schrodinger.application.jaguar.gui.tabs.transition_state_tab module

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin

Bases: object

NAME = 'Transition State'

HELP_TOPIC = 'JAGUAR_TOPIC_TRANSITION_STATE_FOLDER'

SA_LOWEST_HESSIAN = 'Lowest Hessian eigenvector'

SA_LOWEST_NON_TORSIONAL = 'Lowest non-torsional mode'

SA_LOWEST_BOND_STRETCH = 'Lowest bond-stretch mode'

SA_RP_PATH = 'Reactant-product path'

SA_USER = 'User-selected eigenvector'

SA_ACTIVE = 'Active coordinate eigenvector'

SEARCH_ALONG_VALUES = {'Active coordinate eigenvector': -6, 'Lowest Hessian eigenvector': 0, 'Lowest bond-stretch mode': -2, 'Lowest non-torsional mode': -1, 'Reactant-product path': -5, 'User-selected eigenvector': 'User-selected eigenvector'}

STANDARD_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'User-selected eigenvector')

ADDITIONAL_SEARCH_ALONGS = ()

SEARCH_STANDARD = 0

setup()

onHessianRefinementToggled(checked)

repopulateSearchAlongCombo(search_method)

Replace the contents of the search along combo boxes based on the current search method

searchAlongChanged()

Respond to the user changing the search along method by updating the status of the eigenvector input widgets

getMmJagKeywords()

loadSettings(jag_input)

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin, schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.transition_state_top_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/transition_state_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.multi_structures_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/multi_structures_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui' from '/scr/buildbot/savedbuilds/2018-3/NB/build-149/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/transition_state_bottom_ui.py'>, (<class 'schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector'>, 'molecule_sub_tab'))

LST_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'Reactant-product path', 'User-selected eigenvector')

QST_SEARCH_ALONG = ('Reactant-product path',)

ADDITIONAL_SEARCH_ALONGS = (('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'Reactant-product path', 'User-selected eigenvector'), ('Reactant-product path',))

SEARCH_LST = 1

SEARCH_QST = 2

setup()

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

searchMethodChanged()

Respond to the user changing the search method by updating the structure selectors and the search along combo box

getStructures()

Get all of the structures that are loaded into the tab. When LST is selected, the structure types don’t map to the Z-matrices in the standard way, so we have to override the parent function.

Returns:A list of: - the structure to be loaded into ZMAT1 (or None) - the structure to be loaded into ZMAT2 (or None) - the structure to be loaded into ZMAT3 (or None) Return type:list

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.

setStructures(entry_ids, jag_input=None)

Override the parent function so we can properly handle LST jobs (which use zmat 1 and 2 for reactant and product instead of transition state and reactant)

isLst(jag_input)

Does the Jaguar input specify an LST job? This answer isn’t guaranteed to be correct, since there’s no way to distinguish a fully- or partially-specified LST job from a partially-specified QST job if the default initial LST guess is used. If the input is ambiguous and LST or QST is already selected, then we try to keep the setting as is.

Parameters:jag_input (schrodinger.application.jaguar.input.JaguarInput) – A JaguarInput object containing the job settings Returns:True if the specified job is likely to be LST. False otherwise. Return type:bool

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.ActiveTransitionStateTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab

Tab used in place of transition state tab in Transition State Search panel

STANDARD_SEARCH_ALONG = ('Lowest Hessian eigenvector', 'Lowest non-torsional mode', 'Lowest bond-stretch mode', 'User-selected eigenvector', 'Active coordinate eigenvector')

setup()

Setup UI elements

getActiveCoordItem()

Return the combobox item corresponding to “Active coordinate eigenvector” (itrvec=-6)

Returns:The model item corresponding to the Active Coordinates

option in the search-along combo box :rtype: QtGui.QStandardItem

onActiveConstraintsChkChanged(state)

Enable of disable relevant UI elements when constraints are set as active on the optimization tab.

Parameters:state (bool) – Checked or not checked

onHessianRefinementToggled(checked)

Enable active coordinates radio button if active constraints

Parameters:checked (bool) – checked or not checked

repopulateSearchAlongCombo(search_method)

Replace the contents of the search along combo boxes based on the current search method

loadSettings(jag_input)

Restore settings from Jaguar input handle.

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