schrodinger.application.matsci.ml_formulations_gui_utils module¶

Utilities for Machine Learning Formulations GUI

schrodinger.application.matsci.ml_formulations_gui_utils.validate_smiles(smiles)¶

A cached function that wraps the adapter.validate_smarts function to validate the smiles string

Parameters: smiles (str) – The smiles string to validate
Returns: True if the smiles is valid, False otherwise
Return type: bool

class schrodinger.application.matsci.ml_formulations_gui_utils.FormulationData(formulation_info)¶

Bases: PyQt6.QtCore.QObject

Class to hold data for a formulation, the data is passed to widgets as references so that it can be edited by the user.

properties: A dictionary of the properties of the formulation

compositions: A dictionary with the component name as the key and: composition as the value
info: A dictionary of the formulation information where key is the: column name and value is the value of the column of the formulation in the formulation CSV. This used to write the formulation data back to the CSV

property_updated is emitted when the user updates the value of a property in the formulation

property_updated¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(formulation_info)¶

Initialize the FormulationData

Parameters: formulation_info (dict) – A dictionary of the formulation information where key is the column name and value is the value of the column of the formulation in the formulation CSV

fixSmiles(smiles, index)¶

Helper function for the constructor to fix the smiles string and validate it. There can be 3 cases: 1. User provided a valid smiles string, return the smiles and True 2. User provided a compound name (invalid smiles), return the name and False 3. User used predefined missing smiles as a placeholder, return the component name and False

Parameters

smiles (str) – The smiles string to fix
index (str) – The index of the component

Returns

The fixed smiles string and whether the smiles is valid

Return type

tuple(str, bool)

getComponentKey(component)¶

Get the key for the given component from the name of the component

Parameters: component (str) – The component to get the key for
Returns: The key for the component
Return type: str

getComposition()¶

Get the composition of the formulation

Returns: The composition of the formulation where the keys are the COMPONENT and the values are the composition
Return type: dict

getProperties()¶

Get the properties of the formulation

Returns: The properties of the formulation where the keys are the property names and the values are the property values
Return type: dict

addProperty(prop, value)¶

Add a property to the formulation

Parameters

prop (str) – The name of the property to add
value (float) – The value of the property

updateComposition(name, composition)¶

Update the composition of the formulation

Parameters

name (str) – The name of the component to update
composition (float) – The new composition of the component

updateComponent(old_name, new_name)¶

Update the name of the component in the formulation

Parameters

old_name (str) – The old name of the component
new_name (str) – The new name of the component

Raises

ValueError – If the new name already exists, due to duplicate

updateProperties(prop, value)¶

Update the property value of the formulation

Parameters

prop (str) – The name of the property to update
value (float) – The new value of the property

removeProperty(prop)¶

Remove the property from the formulation

Parameters: prop (str) – The name of the property to remove

getCSVData()¶

Get the data for the formulation in the format to write to the CSV file

Returns: The data with the keys as SMILES, COMPOSITION, and Properties as keys and the values as the values of the formulation. The values are empty strings if the value in SMILES is not a valid smiles.
Return type: dict

class schrodinger.application.matsci.ml_formulations_gui_utils.FormulationCSVReader¶

Bases: object

Helper class to read the formulation CSV file

validateHeader(header, required_props=None)¶

Validate the header of the csv file

Parameters

header (list) – The list of header values in the csv file
required_props (list) – The list of required properties that must be present in the csv file

Raises

ValueError – If the headers in the csv file are not valid

getFormulationsFromCSV(csv_reader, required_props=None, skip_props=None)¶

Get the formulations from the CSV reader

Parameters

csv_reader (csv.DictReader) – The csv reader object
required_props (list) – The list of required properties that must be
skip_props (list) – The list of properties to skip

Returns

The list of formulations

Return type

list(FormulationData)

readCSVData(filename, required_props=None)¶

Read the data from the CSV file

Parameters

filename (str) – The filename of the CSV file
required_props (list) – The list of required properties that must be present in the csv file. If None, there will be no requirement of properties

Returns

The list of formulations

Return type

list(FormulationData)

readCSVIOData(csv_io, skip_props=None)¶

Read the data from the CSV StringIO object

Parameters

csv_io (io.StringIO) – The StringIO object of the CSV file
skip_props (list) – The list of properties to skip

Returns

The list of formulations

Return type

list(FormulationData)

class schrodinger.application.matsci.ml_formulations_gui_utils.ScrollableAreaWidget(v_scroll_bar=False)¶

