schrodinger.application.matsci.chargegui module

Classes to aid in assigning charges to atoms in a GUI

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.chargegui.ChargePropertySelector(label, layout=None, tip=None)

Bases: schrodinger.ui.qt.propertyselector.PropertySelectorMenu

A widget that allows the user to pick from a list of properties from a combobox and shows the user the “User” version of the property name (Property Name rather than x_prog_Property_Name)

setVisible(state)

Set the combobox and label visible or hidden

Parameters:state (bool) – Whether to show (True) or hide (False) the widgets

isVisible()

Check if the combobox is visible

Return type:bool Returns:True if visible, False if not

reset()

Reset the combobox

updateProperties(structs)

Fill the combobox with all allowed atom properties available in structs

Parameters:structs (list or None) – If a list, each item is a schrodinger.structure.Structure object. Use None to remove all atom properties but the default

getSelectedProp()

Return the x_prog_property_name form of the selected property

Return type:str or None Returns:The x_prog_property_name value of the selected property or None if no property is selected

static getAllPotentialAtomChargeProperties()

Accumulate a list of all numeric atomic properties in all structures, removing any on the NON_CHARGE_PROPS list

Parameters:structs (list) – Each item is a schrodinger.structure.Structure object. Return type:list Returns:A list of all numeric (r_, i_) atom properties found in structs. The list is sorted alphabetically.

class schrodinger.application.matsci.chargegui.BasisSetSelector(label, basis_set, tip=None, layout=None)

Bases: schrodinger.ui.qt.swidgets.SFrame

A frame that contains a label, line edit and pop up widgets for specifying a basis set

reset()

Reset the widgets

getBasis()

Get the current basis set

Return type:str Returns:The specified basis set

setStructure(struct)

Set the structure for the basis set edit to determine valid basis sets

Parameters:struct (schrodinger.structure.Structure) – The structure to use for checking basis sets

validate()

Check if all widgets are in allowed states

Return type:(False, msg) or True Returns:False and error message if something is wrong, True if everything is OK. Return value is acceptable for an AF2 valiator.

class schrodinger.application.matsci.chargegui.NeighborTreatment(quantum=False, label=None, basis_set='3-21G', layout_type='horizontal', **kwargs)

Bases: schrodinger.ui.qt.swidgets.SFrame

An SFrame that contains a set of widgets that allows the user to pick whether neighboring atoms will be dealt with as atoms, existing charges or on-the-fly ESP charges

methodChanged()

React to changing the treatment method

reset()

Reset all the widgets

updateProperties(structs)

Update the available charge properties based on structs

Parameters:structs (list) – A list of structures to pull charge properties from

validate()

Validate that the widgets are in a proper state

Return type:True or (False, msg) Returns:True if everything is OK or (False, msg) if something is wrong. msg will describe the issue. The return value is consistent with af2 validation methods

getMethod()

Get the current treatment method

Return type:str Returns:The selected treatment method

getBasis()

Get the currently selected basis set if the treatment method requires one

Return type:str or None Returns:A current basis set or None if the current treatment does not use a basis set

getQProp()

Get the currently selected charge property if applicable

Return type:str or None Returns:The current charge property or None if the current treatment does not use a charge property (or none is available). The property will be in the x_prog_property_name format.

getFlags(flag_names=None)

Get the command line flags generated by this set of widgets

Parameters:flag_names (dict) – Used to modify flag names to custom values. Keys are default flag names (BASIS_FLAG, USE_Q_FLAG module constants) and values are the new flag string to use. Return type:list Returns:A list of command line flags and values that capture the current state of these widgets.