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
jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar handle to store the tab settings in
eid (str) – The entry id of the structure in
jag_input
- 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
jag_input (schrodinger.application.jaguar.input.JaguarInput) – The Jaguar settings to base the tab settings on
eid (str) – The entry id of the structure in
jag_input
title (str) – The title of the structure in
jag_input
- 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