atom_vel_block method) (restraintmaker.io.Files.Gromos_blocks.distance_res_spec_block method) (restraintmaker.io.Files.Gromos_blocks.genbox_block method) (restraintmaker.io.Files.Gromos_blocks.lattice_shifts_block method) (restraintmaker.io.Files.Gromos_blocks.timestep_block method) (restraintmaker.io.Files.Gromos_blocks.title_block method)

blocksset (restraintmaker.io.Files.Gromos_files.general_gromos_file attribute) BruteForceRingOptimzer (class in restraintmaker.algorithm.Optimizer) build_disres() (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file method) build_posres() (restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file method)

C

calculate_value_pca_relative_to_pca_of_both_molecules() (in module restraintmaker.algorithm.Optimizer) chain (restraintmaker.utils.Utilities.Atom attribute) check_for_doubles() (in module restraintmaker.utils.Utilities) check_objects_exists() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) check_or_convert_argument() (in module restraintmaker.utils.Utilities) check_restraint_pairs_for_doubles() (in module restraintmaker.utils.Utilities) check_restraint_results() (restraintmaker.test.test_optimizer.test_Optimizer method) cog_distance_restraint() (in module restraintmaker.algorithm.Optimizer) colorize() (in module restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities) CONFIRM (restraintmaker.interface_Pymol.pymol_utilities.program_states.EventType attribute) connect_two_molecules() (restraintmaker.algorithm.Optimizer.BruteForceRingOptimzer method) (restraintmaker.algorithm.Optimizer.GreedyGraphOptimizer method) (restraintmaker.algorithm.Optimizer.MetaMoleculeRingOptimizer method)

content (restraintmaker.io.Files.Gromos_files.general_gromos_file attribute) convert_atoms_to_pdb_molecules() (in module restraintmaker.utils.Utilities) create_file_open_dialog() (in module restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs) create_file_save_dialog() (in module restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs) create_input_dialog() (in module restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs) create_multi_dialog() (in module restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs) create_pymol_objects_for_molecules() (in module restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities) create_pymol_objects_for_restraints() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) CURRENTLY_DISABLED (restraintmaker.interface_Pymol.pymol_utilities.program_states.ActionState attribute) CURRENTLY_ENABLED (restraintmaker.interface_Pymol.pymol_utilities.program_states.ActionState attribute)

D

disres (class in restraintmaker.io.Files.Gromos_files) (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file attribute) distance (restraintmaker.utils.Utilities.RestraintPair attribute) distance_res_spec_block (class in restraintmaker.io.Files.Gromos_blocks) distant_Restraint_Type (class in restraintmaker.io.Files.Gromos_blocks)

do_dirty() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) do_key() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) do_nothing() (in module restraintmaker.utils.Utilities) do_pick() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) do_select() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) do_special() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method)

E

elem (restraintmaker.utils.Utilities.Atom attribute) ElementFilter (class in restraintmaker.algorithm.Filter) EventType (class in restraintmaker.interface_Pymol.pymol_utilities.program_states) execute_at_different_verbosity() (in module restraintmaker.utils.Utilities) export_Gromacs_Distance_Restraints (class in restraintmaker.io.Exporter) export_Gromacs_Position_RESTRAINTS (class in restraintmaker.io.Exporter) export_Gromos_Distance_Restraints (class in restraintmaker.io.Exporter) export_Gromos_Position_RESTRAINTS (class in restraintmaker.io.Exporter)

export_JSON_Distance_Restraints (class in restraintmaker.io.Exporter) export_JSON_Position_RESTRAINTS (class in restraintmaker.io.Exporter) export_restraints() (restraintmaker.io.Exporter._Exporter method) (restraintmaker.io.Exporter.export_Gromacs_Distance_Restraints method) (restraintmaker.io.Exporter.export_Gromacs_Position_RESTRAINTS method) (restraintmaker.io.Exporter.export_Gromos_Distance_Restraints method) (restraintmaker.io.Exporter.export_Gromos_Position_RESTRAINTS method) (restraintmaker.io.Exporter.export_JSON_Distance_Restraints method) (restraintmaker.io.Exporter.export_JSON_Position_RESTRAINTS method)