Bases: PyQt6.QtWidgets.QWidget

Scrollable data area that holds the formulation data

bottom_reached: signal is emitted when the bottom of the scroll area is reached

bottom_reached¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(v_scroll_bar=False)¶

Initialize the ScrollableAreaWidget

Parameters: v_scroll_bar (bool) – Whether to show the vertical scroll bar

setupInternalWidget()¶: Setup the internal widget that holds the data in the scroll area

connectVScrollSync(other_scroll_area)¶

Connect the scroll current scroll area to another scroll area to allow for synchronized vertical scrolling

Parameters: other_scroll_area (ScrollableAreaWidget) – The other scroll area to connect to

connectHScrollSync(other_scroll_area)¶

Connect the scroll current scroll area to another scroll area to allow for synchronized horizontal scrolling

Parameters: other_scroll_area (ScrollableAreaWidget) – The other scroll area to connect to

class schrodinger.application.matsci.ml_formulations_gui_utils.DataRowWidget(layout)¶

Bases: PyQt6.QtWidgets.QWidget

Widget to hold the widgets for a row in the formulation table view. The widget has three sections:

Top section is the frame to display the warnings. Middle section is the frame to display the data. Bottom section is the frame to display the widgets to edit the data. The top and bottom sections are hidden by default.

__init__(layout)¶

Initialize the DataRowWidget

Parameters: layout (QtWidgets.QLayout) – The layout to add the widget to

setRowMessage(message)¶

Set the message to display in the top section of the widget

Parameters: message (str) – The message to display

addDataColumnWidget(widget, fixed_width)¶

Add a widget to the middle section of the widget

Parameters

widget (QtWidgets.QWidget) – The widget to add in the horizontal layout
fixed_width (int) – The width of the widget

addEditColumnWidget(widget)¶

Add a widget to the bottom section of the widget

Parameters: widget (QtWidgets.QWidget) – The widget to add in the horizontal layout

finalizeRowLayout()¶: Hide the top and bottom sections of the widget and add stretch to the sections once all the widgets have been added

toggleMessageVisibility(state)¶

Toggle the visibility of the top section of the widget

Parameters: state (bool) – The state to set the visibility to

toggleEditVisibility()¶: Toggle the visibility of the bottom section of the widget

class schrodinger.application.matsci.ml_formulations_gui_utils.SketcherSMILESDialog(title: str, parent=None)¶

Bases: schrodinger.ui.sketcher_smarts_dialog.SketcherSMARTSDialog

Dialog to show SMILES in sketcher and get the updated SMILES from sketcher

smiles_accepted is emitted when the user accepts the dialog and the new SMILES value is passed as an argument

smiles_accepted¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

accept()¶: Accept the dialog

class schrodinger.application.matsci.ml_formulations_gui_utils.CustomTooltip(text)¶

Bases: PyQt6.QtWidgets.QWidget

A custom tooltip that can be used to display a message

__init__(text)¶

Initialize the tooltip

Parameters: text (str) – The text to display in the tooltip

class schrodinger.application.matsci.ml_formulations_gui_utils.ValueLabel(text, parent_width, layout=None, fixed_width=None, **kwargs)¶

Bases: PyQt6.QtWidgets.QLabel

A label that is used to display a formulation property values

__init__(text, parent_width, layout=None, fixed_width=None, **kwargs)¶

Initialize the label

Parameters

text (str) – The text to display in the label
parent_width (int) – The width of the parent widget
layout (QtWidgets.QLayout) – The layout to add the label to
fixed_width (int) – The fixed width of the label

setElidedText(text)¶

Set the text of the label and elide it if it is too long. Keep the original text as the tooltip

Parameters: text (str) – The text to display in the label

class schrodinger.application.matsci.ml_formulations_gui_utils.ClickableLabel(text, command, parent_width, layout=None, fixed_width=None)¶

Bases: schrodinger.application.matsci.ml_formulations_gui_utils.ValueLabel

A label that behaves like a link and can be clicked

clicked¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(text, command, parent_width, layout=None, fixed_width=None)¶

