schrodinger.application.matsci.reaction_workflow_gui_utils module¶

GUI utilities for reaction workflows.

class schrodinger.application.matsci.reaction_workflow_gui_utils.SequenceData(amin, amax, step, value)¶

Bases: tuple

amax¶: Alias for field number 1

amin¶: Alias for field number 0

step¶: Alias for field number 2

value¶: Alias for field number 3

class schrodinger.application.matsci.reaction_workflow_gui_utils.AtomCollectionFrame(label, tag, n_min, idx_getter, sort=True, layout=None, use_picker=False)¶

Bases: schrodinger.ui.qt.swidgets.SFrame

Manage an atom collection.

showStructures¶: A pyqtSignal emitted by instances of the class.

__init__(label, tag, n_min, idx_getter, sort=True, layout=None, use_picker=False)¶

Create an instance.

Parameters

label (str) – the label for the line edit
tag (str) – an identifying tag
n_min (int) – the minimum number of indices needed when specifying indices
idx_getter (function) – function to get indices
sort (bool) – whether to sort the indices
layout (QLayout or None) – the layout to which this widget will be added or None if there isn’t one
use_picker (bool) – if True then use a picker rather than a define button

layOut()¶: Lay out the widgets.

setIndices(idxs)¶

Set the indices.

Parameters: idxs (list) – the idxs

getIndices()¶

Get the indices.

Return type: list
Returns: the indices

setStructures(structs)¶

Set the structures.

Parameters: structs (list) – contains schrodinger.structure.Structure

setOptionsFromRepresentativeStructure()¶: Set GUI options according to the properties of the representative structure.

isValid()¶

Validate it.

Raise: rxnwfu.InvalidInput if there is a formatting issue

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.ConformerSelection(*args, show_selection_method=False, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SGroupBox

Manage selection of conformers.

MAX_N_CONFORMERS_LABEL = 'Maximum number of conformers:'¶

MIN_N_CONFORMERS_LABEL = 'Minimum number of conformers:'¶

__init__(*args, show_selection_method=False, **kwargs)¶

Parameters: show_selection_method (bool) – whether to show the selection method

updateNConformersLabel()¶: Update the N conformers label.

getRelEnergy()¶

Return the relative energy in kJ/mol.

Return type: float or None
Returns: the relative energy in kJ/mol or None if not using relative energies

getCmd()¶

Return the command line options.

Return type: list
Returns: the command line options which are flags and values

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.ConformationalSearch(*args, show_restrain_atoms=False, show_selection_method=False, show_return_files=True, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SGroupBox

Manage conformational search options.

__init__(*args, show_restrain_atoms=False, show_selection_method=False, show_return_files=True, **kwargs)¶

Create an instance.

Parameters

show_restrain_atoms (bool) – whether to show the restrain atoms widget
show_selection_method (bool) – whether to show the selection method
show_return_files (bool) – whether to show the return files checkbox

csearchEngineChanged()¶: React to a change in conformational search engine.

getSkipEtaRotamers()¶

Return True if eta-rotamers are to be skipped.

Return type: bool
Returns: True if eta-rotamers are to be skipped

getCmd()¶

Return the command line options.

Return type: list
Returns: the command line options which are flags and values

validate(sts)¶

Validate.

Parameters: sts (list[schrodinger.structure.Structure]) – the structures

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.UniformSequence(label, units, start_data, step_data, num_data, parent_layout=None)¶

Bases: schrodinger.ui.qt.swidgets.SFrame

Manage a uniform sequence using three spin boxes.

__init__(label, units, start_data, step_data, num_data, parent_layout=None)¶

Create an instance.

Parameters

label (str) – the label
units (str) – the units
start_data (SequenceData) – the start data
step_data (SequenceData) – the step data
num_data (SequenceData) – the num data
parent_layout (QLayout) – the layout to which this widget will be added

getValues()¶

Return a tuple of current values.

Return type: tuple(float, float, int)
Returns: a (start, step, num) tuple

setEnabled(state)¶

Set the enabled state.

Parameters: state (bool) – True if enabled

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.QMPreOptimization(*args, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SGroupBox

Manage QM pre-optimization.

__init__(*args, **kwargs)¶

Accepts all arguments normally given for a QGroupBox

Parameters

layout_type (string) – Module constants VERTICAL, HORIZONTAL or GRID, for the type of internal layout
parent_layout (QBoxLayout) – The layout to place this SGroupBox into
checkable (bool) – Whether the groupbox is checkable, False by default
checked (bool) – Whether the groupbox should be checked if checkable. Default is True for checkable groupboxes.
tip (str) – The tooltip to apply to the group box
flat (bool) – whether to apply FlatStyle
command (function) – function to call when the checkbox emits a ‘clicked()’ signal
toggled_command (function) – function to call when the checkbox emits a ‘toggled()’ signal

getCmd()¶

Return the command line options.

