adsorpy package¶
Submodules¶
- adsorpy.gui module
RunSimulationInputRunSimulationInput.rsa_configRunSimulationInput.molecules_listRunSimulationInput.rotation_symmetriesRunSimulationInput.reflection_symmetriesRunSimulationInput.rotation_countsRunSimulationInput.lattice_typeRunSimulationInput.site_countRunSimulationInput.lattice_aRunSimulationInput.boundary_conditionRunSimulationInput.simulation_typeRunSimulationInput.dosing_distributionRunSimulationInput.include_rejected_fluxRunSimulationInput.calculate_gap_sizeRunSimulationInput.prlongoutput_flagRunSimulationInput.plot_output_flagRunSimulationInput.seedRunSimulationInput.timestep_limitRunSimulationInput.site_x_coordsRunSimulationInput.site_y_coordsRunSimulationInput.bounding_x_coordRunSimulationInput.bounding_y_coordRunSimulationInput.sticking_probability
BatchSimulationInputFilePickerWidgetset_content()extract_param_docs()from_geojson_str_to_polygon()validate_polygon()SimplePolygonDictPydanticPolygonParamWidgetsParamWidgets.radiusParamWidgets.distanceParamWidgets.x_offsetParamWidgets.y_offsetParamWidgets.quad_segsParamWidgets.scaleParamWidgets.vertsParamWidgets.roundednessParamWidgets.file_nameParamWidgets.ignore_atomsParamWidgets.rollParamWidgets.pitchParamWidgets.yawParamWidgets.z_trimParamWidgets.reference_lattice_spacing
SymmetryWidgetsis_valid_param()MoleculeParametersSurfaceParametersMiscParametersZoomableSvgWidgetZoomableSvgWidget.graphics_changedZoomableSvgWidget.__init__()ZoomableSvgWidget.current_svg_pathZoomableSvgWidget._current_svg_bytesZoomableSvgWidget.resizeEvent()ZoomableSvgWidget.load()ZoomableSvgWidget.load_svg()ZoomableSvgWidget.export_graphics()ZoomableSvgWidget.wheelEvent()ZoomableSvgWidget.staticMetaObject
AutoStateMetaAppStateAppState.seed_inputAppState.step_limitAppState.misc_paramsAppState.molecule_param_listAppState.surface_paramsAppState.coveragesAppState.fraction_of_covered_areaAppState.gap_size_distributionAppState.coveragesChangedAppState.fraction_of_covered_areaChangedAppState.gap_size_distributionChangedAppState.misc_paramsChangedAppState.molecule_param_listChangedAppState.seed_inputChangedAppState.staticMetaObjectAppState.step_limitChangedAppState.surface_paramsChanged
AdsorpyGUIGeneralSettingsGeneralSettings.__init__()GeneralSettings._settingsGeneralSettings.stateGeneralSettings.bg_signalsGeneralSettings.input_metadataGeneralSettings._fetch_setting()GeneralSettings._init_validators()GeneralSettings._init_controls()GeneralSettings._change_bulk_run_value()GeneralSettings._init_feedback_textboxes()GeneralSettings._on_surface_changed()GeneralSettings._on_molecules_changed()GeneralSettings._init_svg_view()GeneralSettings._assemble_layout()GeneralSettings.get_run_sim_default()GeneralSettings._prepare_simulation_inputs()GeneralSettings.run_simulation()GeneralSettings.run_batch_simulation()GeneralSettings._on_simulation_complete()GeneralSettings._on_batch_simulation_complete()GeneralSettings._on_simulation_error()GeneralSettings.export_results()GeneralSettings.error()GeneralSettings.staticMetaObject
MoleculeGenerationMoleculeGeneration.__init__()MoleculeGeneration.param_widgetsMoleculeGeneration.opt_checkboxesMoleculeGeneration._settingsMoleculeGeneration.stateMoleculeGeneration._init_data_storage()MoleculeGeneration._build_left_panel()MoleculeGeneration._update_func_dropdown()MoleculeGeneration._discover_molecule_generators()MoleculeGeneration._build_center_panel()MoleculeGeneration._build_right_panel()MoleculeGeneration._assemble_layout()MoleculeGeneration._fetch_setting()MoleculeGeneration._delete_previous_layout()MoleculeGeneration.build_param_inputs()MoleculeGeneration._create_param_widget()MoleculeGeneration.sync_list_order()MoleculeGeneration._build_symmetry_controls()MoleculeGeneration._build_action_buttons()MoleculeGeneration._update_symmetry_tooltip()MoleculeGeneration.launch_first_time_loader()MoleculeGeneration.get_param_values()MoleculeGeneration.error()MoleculeGeneration.plot_molecule()MoleculeGeneration.add_molecule()MoleculeGeneration.delete_molecule()MoleculeGeneration.show_molecule_settings()MoleculeGeneration.staticMetaObject
SurfaceGenerationSurfaceGeneration.__init__()SurfaceGeneration.stateSurfaceGeneration.surface_countSurfaceGeneration.real_surface_countSurfaceGeneration.stored_paramsSurfaceGeneration.main_splitterSurfaceGeneration._init_validators()SurfaceGeneration._build_left_panel()SurfaceGeneration.staticMetaObjectSurfaceGeneration._init_svg_view()SurfaceGeneration._get_real_surface_site_count()SurfaceGeneration.generate_surface()SurfaceGeneration.error()
BackgroundTaskSignalsBackgroundTaskReorderableListWidget_make_horizontal_line()main()
- adsorpy.molecule_lib module
