schrodinger.application.matsci.guibase module

GUI classes/function shared by multiple Materials Science panels.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.guibase.MultiJobApp(**kwargs)

Bases: schrodinger.ui.qt.appframework2.af2.JobApp

Subclass of AF2 JobApp that allows launching multiple simultanious jobs.

Every panel subclassing this should re-implement getJobCount() and getJobSpec() methods. A start method should NOT be implemented.

validateJobCount(**kwargs)
showLaunchStatus(num_succeeded, njobs)

Show a label at the bottom of the panel with status of the launch.

getJobCount()

Over-ride in the subclass to return the number of jobs that the user would like to start. Used for validation.

:return the number of jobs that the user requests. :rtype: int

multiJobStart()

Custom “start” method. For each job, creates a job sub-directory, cd’s into it, and launches the job there.

:return list of return values from self.launchFromJobSpec() calls.

Each value is a Job object or False, in start mode, or True/False in write mode.

getValidatedOPLSDir(oplsdir=None)

Validate the existing oplsdir or get a requested oplsdir from the user’s selection in the force field selector widget

Parameters

oplsdir (str) – The currently requested oplsdir

Return type

False, None or str

Returns

False if no valid oplsdir can be found, None if there is no custom dir requested, or the path to the custom directory

launchFromJobSpec(sub_jobname, job_num, oplsdir=None)

Re-implemented from JobApp; options and behavior is somewhat differnt.

Starts or write the command for the given subjob.

Returns

Job object on successful start; True on successful write, False on failure.

DrawChildren = 2
DrawWindowBackground = 1
IGNORE_DELAYED_CALLBACKS = False
IgnoreMask = 4
class PaintDeviceMetric

Bases: int

PdmDepth = 6
PdmDevicePixelRatio = 11
PdmDevicePixelRatioScaled = 12
PdmDpiX = 7
PdmDpiY = 8
PdmHeight = 2
PdmHeightMM = 4
PdmNumColors = 5
PdmPhysicalDpiX = 9
PdmPhysicalDpiY = 10
PdmWidth = 1
PdmWidthMM = 3
class RenderFlag

Bases: int

class RenderFlags

Bases: sip.simplewrapper

QWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) QWidget.RenderFlags(QWidget.RenderFlags)

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__init__(**kwargs)
Parameters
  • stop_before (int) – Exit the constructor before specified step.

  • parent (QWidget) – Parent widget, if any.

  • in_knime (bool) – Whether we are currently running under KNIME - a mode in which input selector is hidden, optionally a custom Workspace Structure is specified, and buttom bar has OK & Cancel buttons.

  • workspace_st_file (bool) – Structure to be returned by getWorkspaceStructure() when in_knime is True.

acceptDrops(self) → bool
accessibleDescription(self) → str
accessibleName(self) → str
actionEvent(self, QActionEvent)
actions(self) → List[QAction]
activateWindow(self)
addAction(self, QAction)
addActions(self, Iterable[QAction])
addJaguarMarker(atoms, color=None, icon=None, text='', alt_color=None, highlight=False)

Add a marker to the specified atom(s)

Parameters
  • atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to mark. A list may contain between one and four atoms (inclusive).

  • color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker and icon. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.

  • icon (int) – The icon to draw next to the marker. Should be one the self.MARKER_ICONS constants. If not given, no icon will be drawn.

  • text (str) – The text to display next to the marker. If not given, no text will be displayed. Note that this argument will be ignored when marking a single atom.

  • alt_color (tuple, str, int, or schrodinger.structutils.color) – The alternate marker color. This color is always used for text, and is used for the marker and icon when highlight is True. If not given, color will be used.

  • highlight (bool) – Whether the marker should be highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Returns

The newly created marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If a marker already exists for the specified atoms

Note

Either an icon or text may be displayed on a marker, but not both. If both are given, only the text will be shown.

addMainTaskRunner(runner, taskwidget)

A “main” task runner is a runner that is operated by a task widget (generally a job bar) at the very bottom of the panel. A panel may have more than one main task, but there is always one that is the “current” task. This is useful for panels that have multiple modes, with each mode launching a different job.

The related method, self.setCurrentTask(), is used to switch between main runners that have been added via this function.

Parameters
  • runner (tasks.AbstractTaskRuner) – the task runner

  • taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

addMarker(atoms, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for a group of atoms.

Parameters
  • atoms (list or schrodinger.structure._StructureAtom) – List of atoms to be marked

  • color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

addMarkerFromAsl(asl, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for group of Workspace atoms that match the given ASL. Same atoms continue to be marked even if the Workspace is later modified such that ASL matching changes.

Parameters
  • asl – ASL for the atoms to mark.

  • color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

Returns

Marker object

Return type

markers.Marker

addProjectJobNote(job_id, jobname)

Adds a note to the project annotation file. :param job_id: The ID of the job, as assigned by Maestro :type job_id: string :param jobname: The name of the job, as shown in the job panel :type jobname: string

adjustSize(self)
applyAliasedSettings(settings)

Applies any aliased settings with new values from the dictionary. Any aliases not present in the settings dictionary will be left unchanged.

Parameters

settings (dict) – a dictionary mapping aliases to new values to apply

applySettings(settings, target=None)
autoFillBackground(self) → bool
backgroundRole(self) → QPalette.ColorRole
baseSize(self) → QSize
blockSignals(self, bool) → bool
buildCallbackDicts()

Create a dictionary of all methods that have a maestro_callback decorator.

changeEvent(self, QEvent)
childAt(self, QPoint) → QWidget

childAt(self, int, int) -> QWidget

childEvent(self, QChildEvent)
children(self) → List[QObject]
childrenRect(self) → QRect
childrenRegion(self) → QRegion
cleanup()
clearFocus(self)
clearMask(self)
close(self) → bool
closeEvent(event)

Receives the close event and calls the panel’s ‘close’-decorated appmethod. If the appmethod specifically returns False, the close event will be ignored and the panel will remain open. All other return values (including None) will allow the panel to proceed with closing.

This is a PyQT slot method and should not be explicitly called.

colorCount(self) → int
configDialogSettings()
connectNotify(self, QMetaMethod)
contentsMargins(self) → QMargins
contentsRect(self) → QRect
contextMenuEvent(self, QContextMenuEvent)
contextMenuPolicy(self) → Qt.ContextMenuPolicy
create(self, window: sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)
createBottomBar()
createInputSelector()
createJobDir()
createWindowContainer(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget
currentTaskRunner()
cursor(self) → QCursor
customContextMenuRequested

customContextMenuRequested(self, QPoint) [signal]

customEvent(self, QEvent)
definePanelSettings()

Override this method to define the settings for the panel. The aliased settings provide an interface for saving/restoring panel state as well as for interacting with task/job runners that need to access the panel state in a way that is agnostic to the specifics of widget names and types.

Each panel setting is defined by a tuple that specifies the mapping of alias to panel setting. An optional third element in the tuple can be used to group settings by category. This allows multiple settings to share the same alias.

Each setting can either point to a specific object (usually a qt widget), or a pair of setter/getter functions.

If the mapped object is a string, this will be interpreted by af2 as referring to an attribute on the panel, and a AttributeSettingWrapper instance will automatically be created. For example, specifying the string ‘num_atoms’ will create a mapping to self.num_atoms which will simply get and set the value of that instance member.

Custom setter and getter functions should take the form getter(), returning a value that can be encoded/decoded by JSON, and setter(value), where the type of value is the same as the return type of the getter.

Commonly used objects/widgets should be handled automatically in settings.py. It’s worth considering whether it makes more sense to use a custom setter/getter here or add support for the widget in settings.py.

Returns

a list of tuples defining the custom settings.

Return type

list of tuples. Each tuple can be of type (str, object, str) or (str, (callable, callable), str) where the final str is optional.

Custom settings tuples consists of up to three elements:

  1. alias - a string identier for the setting. Ex. “box_centroid”

  2. either:

    1. an object of a type that is supported by settings.py or

    2. the string name of an existing panel attribute (i.e. member variable), or

    3. a (getter, setter) tuple. The getter should take no arguments, and the setter should take a single value.

  3. optionally, a group identifier. This can be useful if the panel runs two different jobs that both have a parameter with the same name but that needs to map to different widgets. If a setting has a group name, it will be ignored by runners unless the runner name matches the group name.

deleteLater(self)
depth(self) → int
destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)
destroyed

destroyed(self, object: QObject = None) [signal]

devType(self) → int
devicePixelRatio(self) → int
devicePixelRatioF(self) → float
devicePixelRatioFScale() → float
disconnect(self)
disconnectNotify(self, QMetaMethod)
dragEnterEvent(self, QDragEnterEvent)
dragLeaveEvent(self, QDragLeaveEvent)
dragMoveEvent(self, QDragMoveEvent)
dropEvent(self, QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
effectiveWinId(self) → sip.voidptr
ensurePolished(self)
enterEvent(self, QEvent)
error(text, preferences=None, key='')

Display an error dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
find(sip.voidptr) → QWidget
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

focusInEvent(self, QFocusEvent)
focusNextChild(self) → bool
focusNextPrevChild(self, bool) → bool
focusOutEvent(self, QFocusEvent)
focusPolicy(self) → Qt.FocusPolicy
focusPreviousChild(self) → bool
focusProxy(self) → QWidget
focusWidget(self) → QWidget
font(self) → QFont
fontInfo(self) → QFontInfo
fontMetrics(self) → QFontMetrics
foregroundRole(self) → QPalette.ColorRole
frameGeometry(self) → QRect
frameSize(self) → QSize
generateStatus()

Generate the text to put into the status bar

Returns

The text to put into the status bar

Return type

str

geometry(self) → QRect
getAliasedSettings()
getAliasedValue(alias)
getAllJaguarMarkers()

Get all markers._BaseMarker currently loaded into the panel

Returns

An iterator of markers._BaseMarker

Return type

iterator

getAllMarkers()

Get all markers.Marker loaded into the panel

Returns

list(markers.Marker)

Return type

list

getCmdListArgValue(cmdlist, arg)
getConfigDialog()
getContentsMargins(self) → Tuple[int, int, int, int]
getJaguarMarker(atoms)

Retrieve a marker for the specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Returns

The requested marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If no marker exists for the specified atoms

Note

As indicated by the return type, this function only returns schrodinger.maestro.markers._BaseMarker derived markers. Multi atom schrodinger.maestro.markers.Marker type markers are not accessible in this way.

getJobSpec()
getObjValue(obj)
getPanelState()

Gets the current state of the panel in the form of a serializable dict. The state consists of the settings specified in definePanelSettings() as well as the automatically harvested settings.

getPersistenceKey(alias)

Return a unique identifier for saving/restoring a setting in the preferences. Override this method to change the key scheme (this is necessary if creating a common resource which is shared by multiple panels).

