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]

ATOMS = 'atoms'

ATOM_LABELS = 'atom labels'

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

PRODUCT = 2

REACTANT = 1

STRUC_DIFF_WARNING = 'Warning: The %s and %s\nentries contain different %s. This must\nbe resolved before running the job.'

TRANSITION_STATE = 0

chooseEntry(struc_type)

Open the EntrySelector dialog for the specified structure and save the selected entry.

Parameters:struc_type (int) – The structure to select. Must be one of self.TRANSITION_STATE, self.REACTANT, or self.PRODUCT.

getBasis(ignored=None)

getDefaultKeywords()

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

getMmJagKeywords()

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

getStructureTitleForJobname()

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

loadSettings(jag_input)

projectUpdated()

Update the listing of structures when the project is updated. Note that the callback for this function is registered in the base_panel.MultiStructureMixin class so that it can be unregistered when the panel is closed.

reset()

Clear the stored structures

setStructureSelectorsEnabled(transition_state, reactant, product)

Enable or disable the three structure selection rows

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.

setup()

structureCbToggled(struc_type)

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

validate()

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