F

file_ending (restraintmaker.io.Importer.import_Gromacs_Distance_Restraints attribute) (restraintmaker.io.Importer.import_Gromacs_Position_Restraints attribute) (restraintmaker.io.Importer.import_Gromos_Distance_Restraints attribute) (restraintmaker.io.Importer.import_Gromos_Position_Restraints attribute) (restraintmaker.io.Importer.import_JSON_Distance_Restraints attribute) (restraintmaker.io.Importer.import_JSON_Position_Restraints attribute)

file_nr (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard attribute) filter() (restraintmaker.algorithm.Filter.ElementFilter method) (restraintmaker.algorithm.Filter.PropertyFilter method) (restraintmaker.algorithm.Filter.RingFilter method) find_atom_by_property() (in module restraintmaker.utils.Utilities) full_harmonic_distance_restraint (restraintmaker.io.Files.Gromos_blocks.distant_Restraint_Type attribute)

G

genbox_block (class in restraintmaker.io.Files.Gromos_blocks) general_gromos_file (class in restraintmaker.io.Files.Gromos_files) geometric_code (class in restraintmaker.io.Files.Gromos_blocks) get_all_short_pair_restraints() (in module restraintmaker.algorithm.Optimizer) get_all_subclasses() (in module restraintmaker.utils.Utilities) get_args() (restraintmaker.algorithm.Filter.ElementFilter method) (restraintmaker.algorithm.Filter.PropertyFilter method) (restraintmaker.algorithm.Filter.RingFilter method) (restraintmaker.algorithm.Optimizer.BruteForceRingOptimzer method) (restraintmaker.algorithm.Optimizer.GreedyGraphOptimizer method) (restraintmaker.algorithm.Optimizer.MetaMoleculeRingOptimizer method) (restraintmaker.algorithm.Selection.AllSelection method) (restraintmaker.algorithm.Selection.LimitedSelection method) (restraintmaker.algorithm.Selection.MCSSelection method) (restraintmaker.algorithm.Selection.PairSelection method) (restraintmaker.algorithm.Selection.SingleAtomSelection method) (restraintmaker.algorithm.Selection.SphericalSelection method) (restraintmaker.io.Exporter._Exporter method)

get_event_mask() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) get_panel() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) get_prompt() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) gmx_disres (in module restraintmaker.io.Files.Gromacs_files) gmx_posres (in module restraintmaker.io.Files.Gromacs_files) GreedyGraphOptimizer (class in restraintmaker.algorithm.Optimizer) Gromacs_distanceRestraint_file (class in restraintmaker.io.Files.Gromacs_files) Gromacs_positionRestraint_file (class in restraintmaker.io.Files.Gromacs_files)

H

half_harmonic_attractive (restraintmaker.io.Files.Gromos_blocks.distant_Restraint_Type attribute) half_harmonic_repulsive (restraintmaker.io.Files.Gromos_blocks.distant_Restraint_Type attribute)

header (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file attribute) (restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file attribute) help_pymol_with_big_atom_list() (in module restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities)