Parameters

alias (str) – the alias for which we are generating a key

getSettings(target=None, ignore_list=None)
getWorkspaceStructure()

If panel is open in Maestro session, returns the current workspace schrodinger.strucutre.Structure.

If panel is open from outside of Maestro, returns the self.workspace_st if self.workspace_st_file is available. Used while running from command line or starting the panel from KNIME.

Returns None otherwise.

Return type

schrodinger.structure.Structure or None

Returns

Maestro workspace structure or None

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap
grabGesture(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())
grabKeyboard(self)
grabMouse(self)

grabMouse(self, Union[QCursor, Qt.CursorShape])

grabShortcut(self, Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int
graphicsEffect(self) → QGraphicsEffect
graphicsProxyWidget(self) → QGraphicsProxyWidget
gui_closed
hasFocus(self) → bool
hasHeightForWidth(self) → bool
hasMouseTracking(self) → bool
hasTabletTracking(self) → bool
height(self) → int
heightForWidth(self, int) → int
heightMM(self) → int
hide(self)
hideAllJaguarMarkers()

Hide all schrodinger.maestro.markers._BaseMarker markers for this panel

hideAllMarkers()

Hide all schrodinger.maestro.markers.Marker markers for this panel.

hideEvent(self, QHideEvent)
hideLayoutElements(layout)

Hide all elements from the given layout. Used for customizing KNIME panel wrappers.

ignoreMaestroCallbacks()

A context manager for temporarily disabling Maestro callbacks created using the decorators above. (Note that callbacks that have been manually added using maestro.*_callback_add() will not be disabled.)

Example:

def includeEntry(self, entry_id):
    proj = maestro.project_table_get()
    with self.ignoreMaestroCallbacks():
        proj[entry_id].in_workspace = project.IN_WORKSPACE

@maestro_callback.project_changed
def onProjectChanged(self):
    print "This method will not be called during includeEntry."

@maestro_callback.workspace_changed
def onWorkspaceChanged(self):
    print "Neither will this one."
info(text, preferences=None, key='')

Display an information dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

inherits(self, str) → bool
initPainter(self, QPainter)
inputMethodEvent(self, QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHints
inputMethodQuery(self, Qt.InputMethodQuery) → Any
MultiJobApp.insertAction(self, QAction, QAction)
insertActions(self, QAction, Iterable[QAction])
installEventFilter(self, QObject)
isActiveWindow(self) → bool
isAncestorOf(self, QWidget) → bool
isEnabled(self) → bool
isEnabledTo(self, QWidget) → bool
isFullScreen(self) → bool
isHidden(self) → bool
isLeftToRight(self) → bool
isMaximized(self) → bool
isMinimized(self) → bool
isModal(self) → bool
isRightToLeft(self) → bool
isSignalConnected(self, QMetaMethod) → bool
isVisible(self) → bool
isVisibleTo(self, QWidget) → bool
isWidgetType(self) → bool
isWindow(self) → bool
isWindowModified(self) → bool
isWindowType(self) → bool
jobCompleted
jobDir()
jobname()

Return the job name currently set for the current task.

jobnameData()

Provides panel settings that are to be incorporated into job names. If self.default_jobname includes string formatting characters (i.e. %s, {0}, etc.), then this method must be implemented. It should return a tuple or a dictionary to be interpolated into the job name.

jobnameDataChanged()

If the job name includes panel settings, then this method should be called whenever the relevant panel settings are modified

keyPressEvent(self, QKeyEvent)
keyReleaseEvent(self, QKeyEvent)
keyboardGrabber() → QWidget
killTimer(self, int)
lastJobCompleted
launchJobCmd(cmdlist, show_progress_bar=False, auto_add_host=True, use_parallel_flag=True, jobdir=None)

Launches a job control command. Use this to launch scripts that accept the standard job control options arguments like -HOST, -DISP, etc. By default, automatically populates standard arguments from the config dialog, but will not overwrite if they are already found in cmdlist. For example, if -HOST is found in cmdlist, launchJobCmd will ignore the host specified in the config dialog.

This method honors self.start_mode; it can either launch the script or write out a job file to the job directory.

Parameters
  • cmdlist (list) – the command list

  • show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

  • auto_add_host (bool) – Whether or not to automatically add -HOST flag to command when it is not already included.

  • use_parallel_flag (bool) – Whether requesting CPUs > 1 without specifying threads > 1 should be represented by the use of the -PARALLEL X flag (True, default) or -HOST host:X (False). -PARALLEL is a Jaguar flag and may not be appropriate for other programs.

  • jobdir (str) – launch the job from this dir, if provided.

Returns

Job object for started job, or None if job start failed or if writing instead of starting. Panels should in general ignore the return value.

launchLauncher(slauncher, show_progress_bar=False)

Either launches a launcher instance or writes the job invocation command, depending on the state of self.start_mode. This allows the panel’s start method to double as a write method.

Calling launchLauncher() is only necessary if creating a customized launcher using makeLauncher().

Parameters

show_progress_bar (int) – Whether or not to show a progress bar tracking the job’s status.

launchScript(script, script_args=None, input_files=[], structure_output_file=None, output_files=[], aux_modules=[], show_progress_bar=False, **kwargs)

DEPRECATED, add get_job_spec_from_args() to the backend script and launch it using launchJobCmd() or also add getJobSpec() to the panel and launch using launchFromJobSpec().

Creates and launches a script using makeLauncher. For documentation on method parameters, see makeLauncher below. Use this method for scripts that do not themselves integrate with job control.

This method honors self.start_mode; it can either launch the script or write out a job file to the job directory.

Parameters

show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

launcherToCmdList(slauncher)
layOut()
layout(self) → QLayout
layoutDirection(self) → Qt.LayoutDirection
leaveEvent(self, QEvent)
loadPanelState(filename=None)

Load the panel state from a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

loadPersistentOptions()

Load all persistent options from the preferences.

loadSettings(jobname)

Load the GUI state for the job in the CWD with the given name. Default implementation will return False. Each KNIME panel will need to implement a custom version. For example, the panel may want to read the <jobname.sh> file, parse the list of command-line options, and populate the GUI accordintly. If a panel writes key/value file, then it would need to read it here.

Returns

True if panel state was restored, False if saved state was not found.

Return type

bool

locale(self) → QLocale
logicalDpiX(self) → int
logicalDpiY(self) → int
lower(self)
makeLauncher(script, script_args=[], input_files=[], structure_output_file=None, output_files=[], aux_modules=[], **kwargs)

DEPRECATED, add get_job_spec_from_args() to the backend script and launch it using launchJobCmd() or also add getJobSpec() to the panel and launch using launchFromJobSpec().

Create a launcher.Launcher instance using the settings defined by the panel, its config dialog, and specified arguments. Returns a launcher instance ready to be launched or further modified. Use this method for scripts that do not themselves integrate with job control.

Only use this method if you need to modify the launcher before launching it. Otherwise, the method launchScript() is preferred to create the launcher and launch it.

Parameters
  • script (str) – Remote path to the script to be launched. See Launcher documentation for more info. If only launching to localhost is desired, then a local path can be specified.

  • script_args (list of str) – arguments to be added to the script’s command line

  • input_files (list of str) – input files that will be copied to the temporary job directory.

  • structure_output_file (str) – this is the file that will be registered with job control to incorporate at the end of the job

  • output_files (list of str) – additional output files to be copied back from the temporary job directory

  • aux_modules (list of modules) – Additional modules required by the script

Returns

A prepped launcher

Return type

Launcher

mapFrom(self, QWidget, QPoint) → QPoint
mapFromGlobal(self, QPoint) → QPoint
mapFromParent(self, QPoint) → QPoint
mapTo(self, QWidget, QPoint) → QPoint
mapToGlobal(self, QPoint) → QPoint
mapToParent(self, QPoint) → QPoint
mask(self) → QRegion
maximumHeight(self) → int
maximumSize(self) → QSize
maximumWidth(self) → int
metaObject(self) → QMetaObject
metric(self, QPaintDevice.PaintDeviceMetric) → int
minimumHeight(self) → int
minimumSize(self) → QSize
minimumSizeHint(self) → QSize
minimumWidth(self) → int
mouseDoubleClickEvent(self, QMouseEvent)
mouseGrabber() → QWidget
mouseMoveEvent(self, QMouseEvent)
mousePressEvent(self, QMouseEvent)
mouseReleaseEvent(self, QMouseEvent)
move(self, QPoint)

move(self, int, int)

moveEvent(self, QMoveEvent)
moveToThread(self, QThread)
nativeEvent(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]
nativeParentWidget(self) → QWidget
nextInFocusChain(self) → QWidget
normalGeometry(self) → QRect
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

overrideWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
overrideWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
paintEngine(self) → QPaintEngine
paintEvent(self, QPaintEvent)
paintingActive(self) → bool
palette(self) → QPalette
classmethod panel(run=True)

Launch a singleton instance of this class. If the panel has already been instantiated, the existing panel instance will be re-opened and brought to the front.

