schrodinger.application.jaguar.gui.tabs.solvation_tab module

schrodinger.application.jaguar.gui.tabs.solvation_tab.different(value1, value2)

Return True if the given float values are different from each other (tiny differences are not considered).

class schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab(parent, input_selector=None)

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

The Solvent tab that contains only solvent model widgets. This is common part of Solvation tab for multiple panels.

NAME = 'Solvent'
HELP_TOPIC = 'JAGUAR_TOPIC_SOLVATION_FOLDER'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.solvent_tab_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvent_tab_ui.py'>,)
SOLVENTS = [Solvent(name='Water', keyvalue='water', dielectric=80.37, radius=1.4, weight=18.02, density=0.99823), Solvent(name='DMSO', keyvalue='dmso', dielectric=36.7, radius=2.41, weight=78.13, density=1.1014)]
SHOW_DIELECTRIC = False
setup()

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

solventTypeChanged()

Called when a new item is selected from the solvent menu.

calculateProbeRadius()

Calculate the solvent probe radius from the density and molecular weight.

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(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
class schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab

The Solvent tab for the Pka panel.

UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.solvent_tab_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvent_tab_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.solvation_pka_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvation_pka_ui.py'>)
setup()

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

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(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
class schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab

The Solvation tab, which includes solvent model and gas-phase reference energy

NAME = 'Solvation'
UI_MODULES = (<module 'schrodinger.application.jaguar.gui.ui.solvation_solvent_model_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvation_solvent_model_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.solvent_tab_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvent_tab_ui.py'>, <module 'schrodinger.application.jaguar.gui.ui.solvation_gas_phase_ui' from '/scr/buildbot/savedbuilds/2018-2/NB/build-169/internal/lib/python3.6/site-packages/schrodinger/application/jaguar/gui/ui/solvation_gas_phase_ui.py'>)
SHOW_DIELECTRIC = True
SOLVENTS = [Solvent(name='Water', keyvalue='water', dielectric=80.37, radius=1.4, weight=18.02, density=0.99823), Solvent(name='Acetonitrile', keyvalue='acetonitrile', dielectric=37.5, radius=2.19, weight=41.05, density=0.777), Solvent(name='Benzene', keyvalue='benzene', dielectric=2.284, radius=2.6, weight=78.12, density=0.87865), Solvent(name='Carbon tetrachloride', keyvalue='carbon_tet', dielectric=2.238, radius=2.67, weight=153.82, density=1.594), Solvent(name='Chlorobenzene', keyvalue='chlorobenzene', dielectric=5.708, radius=2.72, weight=112.56, density=1.1058), Solvent(name='Chloroform', keyvalue='chloroform', dielectric=4.806, radius=2.52, weight=119.38, density=1.4832), Solvent(name='Cyclohexane', keyvalue='cyclohexane', dielectric=2.023, radius=2.78, weight=84.16, density=0.77855), Solvent(name='1,2-dichloroethane', keyvalue='dichloroethane', dielectric=10.65, radius=2.51, weight=98.96, density=1.2351), Solvent(name='Dichloromethane', keyvalue='dichloromethane', dielectric=8.93, radius=2.33, weight=84.93, density=1.3266), Solvent(name='Dimethylformamide', keyvalue='dimethylformamide', dielectric=36.7, radius=2.49, weight=73.09, density=0.944), Solvent(name='DMSO', keyvalue='dmso', dielectric=36.7, radius=2.41, weight=78.13, density=1.1014), Solvent(name='Ethanol', keyvalue='ethanol', dielectric=24.85, radius=2.27, weight=46.07, density=0.785), Solvent(name='Methanol', keyvalue='methanol', dielectric=33.62, radius=2.0, weight=32.04, density=0.7914), Solvent(name='Nitrobenzene', keyvalue='nitrobenzene', dielectric=35.74, radius=2.73, weight=123.11, density=1.2037), Solvent(name='Tetrahydrofuran', keyvalue='tetrahydrofuran', dielectric=7.6, radius=2.52, weight=72.11, density=0.8892), Solvent(name='Other', keyvalue='other', dielectric=None, radius=None, weight=None, density=None)]
NO_SOLVENT_MODEL = 'None'
SOLVENT_MODELS = {'None': 0, 'PBF': 2, 'SM6': 5, 'SM8': 6}
setup()

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

solventModelChanged()

Called when a new item is selected in the solvent model type menu.

gasPhaseReferenceChanged()

Called when a new radio button is clicked in the gas phase section.

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(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
class schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTabNoOptimized(parent, input_selector=None)

Bases: schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab

A solvation tab that doesn’t allow “Optimized gas-phase structure”.

setup()

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