Application Layer

Menu Links

The following module-level constants define the application's menu structure. These are built at import time from YAML configuration files and registered shortcut wrappers.

REvoDesign.application.menu.CONFIG_EDIT_LINKS = [] module-attribute

REvoDesign.application.menu.TOOLS_MENU_LINKS = (MenuItem('actionRenderPickedSidechainGroup', 'REvoDesign.shortcuts.shortcuts_on_menu:menu_dump_sidechains', kwargs={'dump_all': False}), MenuItem('actionRenderAllSidechains', 'REvoDesign.shortcuts.shortcuts_on_menu:menu_dump_sidechains', kwargs={'dump_all': True}), MenuItem('actionColor_by_pLDDT', 'REvoDesign.shortcuts.wrappers.represents:wrapped_color_by_plddt'), MenuItem('actionShow_Real_Sidechain', 'REvoDesign.shortcuts.wrappers.represents:wrapped_real_sc'), MenuItem('actionColor_by_Mutations', 'REvoDesign.shortcuts.wrappers.represents:wrapped_color_by_mutation'), MenuItem('actionPSSM_to_CSV', 'REvoDesign.shortcuts.wrappers.designs:wrapped_pssm2csv'), MenuItem('actionProfile_Design', 'REvoDesign.shortcuts.wrappers.designs:wrapped_profile_pick_design'), MenuItem('actionSMILES_Conformers', 'REvoDesign.shortcuts.wrappers.ligand_converters:wrapped_smiles_conformer_single'), MenuItem('actionSMILES_Conformers_Batch', 'REvoDesign.shortcuts.wrappers.ligand_converters:wrapped_smiles_conformer_batch'), MenuItem('actionSDF_to_Rosetta_Parameters', 'REvoDesign.shortcuts.wrappers.ligand_converters:wrapper_sdf2rosetta_params'), MenuItem('actionRosettaLigand', 'REvoDesign.shortcuts.wrappers.rosetta_tasks:wrapped_rosettaligand'), MenuItem('actionFastRelax', 'REvoDesign.shortcuts.wrappers.rosetta_tasks:wrapped_fast_relax'), MenuItem('actionRelax_w_Ca_Constraints', 'REvoDesign.shortcuts.wrappers.rosetta_tasks:wrapped_relax_w_ca_constraints'), MenuItem('actionPROSS', 'REvoDesign.shortcuts.wrappers.rosetta_tasks:wrapped_pross'), MenuItem('actionThermoMPNN', 'REvoDesign.shortcuts.wrappers.mutation_effect_predictors:wrapped_thermompnn'), MenuItem('actionESM_1v', 'REvoDesign.shortcuts.wrappers.esm2:wrapped_esm1v'), MenuItem('actionAlter_Box', 'REvoDesign.shortcuts.wrappers.vina_tools:wrapped_alter_box'), MenuItem('actionGet_PCA_Box', 'REvoDesign.shortcuts.wrappers.vina_tools:wrapped_get_pca_box'), MenuItem('actionGet_Box', 'REvoDesign.shortcuts.wrappers.vina_tools:wrapped_alter_box'), MenuItem('actionRemove_Het_Atoms', 'REvoDesign.shortcuts.wrappers.vina_tools:wrapped_rmhet'), MenuItem('actionRFdiffusion_General_Task', 'REvoDesign.shortcuts.wrappers.rfdiffusion_tasks:wrapped_general_rfdiffusion_task'), MenuItem('actionSubstrate_Potential', 'REvoDesign.shortcuts.wrappers.rfdiffusion_tasks:wrapped_visualize_substrate_potentials'), MenuItem('actionRenumber_Residue_Index', 'REvoDesign.shortcuts.wrappers.structure:wrapped_resi_renumber'), MenuItem('actionDump_Sequence', 'REvoDesign.shortcuts.wrappers.exports:wrapped_dump_fasta_from_struct'), MenuItem('actionSetLogLevel', 'REvoDesign.shortcuts.wrappers.utils:wrapped_logger_level_setter'), MenuItem('actionRMSF_to_b_factor', 'REvoDesign.shortcuts.wrappers.represents:wrapped_load_b_factors'), MenuItem('actionMake_Residue_Range', 'REvoDesign.shortcuts.wrappers.utils:wrapped_convert_residue_ranges'), MenuItem('actionShorten_Range', 'REvoDesign.shortcuts.wrappers.utils:wrapped_short_range'), MenuItem('actionRun_GREMLIN', 'REvoDesign.shortcuts.wrappers.evolution:wrapped_gremlin')) module-attribute

REvoDesign.application.menu.MENU_LINKS = (*TOOLS_MENU_LINKS, *CONFIG_EDIT_LINKS, *PREFERENCES_MENU_LINKS, *OTHER_MENU_LINKS) module-attribute

Icon Setter

REvoDesign.application.icon.IconSetter

Cluster Tab Controller

REvoDesign.application.cluster_tab.ClusterTabController

Configure runtime behavior of the clustering tab after setupUi().

install()

Install tooltips, method-specific panel switching, and safe defaults.

sync_from_state()

Apply current configuration-backed widget state to the cluster tab.

confirm_cluster_run()

Require explicit confirmation for the deprecated legacy workflow.

Internationalization

REvoDesign.application.i18n.language_settings.LanguageSwitch

Bases: QWidget

Language switching component, manages the language settings and switching for the application.

Attributes:

Name	Type	Description
bus	ConfigBus	Configuration bus for communication with other components.
window		Main window of the application.
language_settings	list[LanguageNameRegistry]	Dictionary containing language related settings.

restore_from_config()

Restores the language setting from the configuration.

get_language_items()

Returns a tuple of all language items.

Returns:

Type	Description
tuple[LanguageItem, ...]	Tuple of all language items.

add_lan_to_menu(lan_regsitry)

Adds the language item to the language menu.

register_language()

Registers all languages.

switch_language(language)

Switches to the specified language.

Parameters:

Name	Type	Description	Default
language	LanguageItem	Language item to switch to.	required

REvoDesign.application.i18n.language_settings.LanguageItem dataclass

A frozen data class representing a language item.

Attributes:

Name	Type	Description
name	str	The name of the language.
id	str	The unique identifier for the language.
action	Any	An action associated with the language item.

language_file property

Returns the absolute path to the language file.

This property constructs and returns the absolute path to the language file based on the language ID and a predefined directory.

Returns:

Name	Type	Description
str		The absolute path to the language file.

REvoDesign.application.i18n.language_settings.LanguageNameRegistry

Bases: TypedDict

A dictionary representing a language name registry from a JSON file.

Attributes: - code: The language code. - name: The name of the language. - action: The action associated with the language.