Parameters

run (bool) – Whether to launch the panel

Returns

The singleton panel instance

Return type

App

parent(self) → QObject
parentWidget(self) → QWidget
physicalDpiX(self) → int
physicalDpiY(self) → int
pos(self) → QPoint
previousInFocusChain(self) → QWidget
processSettings(settings=None, runner=None)

This method is meant to be used as a callback to a task runner. If it is called with no arguments, it returns a dictionary of all the alieased settings. If settings are passed, the settings are first applied to self, and then the newly modified settings are returned.

Parameters
  • settings (dict or None) – a settings dictionary to apply to this object

  • runner (tasks.AbstractTaskRuner) – the task runner that is invoking this callback. This optional argument is necessary for per-runner grouping of settings

processTaskMessage(message_type, text, options=None, runner=None)

This method is meant to be used as a callback to a task runner, and provides a single point of interaction from the runner to the user.

Parameters
  • message_type (int) – the type of message being sent

  • text (str) – the main text to show the user

  • options – extra options

property(self, str) → Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

question(msg, button1='OK', button2='Cancel', title='Question')

Display a prompt dialog window with specified text. Returns True if first button (default OK) is pressed, False otherwise.

raise_(self)
readShFile(jobname)

Reads the jobname.sh file (written by _write()) and returns the list of command line arguments

receivers(self, PYQT_SIGNAL) → int
rect(self) → QRect
registerJob(job, show_progress_bar=False)

Registers a job with the periodic job check callback and starts timer.

Parameters
  • job (jobcontrol.Job) – job to register

  • show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

releaseKeyboard(self)
releaseMouse(self)
releaseShortcut(self, int)
removeAction(self, QAction)
removeAllJaguarMarkers()

Remove all markers schrodinger.maestro.markers._BaseMarker markers from this panel

removeAllJaguarMarkersForEntry(eid)

Remove all markers for the specified entry id from this panel

Parameters

eid (str) – The entry id to remove markers for

removeAllMarkers()

Remove all schrodinger.maestro.markers.Marker markers from this panel.

removeEventFilter(self, QObject)
removeJaguarMarker(marker)

Removes the specified marker

Parameters

marker (schrodinger.maestro.markers._BaseMarker) – The marker to remove

Raises

ValueError – If there is no marker on the specified atoms

removeJaguarMarkerForAtoms(atoms)

Removes the marker for specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Raises

ValueError – If no marker exists for the specified atoms

removeMarker(marker)

Remove the schrodinger.maestro.markers.Marker

Parameters

marker (schrodinger.maestro.markers.Marker) – Marker to remove

Raises

ValueError – If marker is the wrong type or is not associated with the panel.

render(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))

render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))

repaint(self)

repaint(self, int, int, int, int) repaint(self, QRect) repaint(self, QRegion)

reportValidation(results)

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters

results (validation.ValidationResults) – Set of validation results generated by validate

Returns

if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

resetAllRunners()

Resets all task runners associated with this panel (main tasks and other tasks added via setupTaskRunner). This is called from _reset() and normally does not need to be called directly.

resize(self, QSize)

resize(self, int, int)

resizeEvent(self, QResizeEvent)
restoreCursor(app_wide=True)

Restore the application level cursor to the default. If ‘app_wide’ is True then if will be restored for the entire application, if it’s False, it will be just for this panel.

Parameters

app_wide (bool) – If True then this will restore the cursor for the entire application (including Maestro if running there). If False then this will apply only to this panel.

restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool
run()
runCanvas()

This handles Canvas-specific logic

classmethod runKnime(input_selector_file=None, workspace_st_file=None, jobname=None, run=True, load_settings=True, panel_state_file=None)

Call this static method to instantiate this panel in KNIME mode - where OK & Cancel buttons are shown at the bottom. Pressing OK button cases the job files to be written to the CWD.

Parameters
  • input_selector_file (str) – the filename to be fed into the input selector, replacing interactive input from the user. Required if the panel contains an input selector.

  • workspace_st_file (str) – the filename containing the schrodinger.structure.Structure that replaces the workspace structure in a Maestro session.

  • jobname (str) – Jobname for the panel

  • run (bool) – Whether to launch the panel. If False, just returns the panel instance without starting the event loop.

  • load_settings (bool) – Whether to load previous settings for the given jobname from the CWD.

  • panel_state_file – Unused (added for backwards compatability)

runMaestro()

This can be extended in derived classes to perform maestro-only tasks such as setting up the mini-monitor or connecting maestro callbacks

runMode()
runStandalone()
runSubpanel()
runValidation(silent=False, validate_children=True, stop_on_fail=True)

Runs validation and reports the results (unless run silently).

Parameters
  • silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.

  • validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.

  • stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

sanitizeJobnameText(text)

Modify the given text so it can be used in a job name. White space is replaced with underscores and all other disallowed characters are removed.

Parameters

text (basestring) – The text to sanitize

Returns

The sanitized text

Return type

basestring

saveGeometry(self) → QByteArray
savePersistentOptions()

Store all persistent options to the preferences.

MultiJobApp.scroll(self, int, int)

scroll(self, int, int, QRect)

sender(self) → QObject
senderSignalIndex(self) → int
setAcceptDrops(self, bool)
setAccessibleDescription(self, str)
setAccessibleName(self, str)
setAlias(alias, obj, persistent=False)

Sets an alias to conveniently access an object.

Parameters
  • alias (hashable) – any hashable, but typically a string name

  • obj (object) – the actual object to be referenced

  • persistent (bool) – whether to make the setting persistent

setAliasedValue(alias, value)
setAliases(alias_dict, persistent=False)

Sets multiple aliases at once. Already used aliases are overwritten; other existing aliases are not affected.

Parameters
  • alias_dict (dict) – map of aliases to objects

  • persistent (bool) – whether to make the settings persistent

setAttribute(self, Qt.WidgetAttribute, on: bool = True)
setAutoFillBackground(self, bool)
setBackgroundRole(self, QPalette.ColorRole)
MultiJobApp.setBaseSize(self, int, int)

setBaseSize(self, QSize)

setConfigDialogSettings(new_values)
MultiJobApp.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins)

setContextMenuPolicy(self, Qt.ContextMenuPolicy)
setCurrentTask(index)

Selects the current main task for the panel. Switching to a new task involves several steps. These are 1) saving the current panel state to the task runner, 2) hiding the current task widget (and all others), 3) showing the widget for the new task, and 4) setting the panel state to correspond to the new task runner’s settings.

Parameters

index (int) – the index of the task to be selected. The index for each main task is set sequentially from 0 as each task as added using self.addMainTaskRunner()

setCursor(self, Union[QCursor, Qt.CursorShape])
setDefaults()
setDisabled(self, bool)
setEnabled(self, bool)
setFixedHeight(self, int)
setFixedSize(self, QSize)

setFixedSize(self, int, int)

setFixedWidth(self, int)
setFocus(self)

setFocus(self, Qt.FocusReason)

setFocusPolicy(self, Qt.FocusPolicy)
setFocusProxy(self, QWidget)
setFont(self, QFont)
setForegroundRole(self, QPalette.ColorRole)
setGeometry(self, QRect)

setGeometry(self, int, int, int, int)

setGraphicsEffect(self, QGraphicsEffect)
setHidden(self, bool)
setInputMethodHints(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])
setJobname(jobname)

Set the job name for the current task.

setLayout(self, QLayout)
setLayoutDirection(self, Qt.LayoutDirection)
setLocale(self, QLocale)
setMask(self, QBitmap)

setMask(self, QRegion)

setMaximumHeight(self, int)
MultiJobApp.setMaximumSize(self, int, int)

setMaximumSize(self, QSize)

setMaximumWidth(self, int)
setMinimumHeight(self, int)
MultiJobApp.setMinimumSize(self, int, int)

setMinimumSize(self, QSize)

setMinimumWidth(self, int)
setMouseTracking(self, bool)
setObjValue(obj, value)
setObjectName(self, str)
setPalette(self, QPalette)
setPanelOptions()

See parent class for more options.

self.use_mini_jobbar - whether this panel use the narrow version of the bottom job bar. This is useful for narrow panels where the regular job bar is too wide to fit. Default: False

self.viewname - this identifier is used by the mini-monitor so that it knows which jobs belong to this panel. This is automatically generated from the module and class name of the panel and so it does not need to be set unless the module/class names are generic.

self.program_name - a human-readable text name for the job this panel launches. This shows up in the main job monitor to help the user identify the job. Example: “Glide grid generation”. Default: “Job”

self.omit_one_from_standard_jobname - see documentation in jobnames.py

add_driverhost - If True, the backend supports running -DRIVERHOST to specify a different host for the driver job than subjobs. Only certain workflows support this option.

setPanelState(state)

Resets the panel and then sets the panel to the specified state

Parameters

state (PanelState) – the panel state to set. This object should originate from a call to getPanelState()

setParent(self, QWidget)

setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType])

setPersistent(alias=None)

Set options to be persistent. Any options to be made persistent must be aliased, since the alias is used to form the preference key. If no alias is specified, all aliased settings will be made persistent.