I

id (restraintmaker.utils.Utilities.Atom attribute) import_Gromacs_Distance_Restraints (class in restraintmaker.io.Importer) import_Gromacs_Position_Restraints (class in restraintmaker.io.Importer) import_Gromos_Distance_Restraints (class in restraintmaker.io.Importer) import_Gromos_Position_Restraints (class in restraintmaker.io.Importer) import_JSON_Distance_Restraints (class in restraintmaker.io.Importer) import_JSON_Position_Restraints (class in restraintmaker.io.Importer) import_restraints() (restraintmaker.io.Importer.import_Gromacs_Distance_Restraints method) (restraintmaker.io.Importer.import_Gromacs_Position_Restraints method) (restraintmaker.io.Importer.import_Gromos_Distance_Restraints method) (restraintmaker.io.Importer.import_Gromos_Position_Restraints method) (restraintmaker.io.Importer.import_JSON_Distance_Restraints method) (restraintmaker.io.Importer.import_JSON_Position_Restraints method)

in_disres1 (restraintmaker.test.test_importer.test_Importer attribute) in_disres2 (restraintmaker.test.test_importer.test_Importer attribute) in_disresObj_path1 (restraintmaker.test.test_exporter.test_Exporter attribute) in_disresObj_path2 (restraintmaker.test.test_exporter.test_Exporter attribute) in_pdb1 (restraintmaker.test.test_importer.test_Importer attribute) in_pdb2 (restraintmaker.test.test_importer.test_Importer attribute) in_solution_disres_path1 (restraintmaker.test.test_exporter.test_Exporter attribute) in_solution_disres_path2 (restraintmaker.test.test_exporter.test_Exporter attribute)

L

label (restraintmaker.utils.Utilities.Atom attribute) lattice_shift (class in restraintmaker.io.Files.Gromos_blocks) lattice_shifts_block (class in restraintmaker.io.Files.Gromos_blocks)

LimitedSelection (class in restraintmaker.algorithm.Selection) load() (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file static method) (restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file static method) Logic_Handler (class in restraintmaker.interface_Pymol.RestraintMaker_Logic)

M

maximal_spanning_tree_greedy() (in module restraintmaker.algorithm.Optimizer) maximal_weight_chain() (in module restraintmaker.algorithm.Optimizer) maximal_weight_ring() (in module restraintmaker.algorithm.Optimizer) mcs_selection() (in module restraintmaker.tools_Rdkit.Rdkit_Functions) MCSSelection (class in restraintmaker.algorithm.Selection) MetaMoleculeRingOptimizer (class in restraintmaker.algorithm.Optimizer) module restraintmaker restraintmaker.algorithm restraintmaker.algorithm.Filter restraintmaker.algorithm.Optimizer restraintmaker.algorithm.Selection restraintmaker.interface_Pymol restraintmaker.interface_Pymol.pymol_utilities restraintmaker.interface_Pymol.pymol_utilities.program_states restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs restraintmaker.interface_Pymol.RestraintMaker_Logic restraintmaker.interface_Pymol.RestraintMaker_Pymol restraintmaker.io restraintmaker.io.Exporter restraintmaker.io.Files restraintmaker.io.Files.Gromacs_files restraintmaker.io.Files.Gromos_blocks restraintmaker.io.Files.Gromos_files restraintmaker.io.Importer restraintmaker.restraintMaker restraintmaker.test restraintmaker.test.pickle_input_test_file restraintmaker.test.test_exporter restraintmaker.test.test_files restraintmaker.test.test_importer restraintmaker.test.test_optimizer restraintmaker.test.test_restraintMaker_PyMol restraintmaker.tools_Rdkit restraintmaker.tools_Rdkit.Rdkit_Functions restraintmaker.utils restraintmaker.utils.Utilities restraintmaker.wizard

MOVE (restraintmaker.interface_Pymol.pymol_utilities.program_states.EventType attribute)

N

name (restraintmaker.utils.Utilities.Atom attribute)

node (restraintmaker.algorithm.Optimizer.priority_node attribute) NoOptimalSolutionException

O

order (restraintmaker.io.Files.Gromos_blocks.title_block attribute) order_atoms_by_molecule() (in module restraintmaker.utils.Utilities)

out_gromos_disres_path1 (restraintmaker.test.test_exporter.test_Exporter attribute) out_gromos_disres_path2 (restraintmaker.test.test_exporter.test_Exporter attribute)

