schrodinger.application.jaguar.gui.tabs.input_tab module

class schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase(parent, input_selector=None)

Bases: ProvidesStructuresMixin, BaseTab

A tab for specifying settings for the structures currently selected in the project table. Note that this class is not intended to be directly instantiated. Instead, the InputTab or InputTabPka classes should be used.

Variables:

  • MODEL_CLASS (schrodinger.application.jaguar.gui.input_tab_widgets. SelectedEntriesModel) – The class to use for the table model

  • PROXY_CLASS (schrodinger.application.jaguar.gui.input_tab_widgets. SelectedEntriesProxyModel) – The class to use for the table proxy model

  • VIEW_CLASS (schrodinger.application.jaguar.gui.input_tab_widgets. SelectedEntriesView) – The class to use for the table view

  • strucSourceChanged (QtCore.pyqtSignal) – A signal emitted when the structure source changes from included to selected or vice versa.

strucSourceChanged

A pyqtSignal emitted by instances of the class.

NAME = 'Input'
MODEL_CLASS

alias of InputEntriesModel

PROXY_CLASS

alias of InputEntriesProxyModel

VIEW_CLASS

alias of InputEntriesView

setup()

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

projectUpdated()

When the project is updated, update the selected entries table

workspaceChanged(what_changed)

Update the table whenever the workspace changes in case the user changed the charge of a molecule.

Parameters:

what_changed (str) – A flag indicating what changed in the workspace

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

validate()

Make sure that the tab settings will allow a job to be run successfully. Note that this validation should not be redundant with that performed in getMmJagKeywords. Any tab setting that prevents valid mmjag keywords from being generated should cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate fail. This function should be defined in subclasses if validation is needed.

Returns:

If the validation passes, None is returned. If the validation fails, a string that describes the error is returned.

Return type:

str or NoneType

getStructures()

Get all structures loaded into the tab and their associated Jaguar settings

Returns:

A list of tuples. Each tuple represents a single structure and contains:

Return type:

list

getNumStructures()
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

reset()

Reset any structure specific settings in the table. (The non-struture specific settings will be reset via loadSettings())

useFromComboChanged()

Respond to the user changing the structure source (from included to selected or vice versa).

usingSelected()

Return True if the tab is set to use selected entries. False if the tab is set to use included entries.

getCurrentTableModel()

Get the current model, not the proxy model, for the input view

Return type:

QtCore.QAbstractTableModel

Returns:

The model the table is currently using

getAllTableModels()

Get all table models regardless of whether they are the currently the model for the table view or not. This allows supporting panels such as pKa that switch between multiple models depending on panel options.

The proxy model is not included.

Return type:

list

Returns:

A list of models usable by the table view

class schrodinger.application.jaguar.gui.tabs.input_tab.InputTab(parent, input_selector=None)

Bases: ProvidesTheoryMixin, ProvidesBasisMixin, InputTabBase

An input tab that allows the user to specify basis sets.

HELP_TOPIC = 'JAGUAR_INPUT_TAB'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/builds/core-suite-build/core-suite-build/build/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.input_std_bottom_ui' from '/scr/buildbot/builds/core-suite-build/core-suite-build/build/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/input_std_bottom_ui.py'>)
setup()

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

getDefaultKeywords()

The mmjag default basis set is “”, which would cause a warning, so we set the default basis. Additionally, the mmjag default DFT functional name is “”, which would cause a HF level of theory. Instead, set a default functional of B3LYP-D3.

Returns:

A keyword dictionary with the default basis set and functional.

Return type:

dict

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

getBasis(mixed_name='Mixed')

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

getTheoryLevel()

Get the current theory level

Returns:

The current theory level.

Return type:

str

getAllUsedTheoryLevels()
Returns:

A tuple of all theory levels used

Return type:

tuple

getMethod()

Get the current method.

Returns:

The current method

Return type:

str

getFunctional(cur_struc=None)

Get the current DFT functional.

Parameters:

cur_struc (input_tab_widgets.ProjEntryTuple) – Current structure to get functional for. If not specified, functional will be returned based on default theory setting.

Returns:

The current DFT functional

Return type:

str or None

validate()

Make sure that the tab settings will allow a job to be run successfully. Note that this validation should not be redundant with that performed in getMmJagKeywords. Any tab setting that prevents valid mmjag keywords from being generated should cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate fail. This function should be defined in subclasses if validation is needed.

Returns:

If the validation passes, None is returned. If the validation fails, a string that describes the error is returned.