Parameters

alias (str or None) – the alias to save, or None

setProperty(self, str, Any) → bool
setShortcutAutoRepeat(self, int, enabled: bool = True)
setShortcutEnabled(self, int, enabled: bool = True)
MultiJobApp.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize)

setSizePolicy(self, QSizePolicy)

setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy)

setStatusTip(self, str)
setStyle(self, QStyle)
setStyleSheet(self, str)
MultiJobApp.setTabOrder(QWidget, QWidget)
setTabletTracking(self, bool)
setToolTip(self, str)
setToolTipDuration(self, int)
setUpdatesEnabled(self, bool)
setVisible(self, bool)
setWaitCursor(app_wide=True)

Set the cursor to the wait cursor. This will be an hourglass, clock or similar. Call restoreCursor() to return to the default cursor.

Parameters

app_wide (bool) – If True then this will apply to the entire application (including Maestro if running there). If False then this will apply only to this panel.

setWhatsThis(self, str)
setWindowFilePath(self, str)
setWindowFlag(self, Qt.WindowType, on: bool = True)
setWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
setWindowIcon(self, QIcon)
setWindowIconText(self, str)
setWindowModality(self, Qt.WindowModality)
setWindowModified(self, bool)
setWindowOpacity(self, float)
setWindowRole(self, str)
setWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
setWindowTitle(self, str)
setup()
setupJobCmd(cmdlist, auto_add_host=True, use_parallel_flag=True)

Adds standard arguments HOST, NJOBS, PROJ, DISP, VIEWNAME to the cmdlist if they are set in the config dialog. Settings pre-existing in the cmdlist take precedence over the config dialog settings.

Parameters
  • cmdlist (list) – the command list

  • auto_add_host (bool) – Whether or not to automatically add -HOST flat to command when it is not already included.

  • use_parallel_flag (bool) – Whether requesting CPUs > 1 without specifying threads > 1 should be represented by the use of the -PARALLEL X flag (True, default) or -HOST host:X (False). -PARALLEL is a Jaguar flag and may not be appropriate for other programs.

setupTaskRunner(runner, taskwidget)

Connects a task widget to a task runner and associates the runner with this af2 panel via the panel callbacks.

This method is called by self.addMainTaskRunner() and does not need to be called for main tasks; however, it is useful for setting up other tasks that are not main tasks - for example, if there is a smaller job that gets launched from a button in the middle of the panel somewhere.

Parameters
  • runner (tasks.AbstractTaskRuner) – the task runner

  • taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

sharedPainter(self) → QPainter
show()

Re-show all panel markers when the panel is re-shown. This separate method is needed for QDialog instances.

showAllJaguarMarkers()

Show all schrodinger.maestro.markers._BaseMarker markers for which all marked atoms are in the workspace. Hide all other markers.

showAllMarkers()

Set all schrodinger.maestro.markers.Marker markers to be shown if the relevant atoms are in the workspace. These markers are hidden automatically by Maestro when atoms are excluded.

showEvent(event)

When the panel is shown, call the panel’s ‘show’-decorated methods. Note that restoring a minimized panel will not trigger the ‘show’ methods.

showFullScreen(self)
showMaximized(self)
showMinimized(self)
showNormal(self)
showProgressBarForJob(job, show_lbl=True, start_timer=True)

Show a progress bar that tracks the progress of the specified job

Parameters
  • job (schrodinger.job.jobcontrol.Job) – The job to track

  • show_lbl (bool) – If True, the job progress text description will be shown above the progress bar. If False, the text description will not be shown.

  • start_timer (bool) – If True, the progress bar will automatically be updated and removed when the job is complete. If False, it is the caller’s responsibility to periodically call self.progress_bar.readJobAndUpdateProgress() and to call self.status_bar.hideProgress() when the job is complete.

showSTUDialog(sh_txt, jobname)

Shows dialog with information necessary to start a STU test, including a label that links to the test suite.

Parameters

sh_txt (str) – Text contained within the .sh file

signalsBlocked(self) → bool
size(self) → QSize
sizeHint(self) → QSize
sizeIncrement(self) → QSize
sizePolicy(self) → QSizePolicy
stackUnder(self, QWidget)
startDebug()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
startUp()
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
statusTip(self) → str
style(self) → QStyle
styleSheet(self) → str
syncConfigDialog()
tabletEvent(self, QTabletEvent)
testAttribute(self, Qt.WidgetAttribute) → bool
thread(self) → QThread
timerEvent(self, QTimerEvent)
property title
toolTip(self) → str
toolTipDuration(self) → int
tr(self, str, disambiguation: str = None, n: int = - 1) → str
underMouse(self) → bool
ungrabGesture(self, Qt.GestureType)
unsetCursor(self)
unsetLayoutDirection(self)
unsetLocale(self)
update(self)

update(self, QRect) update(self, QRegion) update(self, int, int, int, int)

updateGeometry(self)
updateJobname(uniquify_custom=True)

Generate a new job name based on the current panel settings

Parameters

uniquify_custom (bool) – Whether we should uniquify custom job name by adding integers to the end. If False, only standard and modified job names will be uniquified. (See JobnameType for an explanation of job name types.)

updateMicroFocus(self)
updateStatusBar()

Updates the status bar.

updatesEnabled(self) → bool
validForceFieldSelectorCustomOPLSDir()

Check whether a force field selector exists and if so whether it is set to use a custom OPLS directory that is valid. :return: whether OPLS directory has issues :rtype: bool

validateOPLSDir(opls_dir=None)

See forcefield.validate_opls_dir()

Parameters

opls_dir (str or None) – the opls dir to validate

Returns

the validation result

Return type

forcefield.OPLSDirResult

visibleRegion(self) → QRegion
warning(text, preferences=None, key='')

Display a warning dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

whatsThis(self) → str
wheelEvent(self, QWheelEvent)
width(self) → int
widthMM(self) → int
winId(self) → sip.voidptr
window(self) → QWidget
windowFilePath(self) → str
windowFlags(self) → Qt.WindowFlags
windowHandle(self) → QWindow
windowIcon(self) → QIcon
windowIconChanged

windowIconChanged(self, QIcon) [signal]

windowIconText(self) → str
windowIconTextChanged

windowIconTextChanged(self, str) [signal]

windowModality(self) → Qt.WindowModality
windowOpacity(self) → float
windowRole(self) → str
windowState(self) → Qt.WindowStates
windowTitle(self) → str
windowTitleChanged

windowTitleChanged(self, str) [signal]

windowType(self) → Qt.WindowType
writeJobCmd(cmdlist)

Writes the job invocation command to a file named “<jobname>.sh” Removes options from the command that are maestro-specific.

Note this may modify the contents of cmdlist

writePanelState(filename=None)

Write the panel state to a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

writeStateAndClose()

Will “write” the job files and close the panel.

x(self) → int
y(self) → int
class schrodinger.application.matsci.guibase.MultiDesmondJobApp(**kwargs)

Bases: schrodinger.application.matsci.guibase.MultiJobApp

Class with functionality for setting up, validating and running multiple Desmond jobs.

setup()
setDefaults()
getModel(index)

Return the model system at the specified index.

Parameters

index (int) – Index of the system to return

Returns

Model system at the specified job index

Return type

cms.Cms

getJobCount()

Return the number of jobs that the user would like to run.

Returns

Number of jobs to run

Return type

int

getStructFromPtEntry()

Get the first included entry in the Workspace if that entry is one of the chosen entries, or the first selected entry if no included entry is chosen.

Return type

(schrodinger.structure.Structure, string) or (None, None)

Returns

one structure from selected or included entries, the structure entry id

customOPLSDirForModel(job_num)

Get the custom OPLS directory (if any) for the model corresponding to job_num

Parameters

job_num (int) – The index of the job number

Return type

str or None

Returns

The opls directory to use, or None if this model does not use it

launchFromJobSpec(sub_jobname, job_num, oplsdir=None)

See parent class for documentation. Here mainly OPLS directory is obtained from structure properties.

validateModelLoaded(**kwargs)
DrawChildren = 2
DrawWindowBackground = 1
IGNORE_DELAYED_CALLBACKS = False
IgnoreMask = 4
class PaintDeviceMetric

Bases: int

PdmDepth = 6
PdmDevicePixelRatio = 11
PdmDevicePixelRatioScaled = 12
PdmDpiX = 7
PdmDpiY = 8
PdmHeight = 2
PdmHeightMM = 4
PdmNumColors = 5
PdmPhysicalDpiX = 9
PdmPhysicalDpiY = 10
PdmWidth = 1
PdmWidthMM = 3
class RenderFlag

Bases: int

class RenderFlags

Bases: sip.simplewrapper

QWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) QWidget.RenderFlags(QWidget.RenderFlags)

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__init__(**kwargs)
Parameters
  • stop_before (int) – Exit the constructor before specified step.

  • parent (QWidget) – Parent widget, if any.

  • in_knime (bool) – Whether we are currently running under KNIME - a mode in which input selector is hidden, optionally a custom Workspace Structure is specified, and buttom bar has OK & Cancel buttons.

  • workspace_st_file (bool) – Structure to be returned by getWorkspaceStructure() when in_knime is True.

acceptDrops(self) → bool
accessibleDescription(self) → str
accessibleName(self) → str
actionEvent(self, QActionEvent)
actions(self) → List[QAction]
activateWindow(self)
addAction(self, QAction)
addActions(self, Iterable[QAction])
addJaguarMarker(atoms, color=None, icon=None, text='', alt_color=None, highlight=False)

Add a marker to the specified atom(s)

Parameters
  • atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to mark. A list may contain between one and four atoms (inclusive).