Return type: list
Returns: the command line options which are flags and values

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.Jaguar(master, title, show_temp_and_press=True, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SGroupBox

Manage Jaguar options.

__init__(master, title, show_temp_and_press=True, **kwargs)¶

Create an instance.

Parameters

master (QtWidgets.QWidget) – the widget that this groupbox belongs to
title (str) – The title for the groupbox
show_temp_and_press (bool) – whether to show the temperature and pressure widgets

getCmd()¶

Return the command line options.

Return type: list
Returns: the command line options which are flags and values

reset()¶: Reset it.

schrodinger.application.matsci.reaction_workflow_gui_utils.get_entries(error, included_entry=False)¶

Return either selected entries or the included entry from the Maestro project table provided that the entries have atoms.

Parameters

error (function) – function to call on error
included_entry (bool) – if True then consider the included entry, if False then consider selected entries

Return type

schrodinger.structure.Structure or list[schrodinger.structure.Structure] or None

Returns

None if any of the entries is missing atoms otherwise a single entry when included_entry or list of entries by default

class schrodinger.application.matsci.reaction_workflow_gui_utils.RGroupFileFrame(layout=None)¶

Bases: schrodinger.ui.qt.swidgets.SFrame

Manage a widget for specifying R-group files.

IMPORT_FILE_COL = 0¶

FILE_NAME_COL = 1¶

DIALOG_ID = 'IMPORT_RGROUP_FILE_ID'¶

filesChanged¶: A pyqtSignal emitted by instances of the class.

__init__(layout=None)¶

Create an instance.

Parameters: layout (QLayout or None) – the layout to which this widget will be added or None if there isn’t one

layOut()¶: Lay out the widgets.

tableSelectionChanged()¶: React to a change in the table’s selection.

deleteSelectedRows()¶: Delete the selected rows.

addRow()¶

Add a row to the table.

Return type: int
Returns: the index of the added row

isFileValid(path)¶

Check if the given R-group file is valid.

Raises: rxnwfu.InvalidInput – if the file is not valid

importFile(idx)¶

Import a file.

Parameters: idx (int) – the index of the row for which to import the file

rows()¶

Return row indices of the table.

Return type: generator
Returns: the row indices

copyFiles(path='')¶

Copy the files.

Parameters: path (str) – the path to which the files will be copied, if not provided will be the cwd
Raises: RuntimeError – if the path is not valid

getFileNames()¶

Return the file names.

Return type: dict
Returns: keys are row indices, values are the file names

numberFiles()¶

Return the number of files.

Return type: int
Returns: the number of files

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.Descriptor(*args, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SGroupBox

Manage a widget for calculating descriptors.

BOLTZMANN = 'Boltzmann average'¶

BOLTZMANN_TIP = 'Boltzmann average the descriptors over conformers using the specified energy structure property and output the average on the lowest energy representative conformer.'¶

LOWEST = 'Lowest energy'¶

LOWEST_TIP = 'Only output descriptors for the lowest energy representative conformer.'¶

__init__(*args, **kwargs)¶: Create an instance.

layOut()¶: Lay out the widgets.

isValid()¶

Check if the energy property is valid.

Return type: bool or (bool, str)
Returns: The bool is True if everything is OK, False if not. str is given if a dialog should pop up to show the given message. If bool is True, str will post as Question dialog.

getCmd()¶

Return the command line options.

Return type: list
Returns: the command line options which are flags and values

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.ColorPairFrame(layout=None, first_text='', second_text='', first_default_color=(255, 165, 0), second_default_color=(0, 0, 255), command=None, tip='')¶

Bases: schrodinger.ui.qt.swidgets.SFrame

Manage a widget for specifying a color pair.

__init__(layout=None, first_text='', second_text='', first_default_color=(255, 165, 0), second_default_color=(0, 0, 255), command=None, tip='')¶

Create an instance.

Parameters

layout (QLayout or None) – the layout to which this widget will be added or None if there isn’t one
first_text (str) – the text for the first color button
second_text (str) – the text for the second color button
first_default_color (tuple) – the default color for the first color button as an RGB tuple
second_default_color (tuple) – the default color for the second color button as an RGB tuple
command (function or None) – slot for the color button’s clicked signal which takes two arguments, first and second, for the current RGB color tuples
tip (str) – the tooltip for this widget

layOut(first_text='', second_text='', first_default_color=(255, 165, 0), second_default_color=(0, 0, 255), command=None, tip='')¶

Lay out the widgets.