Return type:

str or NoneType

getCommonBasis()

If all structures use the same basis set, return the basis set name. Otherwise, return None.

Returns:

The basis set name or None

Return type:

str or NoneType

getCommonMethod()

If all structures use the same method, return the method name. Otherwise, return None.

Returns:

The method name or None

Return type:

str or NoneType

getCommonTheoryLevel()
Returns:

If all current methods are of the same theory level, return the theory level. Otherwise return None.

Return type:

str or None

chargedStrucsPresent()

Determine if the user has specified any molecular charges

Returns:

True if the user has specified a molecular charge for any molecule. False otherwise.

Return type:

bool

getBasisForEid(eid, per_atom_name)

Get the basis set for the specified entry id. If there are per-atom basis sets specified for the structure, the per_atom_name will be returned.

Parameters:

  • eid (str) – The entry id

  • per_atom_name (str) – The name to return if per-atom basis sets are specified

Returns:

The basis set name, or per_atom_name if per-atom basis sets are specified

Return type:

Basis or str

getTheoryLevelForEid(eid)

Get the theory level for the specified entry ID.

Parameters:

eid (int) – Entry ID to get theory level of.

Returns:

Theory level for this entry ID.

Return type:

str

getMethodForEid(eid)

Get the method for the specified entry ID.

Parameters:

eid (int) – Entry ID to get method of.

Returns:

Method for this entry ID.

Return type:

str

class schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka(parent, input_selector=None)

Bases: InputTabBase

An input tab that allows the user to specify pKa atoms.

Variables:

  • set_pka_marker (PyQt5.QtCore.pyqtSignal) –

    A signal emitted when a new pKa atom should be marked in the workspace. Emitted with two arguments:

    • The entry id of the structure to be marked (str)

    • The atom to be marked (schrodinger.structure._StructureAtom)

  • remove_all_pka_markers (PyQt5.QtCore.pyqtSignal) – A signal emitted when the panel is reset and should thus remove all markers from the workspace.

HELP_TOPIC = 'JAGUAR_INPUT_TAB'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.input_pka_top_ui' from '/scr/buildbot/builds/core-suite-build/core-suite-build/build/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/input_pka_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui' from '/scr/buildbot/builds/core-suite-build/core-suite-build/build/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/input_pka_bottom_ui.py'>)
MODEL_CLASS

alias of InputEntriesModelPka

VIEW_CLASS

alias of InputEntriesViewPka

set_pka_marker

A pyqtSignal emitted by instances of the class.

remove_all_pka_markers

A pyqtSignal emitted by instances of the class.

SMARTS = 'SMARTS'
SMARTS_TOOLTIP = ''
AUTO = 'Automatic search'
AUTO_TOOLTIP = 'Application will attempt to locate all pKa atoms in all structures.\nStructures must be in the appropriate protonation form.\nNote that this search is not perfect and may miss some atoms or include others erroneously.'
SELECTION_MICRO_TEXT = 'pKa predictions will run on all structures listed below. The pKa atom must be defined for each structure. Optionally choose an alternate method for identifying these atoms below.'
SELECTION_MACRO_TEXT = 'Macro-pKa predictions will run on all structures listed below. The pKa atom will be automatically defined for each structure.'
PKA = 'pKa'
CHARGE = 'Relative Charge'
setup()

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

isMacroPka()

Whether the current panel mode is Macro-pKa

Return type:

bool

Returns:

True if the panel mode is Macro, False if it is Micro

isRangePka()

Whether the Macro-pKa mode range is for pKa

Return type:

bool

Returns:

True if the Macro range is pKa, False if it is relative charge

swapInSourceModel(source)

Change the source model for the table view to the given model

Parameters:

source (QtCore.QAbstractTableModel) – The model to use

setPkaMarkers(*args, **kwargs)

Turn on workspace atom markers if the sending model is the current table model - ignore signals from other models

updateForRangeType(rtype)

React to a change in which Macro-pKa range type is used

Parameters:

rtype (str) – The new range type

updateRelativeChargeInfo()

Update the label that informs the user about relative charges

updateForMethod(micro)

React to the panel changing between micro and macro mode

Parameters:

micro (bool) – True if the panel is in micro mode, False if in macro mode

onFindCheckToggled(state)

If checked, disable editing of pka atom and enable combobox for choosing of pick mode. Update model to reflect new pick mode. Show smarts selector if new picking mode is SMARTS.