  • color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker and icon. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.

  • icon (int) – The icon to draw next to the marker. Should be one the self.MARKER_ICONS constants. If not given, no icon will be drawn.

  • text (str) – The text to display next to the marker. If not given, no text will be displayed. Note that this argument will be ignored when marking a single atom.

  • alt_color (tuple, str, int, or schrodinger.structutils.color) – The alternate marker color. This color is always used for text, and is used for the marker and icon when highlight is True. If not given, color will be used.

  • highlight (bool) – Whether the marker should be highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Returns

The newly created marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If a marker already exists for the specified atoms

Note

Either an icon or text may be displayed on a marker, but not both. If both are given, only the text will be shown.

addMainTaskRunner(runner, taskwidget)

A “main” task runner is a runner that is operated by a task widget (generally a job bar) at the very bottom of the panel. A panel may have more than one main task, but there is always one that is the “current” task. This is useful for panels that have multiple modes, with each mode launching a different job.

The related method, self.setCurrentTask(), is used to switch between main runners that have been added via this function.

Parameters
  • runner (tasks.AbstractTaskRuner) – the task runner

  • taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

addMarker(atoms, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for a group of atoms.

Parameters
  • atoms (list or schrodinger.structure._StructureAtom) – List of atoms to be marked

  • color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

addMarkerFromAsl(asl, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for group of Workspace atoms that match the given ASL. Same atoms continue to be marked even if the Workspace is later modified such that ASL matching changes.

Parameters
  • asl – ASL for the atoms to mark.

  • color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

Returns

Marker object

Return type

markers.Marker

addProjectJobNote(job_id, jobname)

Adds a note to the project annotation file. :param job_id: The ID of the job, as assigned by Maestro :type job_id: string :param jobname: The name of the job, as shown in the job panel :type jobname: string

adjustSize(self)
applyAliasedSettings(settings)

Applies any aliased settings with new values from the dictionary. Any aliases not present in the settings dictionary will be left unchanged.

Parameters

settings (dict) – a dictionary mapping aliases to new values to apply

applySettings(settings, target=None)
autoFillBackground(self) → bool
backgroundRole(self) → QPalette.ColorRole
baseSize(self) → QSize
blockSignals(self, bool) → bool
buildCallbackDicts()

Create a dictionary of all methods that have a maestro_callback decorator.

changeEvent(self, QEvent)
childAt(self, QPoint) → QWidget

childAt(self, int, int) -> QWidget

childEvent(self, QChildEvent)
children(self) → List[QObject]
childrenRect(self) → QRect
childrenRegion(self) → QRegion
cleanup()
clearFocus(self)
clearMask(self)
close(self) → bool
closeEvent(event)

Receives the close event and calls the panel’s ‘close’-decorated appmethod. If the appmethod specifically returns False, the close event will be ignored and the panel will remain open. All other return values (including None) will allow the panel to proceed with closing.

This is a PyQT slot method and should not be explicitly called.

colorCount(self) → int
configDialogSettings()
connectNotify(self, QMetaMethod)
contentsMargins(self) → QMargins
contentsRect(self) → QRect
contextMenuEvent(self, QContextMenuEvent)
contextMenuPolicy(self) → Qt.ContextMenuPolicy
create(self, window: sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)
createBottomBar()
createInputSelector()
createJobDir()
createWindowContainer(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget
currentTaskRunner()
cursor(self) → QCursor
customContextMenuRequested

customContextMenuRequested(self, QPoint) [signal]

customEvent(self, QEvent)
definePanelSettings()

Override this method to define the settings for the panel. The aliased settings provide an interface for saving/restoring panel state as well as for interacting with task/job runners that need to access the panel state in a way that is agnostic to the specifics of widget names and types.

Each panel setting is defined by a tuple that specifies the mapping of alias to panel setting. An optional third element in the tuple can be used to group settings by category. This allows multiple settings to share the same alias.

Each setting can either point to a specific object (usually a qt widget), or a pair of setter/getter functions.

If the mapped object is a string, this will be interpreted by af2 as referring to an attribute on the panel, and a AttributeSettingWrapper instance will automatically be created. For example, specifying the string ‘num_atoms’ will create a mapping to self.num_atoms which will simply get and set the value of that instance member.

Custom setter and getter functions should take the form getter(), returning a value that can be encoded/decoded by JSON, and setter(value), where the type of value is the same as the return type of the getter.

Commonly used objects/widgets should be handled automatically in settings.py. It’s worth considering whether it makes more sense to use a custom setter/getter here or add support for the widget in settings.py.

Returns

a list of tuples defining the custom settings.

Return type

list of tuples. Each tuple can be of type (str, object, str) or (str, (callable, callable), str) where the final str is optional.

Custom settings tuples consists of up to three elements:

  1. alias - a string identier for the setting. Ex. “box_centroid”

  2. either:

    1. an object of a type that is supported by settings.py or

    2. the string name of an existing panel attribute (i.e. member variable), or

    3. a (getter, setter) tuple. The getter should take no arguments, and the setter should take a single value.

  3. optionally, a group identifier. This can be useful if the panel runs two different jobs that both have a parameter with the same name but that needs to map to different widgets. If a setting has a group name, it will be ignored by runners unless the runner name matches the group name.

deleteLater(self)
depth(self) → int
destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)
destroyed

destroyed(self, object: QObject = None) [signal]

devType(self) → int
devicePixelRatio(self) → int
devicePixelRatioF(self) → float
devicePixelRatioFScale() → float
disconnect(self)
disconnectNotify(self, QMetaMethod)
dragEnterEvent(self, QDragEnterEvent)
dragLeaveEvent(self, QDragLeaveEvent)
dragMoveEvent(self, QDragMoveEvent)
dropEvent(self, QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
effectiveWinId(self) → sip.voidptr
ensurePolished(self)
enterEvent(self, QEvent)
error(text, preferences=None, key='')

Display an error dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
find(sip.voidptr) → QWidget
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

focusInEvent(self, QFocusEvent)
focusNextChild(self) → bool
focusNextPrevChild(self, bool) → bool
focusOutEvent(self, QFocusEvent)
focusPolicy(self) → Qt.FocusPolicy
focusPreviousChild(self) → bool
focusProxy(self) → QWidget
focusWidget(self) → QWidget
font(self) → QFont
fontInfo(self) → QFontInfo
fontMetrics(self) → QFontMetrics
foregroundRole(self) → QPalette.ColorRole
frameGeometry(self) → QRect
frameSize(self) → QSize
generateStatus()

Generate the text to put into the status bar

Returns

The text to put into the status bar

Return type

str

geometry(self) → QRect
getAliasedSettings()
getAliasedValue(alias)
getAllJaguarMarkers()

Get all markers._BaseMarker currently loaded into the panel

Returns

An iterator of markers._BaseMarker

Return type

iterator

getAllMarkers()

Get all markers.Marker loaded into the panel

Returns

list(markers.Marker)

Return type

list

getCmdListArgValue(cmdlist, arg)
getConfigDialog()
getContentsMargins(self) → Tuple[int, int, int, int]
getJaguarMarker(atoms)

Retrieve a marker for the specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Returns

The requested marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If no marker exists for the specified atoms

Note

As indicated by the return type, this function only returns schrodinger.maestro.markers._BaseMarker derived markers. Multi atom schrodinger.maestro.markers.Marker type markers are not accessible in this way.

getJobSpec()
getObjValue(obj)
getPanelState()

Gets the current state of the panel in the form of a serializable dict. The state consists of the settings specified in definePanelSettings() as well as the automatically harvested settings.

getPersistenceKey(alias)

Return a unique identifier for saving/restoring a setting in the preferences. Override this method to change the key scheme (this is necessary if creating a common resource which is shared by multiple panels).

Parameters

alias (str) – the alias for which we are generating a key

getSettings(target=None, ignore_list=None)
getValidatedOPLSDir(oplsdir=None)

Validate the existing oplsdir or get a requested oplsdir from the user’s selection in the force field selector widget

Parameters

oplsdir (str) – The currently requested oplsdir

Return type

False, None or str

Returns

False if no valid oplsdir can be found, None if there is no custom dir requested, or the path to the custom directory

getWorkspaceStructure()

If panel is open in Maestro session, returns the current workspace schrodinger.strucutre.Structure.

If panel is open from outside of Maestro, returns the self.workspace_st if self.workspace_st_file is available. Used while running from command line or starting the panel from KNIME.

Returns None otherwise.

Return type

schrodinger.structure.Structure or None

Returns

Maestro workspace structure or None

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap
grabGesture(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())
grabKeyboard(self)
grabMouse(self)

grabMouse(self, Union[QCursor, Qt.CursorShape])

grabShortcut(self, Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int
graphicsEffect(self) → QGraphicsEffect
graphicsProxyWidget(self) → QGraphicsProxyWidget
gui_closed
hasFocus(self) → bool
hasHeightForWidth(self) → bool
hasMouseTracking(self) → bool
hasTabletTracking(self) → bool
height(self) → int
heightForWidth(self, int) → int
heightMM(self) → int
hide(self)
hideAllJaguarMarkers()

Hide all schrodinger.maestro.markers._BaseMarker markers for this panel

hideAllMarkers()

Hide all schrodinger.maestro.markers.Marker markers for this panel.

hideEvent(self, QHideEvent)
hideLayoutElements(layout)

Hide all elements from the given layout. Used for customizing KNIME panel wrappers.

ignoreMaestroCallbacks()

A context manager for temporarily disabling Maestro callbacks created using the decorators above. (Note that callbacks that have been manually added using maestro.*_callback_add() will not be disabled.)