Parameters

text (str) – The text to display in the label
command (function) – The command to run when the label is clicked
parent_width (int) – The width of the parent widget
layout (QtWidgets.QLayout) – The layout to add the label to
fixed_width (int) – The fixed width of the label

setToolTip(text)¶

Set the tooltip text for the label

Parameters: text (str) – The text to display in the tooltip

updateStyle(color, font_weight='normal')¶

Update the style of the label

Parameters

color (str) – The color of the label
font_weight (str) – The font weight of the label

hideCustomTooltip()¶: Hide the custom tooltip

enterEvent(event)¶

Update the style of the label when the mouse enters the label to behave like hover in a link

Parameters: event (QtCore.QEvent) – The enter event

leaveEvent(event)¶

Update the style of the label when the mouse leaves the label

Parameters: event (QtCore.QEvent) – The leave event

mousePressEvent(event)¶

Emit the clicked signal when the label is clicked

Parameters: event (QtCore.QEvent) – The mouse press event

class schrodinger.application.matsci.ml_formulations_gui_utils.ValueEdit(text, command, fixed_width, validator, read_only=False)¶

Bases: schrodinger.ui.qt.swidgets.SLineEdit

Line edit widget that is used to edit the formulation values

_editing_finished is emitted when the user finishes editing the value and the new value is passed as an argument

__init__(text, command, fixed_width, validator, read_only=False)¶

Parameters

text (str) – The text to display
command (function) – The command to run when the text is changed
fixed_width (int) – The width of the line edit widget
validator (QtGui.QValidator) – The validator to use for the line edit
read_only (bool) – Whether the line edit is read only

class schrodinger.application.matsci.ml_formulations_gui_utils.ClickableProgressBar(value, layout)¶

Bases: PyQt6.QtWidgets.QProgressBar

Progress bar that emits a signal when clicked on clicked

clicked¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(value, layout)¶

Initialize the progress bar

Parameters

value (int) – The value to set the progress bar to
layout (QtWidgets.QLayout) – The layout to add the progress bar to

setValue(value)¶: Override the setValue method to set the tooltip to the value

mousePressEvent(event)¶: Override the mousePressEvent to emit a signal when clicked

class schrodinger.application.matsci.ml_formulations_gui_utils.ComponentsWidget(name, composition, command)¶

Bases: PyQt6.QtWidgets.QWidget, schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin

Widget to hold the component name (can be SMILES) string and the progress bar to display the composition of the component

name_changed is emitted when the user changes the name string using: the sketcher and old and new names are passed as arguments

name_changed¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(name, composition, command)¶

Parameters

name (str) – The name string to display
composition (float) – The composition of the component in the formulation
command (function) – The command to run when the progress bar is clicked

updateComposition(composition)¶

Update the composition of the component

Parameters: composition (float) – The new composition

updateName(name)¶

Update the component name

Parameters: name (str) – The new name of the component

showSketcher()¶: Show the sketcher dialog to edit the SMILES string

class schrodinger.application.matsci.ml_formulations_gui_utils.FormulationRowManager(formulation, composition_layout, properties_layout)¶

Bases: object

Class to manage the widgets in a row of the formulation table view

__init__(formulation, composition_layout, properties_layout)¶

Initialize the FormulationRowManager

Parameters

formulation (ml_formulations_gui_utils.FormulationData) – The formulation data to display in the row
composition_layout (QtWidgets.QLayout) – The layout to add the composition widgets to
properties_layout (QtWidgets.QLayout) – The layout to add the properties widgets to

getTotalComposition()¶

Get the total composition of the formulation

Returns: The total composition of the formulation
Return type: float

addCompositionRow()¶: Add the composition widgets to the composition row

addPropertiesRow()¶: Add the properties values to the properties row

toggleMessageVisibility(state=None)¶: Toggle the visibility of the message in the row

toggleEditVisibility()¶: Toggle the visibility of the edit widgets in the row

compositionUpdated(composition_widget, value)¶

Update the composition of the component in the formulation

Parameters

composition_widget (ComponentsWidget) – The widget that was updated
value (str) – The new value of the composition

nameUpdated(old_name, new_name)¶

Update the name of the component in the formulation

Parameters

old_name (str) – The old name of the component
new_name (str) – The new name of the component

deleteLater()¶: Delete the widgets in the row

class schrodinger.application.matsci.ml_formulations_gui_utils.ScrollableAreaManager(grid_layout, scroll_update)¶

Bases: object

Manager for the scrollable area that holds the formulation data that are separated into two different areas: composition and properties