Parameters:

state (bool) – If checkbox is checked or not

onPickModeComboChanged()

Update model to reflect new pick mode. Show smarts selector if new picking mode is SMARTS.

onPickModeChanged()

Update the model to reflect the new pick mode. If its SMARTS show and hide the define label and connect signals.

showDefineButton()

Show the define label

hideDefineButton()

Hide the define label

getPickingMode()

Determine the current picking mode the tab is in

Returns:

picking mode

Return type:

input_tab_widgets_pka.PickingModes

runSmartsSearch()

Run SMARTS searches on the entries in the entry table if the pick mode is SMARTS

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.

isZwitterionChecked()
isConformationalSearchesChecked()
validate()

Make sure that the tab settings will allow a job to be run successfully. Note that this validation should not be redundant with that performed in getMmJagKeywords. Any tab setting that prevents valid mmjag keywords from being generated should cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate fail. This function should be defined in subclasses if validation is needed.

Returns:

If the validation passes, None is returned. If the validation fails, a string that describes the error is returned.

Return type:

str or NoneType

validateMacroSettings()

Validate any Macro-pKa settings on the input tab

Return type:

str or None

Returns:

An error message, or None if there are no issues

validateMicroSettings()

Validate any Macro-pKa settings on the input tab

Return type:

str or None

Returns:

An error message, or None if there are no issues

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

loadWorkflowSettings(workflow_input, eid)

Load workflow settings from the input file

Parameters:

  • workflow_input (schrodinger.application.jaguar.workflow_input) – The workflow input object created from the input file

  • eid (str or None) – The entry ID of structure that was loaded during this read. If None, the settings are not associated with an entry.

setPickMethodToManual()
setPickMethodToAuto()
reset()

Reset any structure specific settings in the table. (The non-struture specific settings will be reset via loadSettings())

getAllTableModels()

Get all table models regardless of whether they are the currently the model for the table view or not.

Return type:

list

Returns:

A list of models usable by the table view

class schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB(parent, input_selector=None)

Bases: InputTabBase

An input tab that is used with Hydrogen Bond task.

HELP_TOPIC = 'JAGUAR_HYDROGEN_BOND'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.input_hb_top_ui' from '/scr/buildbot/builds/core-suite-build/core-suite-build/build/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/input_hb_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui' from '/scr/buildbot/builds/core-suite-build/core-suite-build/build/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/input_hb_bottom_ui.py'>)
MODEL_CLASS

alias of InputEntriesModelHB

VIEW_CLASS

alias of InputEntriesView

getMmJagKeywords()

There are no jaguar handle keywords that this tab sets, but we need this function to override the one in the base class.

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

isFastMode()

This function return True if ‘Fast Mode’ check box is checked.

Returns:

True if ‘Fast Mode’ check box is toggled.

Return type:

bool

getOptimizationCmd()

This function returns command argument corresponding to the checked optimization option. If ‘Optimize all structure’ option is selected this function returns None.

Returns:

optimization command argument

Return type:

string or None

reset()

This function resets optimization and ‘fast mode’ settings to default state. This function needs to be called every time when input file is loaded.

class schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs(parent, input_selector=None)

Bases: InputTab

An Input tab with sub-tabs on the bottom. Sub-tabs can be set using addSubTabs, which is normally accessed by setting the INPUT_SUB_TABS panel class variable.

Variables:

  • DEFAULT_SUB_TAB_VISIBILITY (bool) – Whether the sub-tabs should be visible by default. Sub-tab visibility can be toggled at any time using setSubTabsVisible, which is connected to the “Atom-Level Settings” button.

  • subTabChanged (PyQt5.QtCore.pyqtSignal) – A signal emitted when the active sub-tab has been changed, or when the sub-tab visibility has been toggled.

  • addJaguarMarker (PyQt5.QtCore.pyqtSignal) –

    A signal emitted when a workspace marker should be added. Emitted with:

    • The list of atoms to add the marker for (list)

    • The marker settings (dict)

    • The name of the sub-tab that the marker is for (str)

  • removeJaguarMarker (PyQt5.QtCore.pyqtSignal) –

    A signal emitted when a workspace marker should be removed. Emitted with:

    • The list of atoms to remove the marker for (list)

    • The name of the sub-tab that the marker is for (str)

  • setMarkerHighlighting (PyQt5.QtCore.pyqtSignal) –

    A signal emitted when the highlighting of a workspace marker should be changed. Emitted with:

    • The list of atoms to change the highlighting for (list)

    • Whether the marker should be highlighted (True) or unhighlighted (False) (bool)