P

PaintSelection (class in restraintmaker.algorithm.Selection) PairSelection (class in restraintmaker.algorithm.Selection) parse_disres_file() (restraintmaker.io.Files.Gromos_files.disres method) parse_pdb_blocks_to_rdkit() (in module restraintmaker.tools_Rdkit.Rdkit_Functions) path (restraintmaker.io.Files.Gromos_files.general_gromos_file attribute) PolyArea() (in module restraintmaker.tools_Rdkit.Rdkit_Functions) PolygonSort() (in module restraintmaker.tools_Rdkit.Rdkit_Functions) posres (restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file attribute)

print() (in module restraintmaker.utils.Utilities) priority (restraintmaker.algorithm.Optimizer.priority_node attribute) priority_node (class in restraintmaker.algorithm.Optimizer) PropertyFilter (class in restraintmaker.algorithm.Filter) provide_services_to_spherical_selection() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) pseudo_H_atom_goc_H_atoms_CH3 (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute) pseudo_H_atoms_goc_of_three_CH3 (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute) pseudo_H_atoms_goc_of_two_CH3 (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute) pymol_selection_to_atom_list() (in module restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities)

R

r1 (restraintmaker.utils.Utilities.RestraintPair attribute) r2 (restraintmaker.utils.Utilities.RestraintPair attribute) react_to_event() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) read_disres_file() (restraintmaker.io.Files.Gromos_files.disres method) real_atom (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute) redraw() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) required_blocks (restraintmaker.io.Files.Gromos_files.disres attribute) (restraintmaker.io.Files.Gromos_files.general_gromos_file attribute) resi (restraintmaker.utils.Utilities.Atom attribute) resn (restraintmaker.utils.Utilities.Atom attribute) restraintmaker module restraintmaker.algorithm module restraintmaker.algorithm.Filter module restraintmaker.algorithm.Optimizer module restraintmaker.algorithm.Selection module restraintmaker.interface_Pymol module restraintmaker.interface_Pymol.pymol_utilities module restraintmaker.interface_Pymol.pymol_utilities.program_states module restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities module restraintmaker.interface_Pymol.pymol_utilities.qt_dialogs module restraintmaker.interface_Pymol.RestraintMaker_Logic module restraintmaker.interface_Pymol.RestraintMaker_Pymol module restraintmaker.io module restraintmaker.io.Exporter module restraintmaker.io.Files module

restraintmaker.io.Files.Gromacs_files module restraintmaker.io.Files.Gromos_blocks module restraintmaker.io.Files.Gromos_files module restraintmaker.io.Importer module restraintmaker.restraintMaker module restraintmaker.test module restraintmaker.test.pickle_input_test_file module restraintmaker.test.test_exporter module restraintmaker.test.test_files module restraintmaker.test.test_importer module restraintmaker.test.test_optimizer module restraintmaker.test.test_restraintMaker_PyMol module restraintmaker.tools_Rdkit module restraintmaker.tools_Rdkit.Rdkit_Functions module restraintmaker.utils module restraintmaker.utils.Utilities module restraintmaker.wizard module RestraintPair (class in restraintmaker.utils.Utilities) Restraints_Wizard (class in restraintmaker.interface_Pymol.RestraintMaker_Pymol) ring_atom_filter() (in module restraintmaker.tools_Rdkit.Rdkit_Functions) RingFilter (class in restraintmaker.algorithm.Filter) run_plugin() (in module restraintmaker.restraintMaker) run_plugin_gui() (in module restraintmaker.restraintMaker)

S

SELECT (restraintmaker.interface_Pymol.pymol_utilities.program_states.EventType attribute) select_atoms_within_sphere() (restraintmaker.algorithm.Selection.PaintSelection method) (restraintmaker.algorithm.Selection.SphericalSelection method) set_action_states() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) set_action_type() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) set_mode() (restraintmaker.interface_Pymol.RestraintMaker_Logic.Logic_Handler method) set_wizard_style() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) setUp() (restraintmaker.test.test_exporter.test_Exporter method) (restraintmaker.test.test_importer.test_Importer method)

