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

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

Bases: object

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

HELP_TOPIC = 'JAGUAR_TOPIC_TRANSITION_STATE_FOLDER'

NAME = 'Transition State'

SA_LOWEST_BOND_STRETCH = 'Lowest bond-stretch mode'

SA_LOWEST_HESSIAN = 'Lowest Hessian eigenvector'

SA_LOWEST_NON_TORSIONAL = 'Lowest non-torsional mode'

SA_RP_PATH = 'Reactant-product path'

SA_USER = 'User-selected eigenvector'

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

SEARCH_STANDARD = 0

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

getMmJagKeywords()

loadSettings(jag_input)

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

setup()

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

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

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',)

SEARCH_LST = 1

SEARCH_QST = 2

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.transition_state_top_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/transition_state_top_ui.pyc'>, <module 'schrodinger.application.jaguar.gui.ui.multi_structures_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/multi_structures_ui.pyc'>, <module 'schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/transition_state_bottom_ui.pyc'>, (<class 'schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector'>, 'molecule_sub_tab'))

getMmJagKeywords()

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

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

searchMethodChanged()

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

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)

setup()