AtomKey_load_radii_from_json()RADIIdiscorectangle()circulium()dogbonium()polygonium()xyz_reader()_rotation_matrix()MoleculeViewerMoleculeViewer.__init__()MoleculeViewer.latticeMoleculeViewer.show_bondsMoleculeViewer.atom_togglesMoleculeViewer.disabled_moleculesMoleculeViewer._init_data()MoleculeViewer._fetch_setting()MoleculeViewer._create_filter_panel()MoleculeViewer._connect_z_filter()MoleculeViewer._create_plot_panel()MoleculeViewer._add_slider_panel()MoleculeViewer.toggle_bonds()MoleculeViewer.update_z_cutoff()MoleculeViewer.apply_atom_filters()MoleculeViewer.setup_bond_controls()MoleculeViewer.update_values()MoleculeViewer.setup_lattice_controls()MoleculeViewer.update_lattice_value()MoleculeViewer.submit_values()MoleculeViewer.toggle_svg_background()MoleculeViewer.transform()MoleculeViewer._circles()MoleculeViewer.draw()MoleculeViewer.staticMetaObject
first_time_loader()_xyz_verifier()_initialise_reader()save_molecule_svg()
- adsorpy.randomsequentialadsorption module
_create_empty_coords()Config_config_loader()BoundaryParametersBoundaryParameters.__init__()BoundaryParameters.molecules_flagBoundaryParameters.boundary_typeBoundaryParameters.soft_flagBoundaryParameters.hard_flagBoundaryParameters.periodic_flagBoundaryParameters.hard_innerBoundaryParameters.molecules_bounding_coordsBoundaryParameters.allowed_idxBoundaryParameters.allowed_boolsBoundaryParameters.extended_gridBoundaryParameters.extended_occupied_byBoundaryParameters.extended_idxBoundaryParameters.close_to_edgeBoundaryParameters.extended_vacantBoundaryParameters.edge_flagBoundaryParameters.mirror_counterBoundaryParameters.mirrorsBoundaryParameters.biggest_diameterBoundaryParameters.treeBoundaryParameters.set_boundary_flags()BoundaryParameters.generate_boundary_conditions()
MoleculeGroupMoleculeGroup.__init__()MoleculeGroup.group_idMoleculeGroup.configMoleculeGroup.moleculeMoleculeGroup.rotation_symmetryMoleculeGroup.reflection_symmetryMoleculeGroup.areaMoleculeGroup.min_radiusMoleculeGroup.max_radiusMoleculeGroup.rotation_countMoleculeGroup.__max_rotationMoleculeGroup.rot_refl_countMoleculeGroup.allowed_rotationsMoleculeGroup.rotated_moleculesMoleculeGroup.rotated_buffer_moleculesMoleculeGroup.molecule_counterMoleculeGroup.occupied_byMoleculeGroup.sticking_probabilityMoleculeGroup.vacantMoleculeGroup.vacancy_countMoleculeGroup.bpMoleculeGroup.gap_distsMoleculeGroup.minmax_gapsMoleculeGroup.generate_rotated_molecules()
CandidateMoleculeCandidateMolecule.molecule_group_idxCandidateMolecule.grid_indexCandidateMolecule.coordinatesCandidateMolecule.moleculeCandidateMolecule.rot_idxCandidateMolecule.molecule_numberCandidateMolecule.close_to_borderCandidateMolecule.existsCandidateMolecule.get_canddata()CandidateMolecule.__init__()
SimulatorSimulator.__init__()Simulator.configSimulator.rngSimulator.surfSimulator.molgroupsSimulator.molgrcountSimulator.bpSimulator.flux_flagSimulator.total_molecule_counterSimulator.outer_radsSimulator.minmax_radsSimulator.mol_dataSimulator.__unclaimedSimulator._calculate_radii()Simulator.attempt_place_molecule()Simulator.update_placement()Simulator.trim_buffer()Simulator.plot_covered_grid()Simulator.svgplot_covered_grid()Simulator.attempt_cascading_placement()Simulator.attempt_random_placement()Simulator.analyse_gap_size()Simulator.check_if_overlap()Simulator.coverageSimulator.fraction_of_covered_area
SurfaceSurface.__init__()Surface.configSurface.lattice_typeSurface.sitesSurface.simple_shape_flagSurface.xsizeSurface.ysizeSurface.zsizeSurface.all_site_countSurface.lattice_aSurface.sticking_probabilitySurface.x_maxSurface.y_maxSurface.areaSurface.grid_indexSurface.grid_coordinatesSurface.bpSurface.treeSurface._estimate_site_count()Surface.generate_grid()Surface._set_xy_max()Surface.generate_custom_surface()Surface.plot_surface_sites()Surface.svgplot_surface_sites()Surface.make_surface_svg_elements()Surface.create_dark_css_style()Surface.create_and_write_svg()
_create_rtree_index()MoleculeDataMoleculeData.max_array_lengthMoleculeData.mol_counterMoleculeData.current_mol_idMoleculeData.mirr_counterMoleculeData.current_mirror_numMoleculeData.last_accessed_idxMoleculeData._header_namesMoleculeData._column_datatypesMoleculeData._heads_dtypesMoleculeData._fill_valsMoleculeData.stored_dataMoleculeData.mol_treeMoleculeData._mirr_namesMoleculeData._mirr_datatypesMoleculeData._mirr_heads_dtypesMoleculeData._mirr_fill_valsMoleculeData.stored_mirr_dataMoleculeData.mirr_treeMoleculeData._otomir_namesMoleculeData._otomir_typesMoleculeData._otomir_heads_dtypesMoleculeData._otomir_fill_valsMoleculeData.orig_to_mirrorsMoleculeData.__init__()MoleculeData.coordsMoleculeData.mirror_coordsMoleculeData.make_struct_array()MoleculeData.add_entry()MoleculeData.add_mirror()
- adsorpy.rsa_calculator module
- adsorpy.rsa_config module
- adsorpy.run_simulation module
- adsorpy.types module