__init__(grid_layout, scroll_update)¶

Initialize the scrollable area manager

Parameters: grid_layout (QtWidgets.QGridLayout) – layout of the parent widget

syncPropertyTitlesHScroll(property_titles)¶

Connect the property titles to the scrollable areas to allow for synchronized horizontal scrolling

Parameters: property_titles (PropertyTitlesArea) – The property titles widget

addRow(formulation)¶

Add the formulation data to the respective areas

Parameters: formulation (ml_formulations_gui_utils.FormulationData) – The formulation data to add to the widgets

reset()¶: Reset the scrollable areas

class schrodinger.application.matsci.ml_formulations_gui_utils.PropertyTitlesArea(properties)¶

Bases: schrodinger.application.matsci.ml_formulations_gui_utils.ScrollableAreaWidget

Widget to hold the property titles for the formulation table

property_clicked is emitted when the user clicks on a property title and: the property name is passed as an argument

property_clicked¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__(properties)¶

Initialize the PropertyTitles widget

Parameters: properties (list) – A list of property names

setupInternalWidget()¶: Override the setupInternalWidget to set the internal widget that holds the property titles

class schrodinger.application.matsci.ml_formulations_gui_utils.FormulationTableWidget¶

Bases: PyQt6.QtWidgets.QWidget

Widget that displays the formulation data in a table format

properties_row_clicked: signal emitted when the properties label is clicked: and the property clicked is passed as an argument

property_labels_clicked¶

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

__init__()¶: Initialize the formulation table widget

displayData(formulations)¶

Display the formulation data in the table

Parameters: formulations (list(ml_formulations_gui_utils.FormulationData)) – list of formulations

loadNextFormulations()¶: Batch load the formulations to the table to avoid freezing the UI

reset()¶: Reset the widgets

class schrodinger.application.matsci.ml_formulations_gui_utils.FormulationPlotFrame¶

Bases: schrodinger.ui.qt.swidgets.SFrame, schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin

Widget that displays the distribution of a property in the formulations

NONE = '(none)'¶

R_2 = 'R$^2$'¶

RMSE = 'RMSE'¶

PEARSON_R = "Pearson's $r$"¶

__init__()¶: Initialize the widget

statsEnabled(state)¶

Enable/disable the statistics checkboxes

Parameters: state (bool) – The state to set the checkboxes to

statsChecked(state)¶

Set the checked state of the statistics checkboxes

Parameters: state (bool) – The state to set the checkboxes to

setProperty(property_name)¶

Set the property to display distribution for

Parameters: property_name (str) – name of the property

loadData(formulations)¶

Load the formulations data

Parameters: formulations (list(ml_formulations_gui_utils.FormulationData)) – list of formulations

getData(property_name)¶

Get the data for the given property

Parameters: property_name (str) – name of the property
Returns: list of property values
Return type: list
Raises: ValueError – if the property name is not a number

getStats(prop_data)¶

Get the statistics for the given property data if the statistics are requested

Parameters: prop_data (list(list)) – list of property values where the first list is the x values and the second list is the y values
Returns: dictionary of statistics where the key is the name of the statistic and the value is the value of the statistic
Return type: dict

addStatsToPlot(plot_data)¶

Add the statistics to the plot as a legend if the statistics are requested

Parameters: plot_data (list(list)) – list of property values where the first list is the

plotScatter()¶: Plot scatter plot of two selected properties.

plotHistogram()¶: Plot the frequency distribution of the selected property

replot()¶: Plot the distribution of the selected property

resetScatter()¶: Reset the scatter plot

reset()¶: Reset the widget

class schrodinger.application.matsci.ml_formulations_gui_utils.FormulationsDataTab(program_name)¶

Bases: schrodinger.ui.qt.swidgets.SFrame

Widget that displays the formulations CSV data in a table format along with the plot

MIN_PLOT_WIDTH = 500¶

INITIAL_SPLIT_SIZE = (100, 100)¶

__init__(program_name)¶

Initialize the widget

Parameters: program_name (str) – The name of the program

showPropertyPlot(property_name)¶: Show the distribution plot frame for the selected property

loadData(formulations)¶

Load the formulations data in the table

Parameters: formulations (list(ml_formulations_gui_utils.FormulationData)) – list of formulations

exportData(filename=None)¶

Export the formulations data to a CSV file

Parameters: filename (str) – The name of the file to export the data to

validateFormulations()¶

Validate the formulations data

Returns: Whether the formulations data is valid. If not valid, the error message is also returned
Return type: bool or bool, str

reset()¶: Reset the widget