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')
STRUC_DIFF_WARNING = 'Warning: The %s and %s\nentries contain different %s. This must\nbe resolved before running the job.'
ATOMS = 'atoms'
ATOM_LABELS = 'atom labels'
setup()

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

reset()

Clear the stored structures

setStructureSelectorsEnabled(transition_state, reactant, product)

Enable or disable the three structure selection rows

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.
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.

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
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
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