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

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/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/molecule_top_ui.pyc'>, <module 'schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/molecule_std_bottom_ui.pyc'>)

getBasis(ignored=None)

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

getMmJagKeywords()

loadSettings(keywords)

setup()

validate()

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.

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

HELP_TOPIC = 'JAGUAR_TOPIC_MOLECULE_FOLDER'

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

NAME = 'Molecule'

createChargeProperties()

Create charge and spin properties in the project table in response to the user clicking on the Create Properties button.

getMmJagKeywords()

loadSettings(keywords)

setup()

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

createChargeProperties()

getStructure()

setStructure(struc)

Change the structure that this tab is representing

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

setup()

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.

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

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

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

PKA_ATOM_PROP = 's_m_pKa_atom'

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.molecule_top_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/molecule_top_ui.pyc'>, <module 'schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui' from '/scr/buildbot/savedbuilds/2017-4/NB/build-152/internal/lib/python2.7/site-packages/schrodinger/application/jaguar/gui/ui/molecule_pka_bottom_ui.pyc'>)

getMmJagKeywords()

isConformationalSearchesChecked()

isZwitterionChecked()

loadSettings(jag_input)

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

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

reset()

setup()

validate()

Make sure that a pka atom has been selected and is a valid atom for the currently selected structure