schrodinger.application.matsci.reaction_workflow_gui_utils module

GUI utilities for reaction workflows.

Copyright Schrodinger, LLC. All rights reserved.

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

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__(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

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__(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 = '<nobr>Boltzmann average the descriptors over conformers </nobr>using the specified energy structure property and output the average on the lowest energy representative conformer.'
LOWEST = 'Lowest energy'
LOWEST_TIP = '<nobr>Only output descriptors for the lowest energy representative </nobr>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
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
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 = '<nobr>Use this option to report the rate constant(s) </nobr>for the rate determining step(s) of the reaction using canonical transition state theory.'
EXTENDED = 'Extended'
EXTENDED_TIP = '<nobr>Use this option to report the rate constants using </nobr>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.