schrodinger.application.jaguar.gui.tabs.multi_structure_tab module

class schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin, schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin, schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab

A parent class for tabs that allow transition state, reactant, and product structures to be selected. MultiStructureTabs also contain a Molecule subtab. Note that this class is not intended to be directly instantiated and instead should be subclassed (such as the IRC tab or Transition State tabs).

ALL_STRUCS = [0, 1, 2]

TRANSITION_STATE = 0

REACTANT = 1

PRODUCT = 2

ENTRY_TYPE_NAMES = ('transition state', 'reactant', 'product')

NEW_STRUC_DIFF_WARNING = '%s and %s entries have different %s.'

ATOMS = 'atoms'

ATOM_LABELS = 'atom labels'

setup()

Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.

setupInWorkspaceColumn()

Set up the In Workspace column.

setInputLoaded(input_loaded: bool)

reset()

Clear the stored structures

onLoadClicked()

Load the selected entries into the structure combos

updateStrucCbsState()

Update the state of all structure checkboxes

strucComboSelectionChanged(struc_type: int)

Set the entry ids based on the combobox selection. :param struc_type: Structure type of current combobox

setStructureSelectorsEnabled(*enabled_list)

Enable or disable the three structure selection rows

onStrucListingsUpdated()

Update the structure warning label and molecule sub tab structure

projectUpdated()

Update the structure combos entries when the project is updated. Note that he callback for this function is registered in the base_panel.MultiStructureMixin class so that it can be unregistered when the panel is closed.

validateStrucCombos() → str

Make sure that the structures are loaded in each of the required structure combos

validate()

Make sure that all of the appropriate structures are loaded and that they all have the same atoms.

structureCbToggled(struc_type)

Respond to the specified structure inclusion checkbox being toggled by including or excluding the relevant structure from the workspace.

getStructures()

Get all of the structures that are loaded into the tab. Each structure will be a schrodinger.structure.Structure object containing the loaded structure, or None if no structure has been loaded.

Returns

A list of: - the transition state structure - the reactant structure - the product structure

Return type

list

loadEntriesIntoStrucCombos()

Load and select the structures in structure combos according to the given entry ids

setStructures(entry_ids, jag_input=None)

Load the specified entry IDs into the tab

Parameters

• entry_ids (list) –

  A list of:

  • the transition state structure entry ID

  • the reactant structure entry ID

  • the product structure entry ID

  Note that this value must be a list, not a tuple.

• jag_input (schrodinger.application.jaguar.input.JaguarInput) – A JaguarInput object containing the job settings. Note that this argument is only used for the Transition State tab version of this function in order to determine if the search method is LST, as this will affect how the structures are loaded.

getRepresentativeStructure()

Retrieve one structure that can be used for basis selector calculations.

Returns

A single representative structure, or None if no structures are loaded.

Return type

schrodinger.structure.Structure or NoneType

enableStructureCombos(should_enable: bool)

Enable all the structure combos and corresponding structure type column entry

Parameters

should_enable – Should the structure combos be enabled

getEids()

Get the entry ids loaded into the tab

Returns

A tuple of - A list of entry ids loaded into the tab - Whether the structures have matching atoms and atom names (bool)

Return type

tuple

getStructureTitleForJobname()

Get the structure title to be used in the job name. If the tab includes multiple structures, then MULTIPLE_STRUC_JOB_TITLE should be returned. If no structures have been specified yet, then None should be returned.

Returns

The structure title

Return type

str or NoneType

getDefaultKeywords()

Get the default keywords for this tab. Note that defaults that exist in mmjag should not be explicitly set here.

getMmJagKeywords()

Return all keywords that should be put into the mmjag handle. This function should be defined in subclasses.

Returns

All keywords that should be put into the mmjag handle

Return type

dict

Raises

schrodinger.application.jaguar.gui.utils.JaguarSettingError – If any settings are invalid.

getBasis(ignored=None)

Get the currently selected basis. If more than one basis set is specified, mixed_name will be returned. If the tab does not allow for specifying multiple basis sets, then this argument may be ignored.

Parameters

mixed_name (str) – The name to return if more than one basis set is specified

Returns

The currently selected basis

Return type

str

loadSettings(jag_input)

Restore tab settings from mmjag keywords. This function should be defined in subclasses.

Parameters

jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar settings to base the tab settings on