    • The name of the sub-tab that the marker is for (str)

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.input_top_ui' from '/scr/buildbot/builds/core-suite-build/core-suite-build/build/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/input_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.input_std_bottom_ui' from '/scr/buildbot/builds/core-suite-build/core-suite-build/build/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/input_std_bottom_ui.py'>)
DEFAULT_SUB_TAB_VISIBILITY = False
SUB_TAB_NAME = '%s (%i)'
subTabChanged

A pyqtSignal emitted by instances of the class.

addJaguarMarker

A pyqtSignal emitted by instances of the class.

removeJaguarMarker

A pyqtSignal emitted by instances of the class.

setMarkerHighlighting

A pyqtSignal emitted by instances of the class.

addSubTabs(sub_tab_classes)

Add a sub tab for each of the specified classes. Note that this function should be called only once per instance.

Parameters:

sub_tab_classes (iterable) – An iterable of schrodinger.application.jaguar. gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab sub-classes to be instantiated.

getChargeConstraintSubTab()

Get the subtab that holds the charge constraint settings

Return type:

schrodinger.application.jaguar.gui.input_sub_tabs. ChargeConstraintsSubTab

Returns:

The charge constraint subtab, or None if no such tab exists

getBasisSetSubTab()

Get the subtab that holds the by-atom basis set settings

Return type:

schrodinger.application.jaguar.gui.input_sub_tabs. BasisSetSubTab

Returns:

The by-atom basis set subtab, or None if no such tab exists

getSubTab(sub_tab_class)

Get the sub-tab of the specified class

Parameters:

sub_tab_class (type) – The class of the sub-tab to retrieve

setup()

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

projectUpdated()

Whenever the project is updated, update the structure titles and the structures shown in the sub tabs.

reset()

Reset any structure specific settings in the table. (The non-struture specific settings will be reset via loadSettings())

setSubTabsVisible(visible=None)

Set whether the sub-tabs are visible in response to the user clicking on the “Atom-Level Settings” button.

Parameters:

visible (bool or NoneType) – Should the sub-tabs be made visible. If not specified, the visibility will be toggled.

subTabsVisible()

Are the sub-tabs currently visible?

Returns:

True if the sub-tabs are visible. False otherwise.

Return type:

bool

validate()

Make sure that the tab settings will allow a job to be run successfully. Note that this validation should not be redundant with that performed in getMmJagKeywords. Any tab setting that prevents valid mmjag keywords from being generated should cause getMmJagKeywords to raise a JaguarSettingError. Any tab setting that allows mmjag keywords to be successfully generated but will result in a job failure should cause a validate fail. This function should be defined in subclasses if validation is needed.

Returns:

If the validation passes, None is returned. If the validation fails, a string that describes the error is returned.

Return type:

str or NoneType

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, title)

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

Parameters:
activeSubTab()

Get the active sub tab

Returns:

The active sub-tab or None if the sub-tabs are not visible

Return type:

schrodinger.application.jaguar.gui.input_sub_tabs. base_sub_tab.BaseSubTab or NoneType

activeSubTabName()

Get the name of the active sub-tab

Returns:

The name of the active sub-tab or None if the sub-tabs are not visible

Return type:

str or NoneType

activate()

Activate the appropriate sub-tab (if any) when this tab is activated

deactivate()

Deactivate the active sub-tab (if any)

displayedEntryIds()

Return the entry IDs for all structures that are currently displayed in the input table

Returns:

A set of entry ids

Return type:

set

perAtomBasisSetsPresent()

Have any per-atom basis sets been set?

Returns:

True if there are per-atom basis sets for any currently selected structures. False otherwise.

Return type:

bool

getCommonBasis()

If all structures use the same basis set and there are no per-atom basis sets, return the basis set name. Otherwise, return None.

Returns:

The basis set name or None

Return type:

str or NoneType

theoryChanged(theory_level)

If there is a Charge Constraints sub-tab, disable or enable it when the level of theory changes.

Parameters:

theory_level (str) – The current level of theory. Should be one of “DFT”, “HF”, “LMP2”, “RIMP2” or “Mixed”.

useFromComboChanged()

Update the sub-tabs when the user changes the structure source (from included to selected or vice versa).

class schrodinger.application.jaguar.gui.tabs.input_tab.InputTabCoordinateScan(parent, input_selector=None)

Bases: InputTab

Input tab used in Rigid and Relaxed Coordinate scan GUIs. It modifies ‘Input structures from’ combo box to include only the ‘Workspace (included)’ item.

setup()

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