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 onefirst_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 onebtn_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 structurefirst_idxs (list) – superposition indices for the first structure
second_st (
schrodinger.structure.Structure
) – the second structuresecond_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
- 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 structurefirst_idxs (list) – superposition indices for the first structure
second_st (
schrodinger.structure.Structure
) – the second structuresecond_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 = '<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.