Example:

def includeEntry(self, entry_id):
    proj = maestro.project_table_get()
    with self.ignoreMaestroCallbacks():
        proj[entry_id].in_workspace = project.IN_WORKSPACE

@maestro_callback.project_changed
def onProjectChanged(self):
    print "This method will not be called during includeEntry."

@maestro_callback.workspace_changed
def onWorkspaceChanged(self):
    print "Neither will this one."
info(text, preferences=None, key='')

Display an information dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

inherits(self, str) → bool
initPainter(self, QPainter)
inputMethodEvent(self, QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHints
inputMethodQuery(self, Qt.InputMethodQuery) → Any
MultiDesmondJobApp.insertAction(self, QAction, QAction)
insertActions(self, QAction, Iterable[QAction])
installEventFilter(self, QObject)
isActiveWindow(self) → bool
isAncestorOf(self, QWidget) → bool
isEnabled(self) → bool
isEnabledTo(self, QWidget) → bool
isFullScreen(self) → bool
isHidden(self) → bool
isLeftToRight(self) → bool
isMaximized(self) → bool
isMinimized(self) → bool
isModal(self) → bool
isRightToLeft(self) → bool
isSignalConnected(self, QMetaMethod) → bool
isVisible(self) → bool
isVisibleTo(self, QWidget) → bool
isWidgetType(self) → bool
isWindow(self) → bool
isWindowModified(self) → bool
isWindowType(self) → bool
jobCompleted
jobDir()
jobname()

Return the job name currently set for the current task.

jobnameData()

Provides panel settings that are to be incorporated into job names. If self.default_jobname includes string formatting characters (i.e. %s, {0}, etc.), then this method must be implemented. It should return a tuple or a dictionary to be interpolated into the job name.

jobnameDataChanged()

If the job name includes panel settings, then this method should be called whenever the relevant panel settings are modified

keyPressEvent(self, QKeyEvent)
keyReleaseEvent(self, QKeyEvent)
keyboardGrabber() → QWidget
killTimer(self, int)
lastJobCompleted
launchJobCmd(cmdlist, show_progress_bar=False, auto_add_host=True, use_parallel_flag=True, jobdir=None)

Launches a job control command. Use this to launch scripts that accept the standard job control options arguments like -HOST, -DISP, etc. By default, automatically populates standard arguments from the config dialog, but will not overwrite if they are already found in cmdlist. For example, if -HOST is found in cmdlist, launchJobCmd will ignore the host specified in the config dialog.

This method honors self.start_mode; it can either launch the script or write out a job file to the job directory.

Parameters
  • cmdlist (list) – the command list

  • show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

  • auto_add_host (bool) – Whether or not to automatically add -HOST flag to command when it is not already included.

  • use_parallel_flag (bool) – Whether requesting CPUs > 1 without specifying threads > 1 should be represented by the use of the -PARALLEL X flag (True, default) or -HOST host:X (False). -PARALLEL is a Jaguar flag and may not be appropriate for other programs.

  • jobdir (str) – launch the job from this dir, if provided.

Returns

Job object for started job, or None if job start failed or if writing instead of starting. Panels should in general ignore the return value.

launchLauncher(slauncher, show_progress_bar=False)

Either launches a launcher instance or writes the job invocation command, depending on the state of self.start_mode. This allows the panel’s start method to double as a write method.

Calling launchLauncher() is only necessary if creating a customized launcher using makeLauncher().

Parameters

show_progress_bar (int) – Whether or not to show a progress bar tracking the job’s status.

launchScript(script, script_args=None, input_files=[], structure_output_file=None, output_files=[], aux_modules=[], show_progress_bar=False, **kwargs)

DEPRECATED, add get_job_spec_from_args() to the backend script and launch it using launchJobCmd() or also add getJobSpec() to the panel and launch using launchFromJobSpec().

Creates and launches a script using makeLauncher. For documentation on method parameters, see makeLauncher below. Use this method for scripts that do not themselves integrate with job control.

This method honors self.start_mode; it can either launch the script or write out a job file to the job directory.

Parameters

show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

launcherToCmdList(slauncher)
layOut()
layout(self) → QLayout
layoutDirection(self) → Qt.LayoutDirection
leaveEvent(self, QEvent)
loadPanelState(filename=None)

Load the panel state from a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

loadPersistentOptions()

Load all persistent options from the preferences.

loadSettings(jobname)

Load the GUI state for the job in the CWD with the given name. Default implementation will return False. Each KNIME panel will need to implement a custom version. For example, the panel may want to read the <jobname.sh> file, parse the list of command-line options, and populate the GUI accordintly. If a panel writes key/value file, then it would need to read it here.

Returns

True if panel state was restored, False if saved state was not found.

Return type

bool

locale(self) → QLocale
logicalDpiX(self) → int
logicalDpiY(self) → int
lower(self)
makeLauncher(script, script_args=[], input_files=[], structure_output_file=None, output_files=[], aux_modules=[], **kwargs)

DEPRECATED, add get_job_spec_from_args() to the backend script and launch it using launchJobCmd() or also add getJobSpec() to the panel and launch using launchFromJobSpec().

Create a launcher.Launcher instance using the settings defined by the panel, its config dialog, and specified arguments. Returns a launcher instance ready to be launched or further modified. Use this method for scripts that do not themselves integrate with job control.

Only use this method if you need to modify the launcher before launching it. Otherwise, the method launchScript() is preferred to create the launcher and launch it.

Parameters
  • script (str) – Remote path to the script to be launched. See Launcher documentation for more info. If only launching to localhost is desired, then a local path can be specified.

  • script_args (list of str) – arguments to be added to the script’s command line

  • input_files (list of str) – input files that will be copied to the temporary job directory.

  • structure_output_file (str) – this is the file that will be registered with job control to incorporate at the end of the job

  • output_files (list of str) – additional output files to be copied back from the temporary job directory

  • aux_modules (list of modules) – Additional modules required by the script

Returns

A prepped launcher

Return type

Launcher

mapFrom(self, QWidget, QPoint) → QPoint
mapFromGlobal(self, QPoint) → QPoint
mapFromParent(self, QPoint) → QPoint
mapTo(self, QWidget, QPoint) → QPoint
mapToGlobal(self, QPoint) → QPoint
mapToParent(self, QPoint) → QPoint
mask(self) → QRegion
maximumHeight(self) → int
maximumSize(self) → QSize
maximumWidth(self) → int
metaObject(self) → QMetaObject
metric(self, QPaintDevice.PaintDeviceMetric) → int
minimumHeight(self) → int
minimumSize(self) → QSize
minimumSizeHint(self) → QSize
minimumWidth(self) → int
mouseDoubleClickEvent(self, QMouseEvent)
mouseGrabber() → QWidget
mouseMoveEvent(self, QMouseEvent)
mousePressEvent(self, QMouseEvent)
mouseReleaseEvent(self, QMouseEvent)
move(self, QPoint)

move(self, int, int)

moveEvent(self, QMoveEvent)
moveToThread(self, QThread)
multiJobStart()

Custom “start” method. For each job, creates a job sub-directory, cd’s into it, and launches the job there.

:return list of return values from self.launchFromJobSpec() calls.

Each value is a Job object or False, in start mode, or True/False in write mode.

nativeEvent(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]
nativeParentWidget(self) → QWidget
nextInFocusChain(self) → QWidget
normalGeometry(self) → QRect
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

overrideWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
overrideWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
paintEngine(self) → QPaintEngine
paintEvent(self, QPaintEvent)
paintingActive(self) → bool
palette(self) → QPalette
classmethod panel(run=True)

Launch a singleton instance of this class. If the panel has already been instantiated, the existing panel instance will be re-opened and brought to the front.

Parameters

run (bool) – Whether to launch the panel

Returns

The singleton panel instance

Return type

App

parent(self) → QObject
parentWidget(self) → QWidget
physicalDpiX(self) → int
physicalDpiY(self) → int
pos(self) → QPoint
previousInFocusChain(self) → QWidget
processSettings(settings=None, runner=None)

This method is meant to be used as a callback to a task runner. If it is called with no arguments, it returns a dictionary of all the alieased settings. If settings are passed, the settings are first applied to self, and then the newly modified settings are returned.

Parameters
  • settings (dict or None) – a settings dictionary to apply to this object

  • runner (tasks.AbstractTaskRuner) – the task runner that is invoking this callback. This optional argument is necessary for per-runner grouping of settings

processTaskMessage(message_type, text, options=None, runner=None)

This method is meant to be used as a callback to a task runner, and provides a single point of interaction from the runner to the user.

Parameters
  • message_type (int) – the type of message being sent

  • text (str) – the main text to show the user

  • options – extra options

property(self, str) → Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

question(msg, button1='OK', button2='Cancel', title='Question')

Display a prompt dialog window with specified text. Returns True if first button (default OK) is pressed, False otherwise.

raise_(self)
readShFile(jobname)

Reads the jobname.sh file (written by _write()) and returns the list of command line arguments

receivers(self, PYQT_SIGNAL) → int
rect(self) → QRect
registerJob(job, show_progress_bar=False)

Registers a job with the periodic job check callback and starts timer.

