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: 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: 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: 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: 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: 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: 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: 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: 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: 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: MaestroCallbackWidgetMixin, 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: 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: 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.