Parameters

first_text (str) – the text for the first color button
second_text (str) – the text for the second color button
first_default_color (tuple) – the default color for the first color button as an RGB tuple
second_default_color (tuple) – the default color for the second color button as an RGB tuple
command (function or None) – slot for the color button’s clicked signal which takes two arguments, first and second, for the current RGB color tuples
tip (str) – the tooltip for this widget

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.WorkspaceSuperpositionFrame(layout=None, btn_text='Superpose', tip='', command=None, first_name='first', second_name='second')¶

Bases: schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackWidgetMixin, schrodinger.ui.qt.swidgets.SFrame

Manage a widget for showing a pair of superposed structures in the Maestro workspace.

__init__(layout=None, btn_text='Superpose', tip='', command=None, first_name='first', second_name='second')¶

Create an instance.

Parameters

layout (QLayout or None) – the layout to which this widget will be added or None if there isn’t one
btn_text (str) – the text for superpose button
tip (str) – the tooltip for this widget
command (function or None) – slot for the superposition button’s clicked signal
first_name (str) – a name for identifying the first structure
second_name (str) – a name for identifying the second structure

layOut(btn_text='', tip='', command=None)¶

Lay out the widgets.

Parameters

btn_text (str) – the text for superpose button
tip (str) – the tooltip for this widget
command (function or None) – slot for the superposition button’s clicked signal

isValid(first_st, first_idxs, second_st, second_idxs)¶

Validate it, return True if valid, (False, msg) otherwise.

Parameters

first_st (schrodinger.structure.Structure) – the first structure
first_idxs (list) – superposition indices for the first structure
second_st (schrodinger.structure.Structure) – the second structure
second_idxs (list) – superposition indices for the second structure

Return type

bool or pair tuple

Returns

True if valid, (False, msg) otherwise

static getProjectStructure(st)¶

Return the current project row structure for the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: schrodinger.structure.Structure
Returns: the project row structure

showSuperposed(first_st, first_idxs, second_st, second_idxs)¶

Show the superposed structures in the Maestro workspace.

Parameters

first_st (schrodinger.structure.Structure) – the first structure
first_idxs (list) – superposition indices for the first structure
second_st (schrodinger.structure.Structure) – the second structure
second_idxs (list) – superposition indices for the second structure

reset()¶: Reset it.

class schrodinger.application.matsci.reaction_workflow_gui_utils.RateConstants(*args, **kwargs)¶

Bases: schrodinger.ui.qt.swidgets.SGroupBox

Manage rate constants.

STANDARD = 'Standard'¶

STANDARD_TIP = 'Use this option to report the rate constant(s) for the rate determining step(s) of the reaction using canonical transition state theory.'¶

EXTENDED = 'Extended'¶

EXTENDED_TIP = 'Use this option to report the rate constants using a more extensive analysis that is based on transition state theory.'¶

__init__(*args, **kwargs)¶

Accepts all arguments normally given for a QGroupBox

Parameters

layout_type (string) – Module constants VERTICAL, HORIZONTAL or GRID, for the type of internal layout
parent_layout (QBoxLayout) – The layout to place this SGroupBox into
checkable (bool) – Whether the groupbox is checkable, False by default
checked (bool) – Whether the groupbox should be checked if checkable. Default is True for checkable groupboxes.
tip (str) – The tooltip to apply to the group box
flat (bool) – whether to apply FlatStyle
command (function) – function to call when the checkbox emits a ‘clicked()’ signal
toggled_command (function) – function to call when the checkbox emits a ‘toggled()’ signal

getFlags()¶

Return command line flags.

Raises: AssertionError – unknown option
Return type: list
Returns: command line flags

reset()¶: Reset.

class schrodinger.application.matsci.reaction_workflow_gui_utils.ReactionWorkflowFrame(layout=None)¶

Bases: schrodinger.ui.qt.swidgets.SFrame

Manage a widget for reaction workflow options.

__init__(layout=None)¶

Create an instance.

Parameters: layout (QLayout or None) – the layout to which this widget will be added or None if there isn’t one

layOut()¶: Lay out the widgets.

getCmd(job_name=None)¶

Return the command line options.

Parameters: job_name (str or None) – the job name if there is one
Return type: list
Returns: the command line options which are flags and values

closeEvent(event)¶

React to a close event.

Parameters: event (QtGui.QCloseEvent) – the event

projectUpdated()¶: React to a change in the project.

resetJMSWF()¶: Reset the JMSWF.

reset()¶: Reset it.

checkRxnWFStructures()¶

Check the reaction workflow structures.

Return type: bool or (bool, str)
Returns: The bool is True if everything is OK, False if not. str is given if a dialog should pop up to show the given message. If bool is True, str will post as Question dialog.