Parameters
  • job (jobcontrol.Job) – job to register

  • show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

releaseKeyboard(self)
releaseMouse(self)
releaseShortcut(self, int)
removeAction(self, QAction)
removeAllJaguarMarkers()

Remove all markers schrodinger.maestro.markers._BaseMarker markers from this panel

removeAllJaguarMarkersForEntry(eid)

Remove all markers for the specified entry id from this panel

Parameters

eid (str) – The entry id to remove markers for

removeAllMarkers()

Remove all schrodinger.maestro.markers.Marker markers from this panel.

removeEventFilter(self, QObject)
removeJaguarMarker(marker)

Removes the specified marker

Parameters

marker (schrodinger.maestro.markers._BaseMarker) – The marker to remove

Raises

ValueError – If there is no marker on the specified atoms

removeJaguarMarkerForAtoms(atoms)

Removes the marker for specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Raises

ValueError – If no marker exists for the specified atoms

removeMarker(marker)

Remove the schrodinger.maestro.markers.Marker

Parameters

marker (schrodinger.maestro.markers.Marker) – Marker to remove

Raises

ValueError – If marker is the wrong type or is not associated with the panel.

render(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))

render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))

repaint(self)

repaint(self, int, int, int, int) repaint(self, QRect) repaint(self, QRegion)

reportValidation(results)

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters

results (validation.ValidationResults) – Set of validation results generated by validate

Returns

if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

resetAllRunners()

Resets all task runners associated with this panel (main tasks and other tasks added via setupTaskRunner). This is called from _reset() and normally does not need to be called directly.

resize(self, QSize)

resize(self, int, int)

resizeEvent(self, QResizeEvent)
restoreCursor(app_wide=True)

Restore the application level cursor to the default. If ‘app_wide’ is True then if will be restored for the entire application, if it’s False, it will be just for this panel.

Parameters

app_wide (bool) – If True then this will restore the cursor for the entire application (including Maestro if running there). If False then this will apply only to this panel.

restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool
run()
runCanvas()

This handles Canvas-specific logic

classmethod runKnime(input_selector_file=None, workspace_st_file=None, jobname=None, run=True, load_settings=True, panel_state_file=None)

Call this static method to instantiate this panel in KNIME mode - where OK & Cancel buttons are shown at the bottom. Pressing OK button cases the job files to be written to the CWD.

Parameters
  • input_selector_file (str) – the filename to be fed into the input selector, replacing interactive input from the user. Required if the panel contains an input selector.

  • workspace_st_file (str) – the filename containing the schrodinger.structure.Structure that replaces the workspace structure in a Maestro session.

  • jobname (str) – Jobname for the panel

  • run (bool) – Whether to launch the panel. If False, just returns the panel instance without starting the event loop.

  • load_settings (bool) – Whether to load previous settings for the given jobname from the CWD.

  • panel_state_file – Unused (added for backwards compatability)

runMaestro()

This can be extended in derived classes to perform maestro-only tasks such as setting up the mini-monitor or connecting maestro callbacks

runMode()
runStandalone()
runSubpanel()
runValidation(silent=False, validate_children=True, stop_on_fail=True)

Runs validation and reports the results (unless run silently).

Parameters
  • silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.

  • validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.

  • stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

sanitizeJobnameText(text)

Modify the given text so it can be used in a job name. White space is replaced with underscores and all other disallowed characters are removed.

Parameters

text (basestring) – The text to sanitize

Returns

The sanitized text

Return type

basestring

saveGeometry(self) → QByteArray
savePersistentOptions()

Store all persistent options to the preferences.

MultiDesmondJobApp.scroll(self, int, int)

scroll(self, int, int, QRect)

sender(self) → QObject
senderSignalIndex(self) → int
setAcceptDrops(self, bool)
setAccessibleDescription(self, str)
setAccessibleName(self, str)
setAlias(alias, obj, persistent=False)

Sets an alias to conveniently access an object.

Parameters
  • alias (hashable) – any hashable, but typically a string name

  • obj (object) – the actual object to be referenced

  • persistent (bool) – whether to make the setting persistent

setAliasedValue(alias, value)
setAliases(alias_dict, persistent=False)

Sets multiple aliases at once. Already used aliases are overwritten; other existing aliases are not affected.

Parameters
  • alias_dict (dict) – map of aliases to objects

  • persistent (bool) – whether to make the settings persistent

setAttribute(self, Qt.WidgetAttribute, on: bool = True)
setAutoFillBackground(self, bool)
setBackgroundRole(self, QPalette.ColorRole)
MultiDesmondJobApp.setBaseSize(self, int, int)

setBaseSize(self, QSize)

setConfigDialogSettings(new_values)
MultiDesmondJobApp.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins)

setContextMenuPolicy(self, Qt.ContextMenuPolicy)
setCurrentTask(index)

Selects the current main task for the panel. Switching to a new task involves several steps. These are 1) saving the current panel state to the task runner, 2) hiding the current task widget (and all others), 3) showing the widget for the new task, and 4) setting the panel state to correspond to the new task runner’s settings.

Parameters

index (int) – the index of the task to be selected. The index for each main task is set sequentially from 0 as each task as added using self.addMainTaskRunner()

setCursor(self, Union[QCursor, Qt.CursorShape])
setDisabled(self, bool)
setEnabled(self, bool)
setFixedHeight(self, int)
setFixedSize(self, QSize)

setFixedSize(self, int, int)

setFixedWidth(self, int)
setFocus(self)

setFocus(self, Qt.FocusReason)

setFocusPolicy(self, Qt.FocusPolicy)
setFocusProxy(self, QWidget)
setFont(self, QFont)
setForegroundRole(self, QPalette.ColorRole)
setGeometry(self, QRect)

setGeometry(self, int, int, int, int)

setGraphicsEffect(self, QGraphicsEffect)
setHidden(self, bool)
setInputMethodHints(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])
setJobname(jobname)

Set the job name for the current task.

setLayout(self, QLayout)
setLayoutDirection(self, Qt.LayoutDirection)
setLocale(self, QLocale)
setMask(self, QBitmap)

setMask(self, QRegion)

setMaximumHeight(self, int)
MultiDesmondJobApp.setMaximumSize(self, int, int)

setMaximumSize(self, QSize)

setMaximumWidth(self, int)
setMinimumHeight(self, int)
MultiDesmondJobApp.setMinimumSize(self, int, int)

setMinimumSize(self, QSize)

setMinimumWidth(self, int)
setMouseTracking(self, bool)
setObjValue(obj, value)
setObjectName(self, str)
setPalette(self, QPalette)
setPanelOptions()

See parent class for more options.

self.use_mini_jobbar - whether this panel use the narrow version of the bottom job bar. This is useful for narrow panels where the regular job bar is too wide to fit. Default: False

self.viewname - this identifier is used by the mini-monitor so that it knows which jobs belong to this panel. This is automatically generated from the module and class name of the panel and so it does not need to be set unless the module/class names are generic.

self.program_name - a human-readable text name for the job this panel launches. This shows up in the main job monitor to help the user identify the job. Example: “Glide grid generation”. Default: “Job”

self.omit_one_from_standard_jobname - see documentation in jobnames.py

add_driverhost - If True, the backend supports running -DRIVERHOST to specify a different host for the driver job than subjobs. Only certain workflows support this option.

setPanelState(state)

Resets the panel and then sets the panel to the specified state

Parameters

state (PanelState) – the panel state to set. This object should originate from a call to getPanelState()

setParent(self, QWidget)

setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType])

setPersistent(alias=None)

Set options to be persistent. Any options to be made persistent must be aliased, since the alias is used to form the preference key. If no alias is specified, all aliased settings will be made persistent.

Parameters

alias (str or None) – the alias to save, or None

setProperty(self, str, Any) → bool
setShortcutAutoRepeat(self, int, enabled: bool = True)
setShortcutEnabled(self, int, enabled: bool = True)
MultiDesmondJobApp.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize)

setSizePolicy(self, QSizePolicy)

setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy)

setStatusTip(self, str)
setStyle(self, QStyle)
setStyleSheet(self, str)
MultiDesmondJobApp.setTabOrder(QWidget, QWidget)
setTabletTracking(self, bool)
setToolTip(self, str)
setToolTipDuration(self, int)
setUpdatesEnabled(self, bool)
setVisible(self, bool)
setWaitCursor(app_wide=True)

Set the cursor to the wait cursor. This will be an hourglass, clock or similar. Call restoreCursor() to return to the default cursor.

Parameters

app_wide (bool) – If True then this will apply to the entire application (including Maestro if running there). If False then this will apply only to this panel.

setWhatsThis(self, str)
setWindowFilePath(self, str)
setWindowFlag(self, Qt.WindowType, on: bool = True)
setWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
setWindowIcon(self, QIcon)
setWindowIconText(self, str)
setWindowModality(self, Qt.WindowModality)
setWindowModified(self, bool)
setWindowOpacity(self, float)
setWindowRole(self, str)
setWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
setWindowTitle(self, str)
setupJobCmd(cmdlist, auto_add_host=True, use_parallel_flag=True)

Adds standard arguments HOST, NJOBS, PROJ, DISP, VIEWNAME to the cmdlist if they are set in the config dialog. Settings pre-existing in the cmdlist take precedence over the config dialog settings.

Parameters
  • cmdlist (list) – the command list

  • auto_add_host (bool) – Whether or not to automatically add -HOST flat to command when it is not already included.

  • use_parallel_flag (bool) – Whether requesting CPUs > 1 without specifying threads > 1 should be represented by the use of the -PARALLEL X flag (True, default) or -HOST host:X (False). -PARALLEL is a Jaguar flag and may not be appropriate for other programs.

setupTaskRunner(runner, taskwidget)

Connects a task widget to a task runner and associates the runner with this af2 panel via the panel callbacks.

This method is called by self.addMainTaskRunner() and does not need to be called for main tasks; however, it is useful for setting up other tasks that are not main tasks - for example, if there is a smaller job that gets launched from a button in the middle of the panel somewhere.