SingleAtomSelection (class in restraintmaker.algorithm.Selection) SIZE (restraintmaker.interface_Pymol.pymol_utilities.program_states.EventType attribute) SphericalSelection (class in restraintmaker.algorithm.Selection) std_fc (restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file attribute) std_funct (restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file attribute) std_index (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file attribute) std_low (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file attribute) std_up1 (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file attribute) std_up2 (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file attribute)

T

test_bruteForce_optimizer() (restraintmaker.test.test_optimizer.test_Optimizer method) test_cog_optimizer() (restraintmaker.test.test_optimizer.test_Optimizer method) test_Exporter (class in restraintmaker.test.test_exporter) test_Exporter_Gromacs_construct() (restraintmaker.test.test_exporter.test_Exporter method) test_Exporter_Gromacs_export_disresDat() (restraintmaker.test.test_exporter.test_Exporter method) test_Exporter_Gromacs_getargs() (restraintmaker.test.test_exporter.test_Exporter method) test_file_dir (in module restraintmaker.test.pickle_input_test_file) (restraintmaker.test.test_exporter.test_Exporter attribute) (restraintmaker.test.test_importer.test_Importer attribute) test_files_IO (restraintmaker.test.test_exporter.test_Exporter attribute) test_files_io (restraintmaker.test.test_importer.test_Importer attribute) test_files_structures (restraintmaker.test.test_importer.test_Importer attribute) test_Importer (class in restraintmaker.test.test_importer) test_Importer_Gromos_construct() (restraintmaker.test.test_importer.test_Importer method)

test_Importer_Gromos_import_disresDat() (restraintmaker.test.test_importer.test_Importer method) test_Importer_Gromos_import_file_notFound() (restraintmaker.test.test_importer.test_Importer method) test_Optimizer (class in restraintmaker.test.test_optimizer) test_prim_optimizer() (restraintmaker.test.test_optimizer.test_Optimizer method) test_shortest_optimizer() (restraintmaker.test.test_optimizer.test_Optimizer method) timer() (in module restraintmaker.test.test_restraintMaker_PyMol) timestep_block (class in restraintmaker.io.Files.Gromos_blocks) title_block (class in restraintmaker.io.Files.Gromos_blocks) to_string() (restraintmaker.io.Files.Gromos_blocks.atom_pair_distanceRes method) (restraintmaker.io.Files.Gromos_blocks.atomP method) (restraintmaker.io.Files.Gromos_blocks.atomV method) (restraintmaker.io.Files.Gromos_blocks.lattice_shift method) trigger_event() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method) try_to_get_args() (in module restraintmaker.interface_Pymol.pymol_utilities.pymol_utitlities)

U

update() (restraintmaker.algorithm.Selection.AllSelection method) (restraintmaker.algorithm.Selection.MCSSelection method)

update_menu() (restraintmaker.interface_Pymol.RestraintMaker_Pymol.Restraints_Wizard method)

V

virtual_atoms_cog (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute) virtual_atoms_com (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute) virtual_H_atom_aliphaticC (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute)

virtual_H_atom_aliphaticC_strange (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute) virtual_H_atom_aromaticC (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute) virtual_H_atoms_goc_aliph (restraintmaker.io.Files.Gromos_blocks.geometric_code attribute)

W

write() (restraintmaker.io.Files.Gromacs_files.Gromacs_distanceRestraint_file method) (restraintmaker.io.Files.Gromacs_files.Gromacs_positionRestraint_file method) (restraintmaker.io.Files.Gromos_files.general_gromos_file method)

X

x (restraintmaker.utils.Utilities.Atom attribute)

Y

y (restraintmaker.utils.Utilities.Atom attribute)

Z

z (restraintmaker.utils.Utilities.Atom attribute)