schrodinger.application.jaguar.gui.tabs.molecule_tab module¶

class schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase(parent, input_selector=None)¶

Bases: schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab

The base class for all molecule tabs. This class defines functionality for the top half of the tab, which is constant between subclasses.

NAME = 'Molecule'¶

HELP_TOPIC = 'JAGUAR_TOPIC_MOLECULE_FOLDER'¶

MULTIPLE_STRUC_WARNING = 'Warning: Charge and spin multiplicity\ncannot be changed when more than one\nentry is selected.'¶

CHARGE_SPIN_INCONSISTANT_WARNING = 'Warning: Charge and spin multiplicity are inconsistent.'¶

setup()¶: Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.

createChargeProperties()¶: Create charge and spin properties in the project table in response to the user clicking on the Create Properties button.

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.

loadSettings(keywords)¶

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

class schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab(parent, input_selector=None)¶

Bases: schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin, schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase

The standard molecule tab

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.molecule_top_ui' from '/scr/buildbot/savedbuilds/2024-4/NB/build-117/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/molecule_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui' from '/scr/buildbot/savedbuilds/2024-4/NB/build-117/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/molecule_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.

Returns: A keyword dictionary with the default basis set
Return type: dict

getBasis(ignored=None)¶

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

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.

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

loadSettings(keywords)¶

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

class schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka(parent, input_selector=None)¶

Bases: schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase

The molecule tab used in the PKA panel

MULTIPLE_STRUC_PICK_WARNING = 'Warning: Pick options cannot be used when\nmore than one entry is in the Workspace'¶

FILE_PICK_WARNING = 'Warning: Pick options cannot be used when\nusing structures from files.'¶

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.molecule_top_ui' from '/scr/buildbot/savedbuilds/2024-4/NB/build-117/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/molecule_top_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui' from '/scr/buildbot/savedbuilds/2024-4/NB/build-117/internal/lib/python3.11/site-packages/schrodinger/application/jaguar/gui/ui/molecule_pka_bottom_ui.py'>)¶

PKA_ATOM_PROP = 's_m_pKa_atom'¶

setup()¶: Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.

reset()¶: Reset the tab to its original state. Note that this function is only necessary for settings that are not stored in the mmjag handle. For mmjag settings, reset will be carried out using loadSettings with a default schrodinger.application.jaguar.input.JaguarInput object. This function should only be defined in subclasses if there are any settings that cannot be reset via loadSettings.

pickThisAtom(atom_num)¶

Respond to the atom picking at atom in the “Use this atom” section.

Parameters: atom_num (int) – The atom number that was just picked

pickProjTableAtom(atom_num)¶

Respond to the atom picking at atom in the “Use pKa atoms from the project table” section.

Parameters: atom_num (int) – The atom number that was just picked

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.

validate()¶: Make sure that a pka atom has been selected and is a valid atom for the currently selected structure

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

isZwitterionChecked()¶

isConformationalSearchesChecked()¶

class schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector(parent, input_selector=None)¶

Bases: schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab

A Molecule tab that does not use the input selector

setup()¶: Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.

setStructure(struc)¶

Change the structure that this tab is representing

Parameters: struc (schrodinger.structure.Structure) – The structure

structureUpdated()¶: React to a change in the structure described by self._struc. i.e. The schrodinger.structure.Structure object passed to setStructure has not changed, but the structure described by that object has.

getStructure()¶: Get the structure that this panel is currently representing

createChargeProperties()¶: Create charge and spin properties in the project table in response to the user clicking on the Create Properties button.