Package schrodinger :: Package application :: Package jaguar :: Package gui :: Package tabs :: Module solvation_tab :: Class SolvationTab

[frames] | no frames]

Class SolvationTab

PyQt4.QtGui.QWidget --+        
                      |        
       base_tab.BaseTab --+    
                          |    
                 SolventTab --+
                              |
                             SolvationTab

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

Instance Methods

[hide private]

setup(self)
Perform tab specific initialization.

solventModelChanged(self)
Called when a new item is selected in the solvent model type menu.

gasPhaseReferenceChanged(self)
Called when a new radio button is clicked in the gas phase section.

dict

getMmJagKeywords(self)
Return all keywords that should be put into the mmjag handle.

dict

_getSolventModelKeyword(self)
Get the solvent model keyword

dict

_getOtherSolventKeywords(self)
Get the dielectric and probe radius keywords if the solvent type is set to "other".

dict

_getGasPhaseKeywords(self)
Get the gas phase reference energy keywords

loadSettings(self, jag_input)
Restore tab settings from mmjag keywords.

_checkSolventSettings(self, jag_input)
Make sure that the solvent settings are consistent.

_loadSolventModelAndTypeSettings(self, jag_input)
Load the solvent model and solvent type settings.

_loadOtherSolventSettings(self, jag_input)
Load the solvent settings for an "other" solvent

_loadGasPhaseSettings(self, jag_input)
Load the gas phase reference energy settings

Inherited from SolventTab: calculateProbeRadius, solventTypeChanged

Inherited from SolventTab (private): _getSolventTypeKeyword

Inherited from base_tab.BaseTab: __init__, activate, deactivate, error, getDefaultKeywords, loadPerAtomSettings, reset, saveSettings, validate, warning

Inherited from base_tab.BaseTab (private): _populateUi

Class Variables

[hide private]

str NAME = "Solvation"
The name of the tab

tuple UI_MODULES = ui.solvation_solvent_model_ui, ui.solvent_tab_ui,...
A tuple of ui modules defining the tab widgets.

SHOW_DIELECTRIC = True
hash(x)

SOLVENTS = [Solvent("Water", mm.MMJAG_SOLVENT_WATER, 80.37, 1....

SOLVENT_MODELS = OrderedDict([("None", mm.MMJAG_ISOLV_OFF), ("...

Inherited from SolventTab: HELP_TOPIC

Instance Variables

[hide private]

Inherited from base_tab.BaseTab: input_selector, task_name, ui

Method Details

[hide private]

setup(self)

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

Overrides: base_tab.BaseTab.setup: (inherited documentation)

getMmJagKeywords(self)

Return all keywords that should be put into the mmjag handle. This function should be defined in subclasses.

Returns: dict

All keywords that should be put into the mmjag handle

Raises:

schrodinger.application.jaguar.gui.utils.JaguarSettingError - If any settings are invalid.

Overrides: base_tab.BaseTab.getMmJagKeywords

(inherited documentation)

_getSolventModelKeyword(self)

Get the solvent model keyword

Returns: dict: A dictionary of keywords

_getOtherSolventKeywords(self)

Get the dielectric and probe radius keywords if the solvent type is set to "other".

Returns: dict: If the solvent type is set to "Other", a dictionary of dielectric and probe radius keywords. Otherwise, an empty dictionary.

Note: The molecular weight and density options are used to compute the probe radius

_getGasPhaseKeywords(self)

Get the gas phase reference energy keywords

Returns: dict: A dictionary of keywords

loadSettings(self, jag_input)

Restore tab settings from mmjag keywords. This function should be defined in subclasses.

Parameters:

jag_input - The Jaguar settings to base the tab settings on

Overrides: base_tab.BaseTab.loadSettings

(inherited documentation)

_checkSolventSettings(self, jag_input)

Make sure that the solvent settings are consistent. Issue warnings for any inconsistencies.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar settings to check

_loadSolventModelAndTypeSettings(self, jag_input)

Load the solvent model and solvent type settings. If solvent model is not PBF, then a solvent type of water is used regardless of the jag_input setting.

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar settings to load

_loadOtherSolventSettings(self, jag_input)

Load the solvent settings for an "other" solvent

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar settings to load

Note: If we load probe radius, we have to clear the molecular weight and density values, since they no longer match the probe radius and will overwrite it the next time calculateProbeRadius() is called. As a result, we only load the probe radius if it's different than what's already in the panel so that we don't unnecessarily clear the molecular weight and density values.

_loadGasPhaseSettings(self, jag_input)

Load the gas phase reference energy settings

Parameters:

jag_input (schrodinger.application.jaguar.input.JaguarInput) - The Jaguar settings to load

Class Variable Details

[hide private]

UI_MODULES

A tuple of ui modules defining the tab widgets. These ui modules should be listed top to bottom. Optionally, a tuple of (tab class, attribute name) may be listed instead of a ui file to include a subtab.

Type:: tuple

Value:

ui.solvation_solvent_model_ui, ui.solvent_tab_ui, ui.solvation_gas_pha
se_ui

SOLVENTS

Value:

[Solvent("Water", mm.MMJAG_SOLVENT_WATER, 80.37, 1.4, 18.02, 0.99823),
 Solvent("Acetonitrile", mm.MMJAG_SOLVENT_ACETONITRILE, 37.5, 2.19, 41
.05, 0.777), Solvent("Benzene", mm.MMJAG_SOLVENT_BENZENE, 2.284, 2.60,
 78.12, 0.87865), Solvent("Carbon tetrachloride", mm.MMJAG_SOLVENT_CAR
BON_TETRACHLORIDE, 2.238, 2.67, 153.82, 1.5940), Solvent("Chlorobenzen
e", mm.MMJAG_SOLVENT_CHLOROBENZENE, 5.708, 2.72, 112.56, 1.1058), Solv
ent("Chloroform", mm.MMJAG_SOLVENT_CHLOROFORM, 4.806, 2.52, 119.38, 1.
4832), Solvent("Cyclohexane", mm.MMJAG_SOLVENT_CYCLOHEXANE, 2.023, 2.7
...

SOLVENT_MODELS

Value:

OrderedDict([("None", mm.MMJAG_ISOLV_OFF), ("PBF", mm.MMJAG_ISOLV_PBF)
, ("SM6", mm.MMJAG_ISOLV_SM6), ("SM8", mm.MMJAG_ISOLV_SM8),])