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

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateBasisSetSubTab(parent=None)

Bases: schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab

Sub tab for per-atom basis sets in transition state tab.

getAtomNumsForEntry(eid: int) → list[int]

Overrides the parent method to retrieve the list of atom numbers for all the rows present in the table.

Returns

A list of atom numbers present in the table.

class schrodinger.application.jaguar.gui.tabs.transition_state_tab.PerAtomBasisPopUp(parent)

Bases: schrodinger.ui.qt.pop_up_widgets.PopUp

Pop-up to select per-atom basis set

setup()

Subclass-specific initialization. Subclasses can re-implement this function with custom set up code.

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, schrodinger.ui.qt.appframework2.markers.MarkerMixin

Transition State tab.

Variables

searchMethodChanged (PyQt5.QtCore.pyqtSignal) – a signal emitted when the search method changes

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.multi_structures_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/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/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/transition_state_bottom_ui.py'>, (<class 'schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector'>, 'molecule_sub_tab'), <module 'schrodinger.application.jaguar.gui.tabs.per_atom_basis_pop_up.per_atom_basis_ui' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/tabs/per_atom_basis_pop_up/per_atom_basis_ui.py'>)
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
searchMethodChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

setup()

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

resetPAB()

Reset per-atom basis pop-up

reset()

Clear the stored structures

onLoadClicked()

Load the entries into the structure combos

projectUpdated()

Update the entries in the structure combos on project updates.

loadEntriesIntoStrucCombos()

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

strucComboSelectionChanged(struc_type: int)

Update the selections on the structure combos to avoid duplicate selection.

Parameters

struc_type – Type of the structure combo whose selection is changed

onSearchMethodChanged()

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

saveSettings(jag_input, eid)

Save tab settings in jaguar handle. It is only used for settings which are not defined using keywords (typically per-atom settings). This function should be defined in subclasses for any tabs that contain per- atom settings.

Parameters
loadPerAtomSettings(jag_input, eid=None, title=None)

Restore per-atom tab settings from mmjag keywords. This function should be defined in subclasses for any tabs that contain per-atom settings.

Parameters
addPABJaguarMarker(atoms: list[schrodinger.structure._structure.StructureAtom], settings: dict)

Add a workspace marker corresponding to the selected atoms for per-atom basis setting. Marker is also added to all the atoms with same name across the loaded structures

Parameters

  • atoms – List of atoms to add the marker for

  • settings – The marker settings

removePABJaguarMarker(atoms: list[schrodinger.structure._structure.StructureAtom])

Remove the workspace markers corresponding to the given atoms per-atom basis setting. Also remove markers corresponding to all the atoms with same name across the loaded structures

Parameters

atoms – List of atoms to remove the marker for

setPABJaguarMarkerHighlighting(atoms: list[schrodinger.structure._structure.StructureAtom], highlight: bool)

Change the workspace marker highlighting for the specified atom marker.

Parameters

  • atoms – A list of atoms to change the highlighting for

  • highlight – Whether to highlight the specified marker

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

onSearchMethodChanged()

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

getActiveCoordItem()

Return the combobox item corresponding to “Active coordinate eigenvector” (itrvec=-6) or None if combobox does not have this item.

Returns

The model item corresponding to the Active Coordinates option in the search-along combo box

Return type

QtGui.QStandardItem or None

onActiveConstraintsChkChanged(state)

Enable or 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