Parameters
  • runner (tasks.AbstractTaskRuner) – the task runner

  • taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

sharedPainter(self) → QPainter
show()

Re-show all panel markers when the panel is re-shown. This separate method is needed for QDialog instances.

showAllJaguarMarkers()

Show all schrodinger.maestro.markers._BaseMarker markers for which all marked atoms are in the workspace. Hide all other markers.

showAllMarkers()

Set all schrodinger.maestro.markers.Marker markers to be shown if the relevant atoms are in the workspace. These markers are hidden automatically by Maestro when atoms are excluded.

showEvent(event)

When the panel is shown, call the panel’s ‘show’-decorated methods. Note that restoring a minimized panel will not trigger the ‘show’ methods.

showFullScreen(self)
showLaunchStatus(num_succeeded, njobs)

Show a label at the bottom of the panel with status of the launch.

showMaximized(self)
showMinimized(self)
showNormal(self)
showProgressBarForJob(job, show_lbl=True, start_timer=True)

Show a progress bar that tracks the progress of the specified job

Parameters
  • job (schrodinger.job.jobcontrol.Job) – The job to track

  • show_lbl (bool) – If True, the job progress text description will be shown above the progress bar. If False, the text description will not be shown.

  • start_timer (bool) – If True, the progress bar will automatically be updated and removed when the job is complete. If False, it is the caller’s responsibility to periodically call self.progress_bar.readJobAndUpdateProgress() and to call self.status_bar.hideProgress() when the job is complete.

showSTUDialog(sh_txt, jobname)

Shows dialog with information necessary to start a STU test, including a label that links to the test suite.

Parameters

sh_txt (str) – Text contained within the .sh file

signalsBlocked(self) → bool
size(self) → QSize
sizeHint(self) → QSize
sizeIncrement(self) → QSize
sizePolicy(self) → QSizePolicy
stackUnder(self, QWidget)
startDebug()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
startUp()
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
statusTip(self) → str
style(self) → QStyle
styleSheet(self) → str
syncConfigDialog()
tabletEvent(self, QTabletEvent)
testAttribute(self, Qt.WidgetAttribute) → bool
thread(self) → QThread
timerEvent(self, QTimerEvent)
property title
toolTip(self) → str
toolTipDuration(self) → int
tr(self, str, disambiguation: str = None, n: int = - 1) → str
underMouse(self) → bool
ungrabGesture(self, Qt.GestureType)
unsetCursor(self)
unsetLayoutDirection(self)
unsetLocale(self)
update(self)

update(self, QRect) update(self, QRegion) update(self, int, int, int, int)

updateGeometry(self)
updateJobname(uniquify_custom=True)

Generate a new job name based on the current panel settings

Parameters

uniquify_custom (bool) – Whether we should uniquify custom job name by adding integers to the end. If False, only standard and modified job names will be uniquified. (See JobnameType for an explanation of job name types.)

updateMicroFocus(self)
updateStatusBar()

Updates the status bar.

updatesEnabled(self) → bool
validForceFieldSelectorCustomOPLSDir()

Check whether a force field selector exists and if so whether it is set to use a custom OPLS directory that is valid. :return: whether OPLS directory has issues :rtype: bool

validateJobCount(**kwargs)
validateOPLSDir(opls_dir=None)

See forcefield.validate_opls_dir()

Parameters

opls_dir (str or None) – the opls dir to validate

Returns

the validation result

Return type

forcefield.OPLSDirResult

visibleRegion(self) → QRegion
warning(text, preferences=None, key='')

Display a warning dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

whatsThis(self) → str
wheelEvent(self, QWheelEvent)
width(self) → int
widthMM(self) → int
winId(self) → sip.voidptr
window(self) → QWidget
windowFilePath(self) → str
windowFlags(self) → Qt.WindowFlags
windowHandle(self) → QWindow
windowIcon(self) → QIcon
windowIconChanged

windowIconChanged(self, QIcon) [signal]

windowIconText(self) → str
windowIconTextChanged

windowIconTextChanged(self, str) [signal]

windowModality(self) → Qt.WindowModality
windowOpacity(self) → float
windowRole(self) → str
windowState(self) → Qt.WindowStates
windowTitle(self) → str
windowTitleChanged

windowTitleChanged(self, str) [signal]

windowType(self) → Qt.WindowType
writeJobCmd(cmdlist)

Writes the job invocation command to a file named “<jobname>.sh” Removes options from the command that are maestro-specific.

Note this may modify the contents of cmdlist

writePanelState(filename=None)

Write the panel state to a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

writeStateAndClose()

Will “write” the job files and close the panel.

x(self) → int
y(self) → int
class schrodinger.application.matsci.guibase.MultiCmdJobApp(**kwargs)

Bases: schrodinger.application.matsci.guibase.MultiDesmondJobApp

Class with functionality for setting up, validating and running multiple Desmond jobs with GPU subhosts via commands.

Note: multiJobStart() fires off multiple jobs by launchJobCmd(), which calls setupJobCmd() to add HOST and SUBHOST flags.

multiJobStart()

Custom “start” method. For each job, creates a job sub-directory, cd’s into it, and launches the job there.

:return list of return values from self.launchFromJobSpec() calls.

Each value is a Job object or False, in start mode, or True/False in write mode.

getJobCmd(jobname, job_number, cmd=None)

Must be inherited by subclasses to yield a command list

Parameters
  • jobname (str) – The job name

  • job_number (int) – the job number

  • cmd (list) – The list of command args to this point

Return type

list of str

Returns

a list of the command args for job submission

setupJobCmd(cmdlist, auto_add_host=True, auto_add_subhost=True, **kwargs)

Adds arguments such as HOST, SUBHOST, and GPU flags to cmdlist beyond the parent class method if they are set in the config dialog. Settings pre-existing in the cmdlist take precedence over the config dialog settings.

Parameters
  • cmdlist (list) – the command list

  • auto_add_host (bool) – Whether or not to automatically add -HOST flat to command when it is not already included.

  • auto_add_subhost (bool) – Whether or not to automatically add -SUBHOST flat to command when it is not already included.

DrawChildren = 2
DrawWindowBackground = 1
IGNORE_DELAYED_CALLBACKS = False
IgnoreMask = 4
class PaintDeviceMetric

Bases: int

PdmDepth = 6
PdmDevicePixelRatio = 11
PdmDevicePixelRatioScaled = 12
PdmDpiX = 7
PdmDpiY = 8
PdmHeight = 2
PdmHeightMM = 4
PdmNumColors = 5
PdmPhysicalDpiX = 9
PdmPhysicalDpiY = 10
PdmWidth = 1
PdmWidthMM = 3
class RenderFlag

Bases: int

class RenderFlags

Bases: sip.simplewrapper

QWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) QWidget.RenderFlags(QWidget.RenderFlags)

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__init__(**kwargs)
Parameters
  • stop_before (int) – Exit the constructor before specified step.

  • parent (QWidget) – Parent widget, if any.

  • in_knime (bool) – Whether we are currently running under KNIME - a mode in which input selector is hidden, optionally a custom Workspace Structure is specified, and buttom bar has OK & Cancel buttons.

  • workspace_st_file (bool) – Structure to be returned by getWorkspaceStructure() when in_knime is True.

acceptDrops(self) → bool
accessibleDescription(self) → str
accessibleName(self) → str
actionEvent(self, QActionEvent)
actions(self) → List[QAction]
activateWindow(self)
addAction(self, QAction)
addActions(self, Iterable[QAction])
addJaguarMarker(atoms, color=None, icon=None, text='', alt_color=None, highlight=False)

Add a marker to the specified atom(s)

Parameters
  • atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to mark. A list may contain between one and four atoms (inclusive).

  • color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker and icon. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.

  • icon (int) – The icon to draw next to the marker. Should be one the self.MARKER_ICONS constants. If not given, no icon will be drawn.

  • text (str) – The text to display next to the marker. If not given, no text will be displayed. Note that this argument will be ignored when marking a single atom.

  • alt_color (tuple, str, int, or schrodinger.structutils.color) – The alternate marker color. This color is always used for text, and is used for the marker and icon when highlight is True. If not given, color will be used.

  • highlight (bool) – Whether the marker should be highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Returns

The newly created marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If a marker already exists for the specified atoms

Note

Either an icon or text may be displayed on a marker, but not both. If both are given, only the text will be shown.

addMainTaskRunner(runner, taskwidget)

A “main” task runner is a runner that is operated by a task widget (generally a job bar) at the very bottom of the panel. A panel may have more than one main task, but there is always one that is the “current” task. This is useful for panels that have multiple modes, with each mode launching a different job.

The related method, self.setCurrentTask(), is used to switch between main runners that have been added via this function.

Parameters
  • runner (tasks.AbstractTaskRuner) – the task runner

  • taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

addMarker(atoms, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for a group of atoms.

Parameters
  • atoms (list or schrodinger.structure._StructureAtom) – List of atoms to be marked

  • color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

addMarkerFromAsl(asl, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for group of Workspace atoms that match the given ASL. Same atoms continue to be marked even if the Workspace is later modified such that ASL matching changes.

Parameters
  • asl – ASL for the atoms to mark.

  • color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

Returns

Marker object

Return type

markers.Marker

addProjectJobNote(job_id, jobname)

Adds a note to the project annotation file. :param job_id: The ID of the job, as assigned by Maestro :type job_id: string :param jobname: The name of the job, as shown in the job panel :type jobname: string

adjustSize(self)
applyAliasedSettings(settings)

Applies any aliased settings with new values from the dictionary. Any aliases not present in the settings dictionary will be left unchanged.

Parameters

settings (dict) – a dictionary mapping aliases to new values to apply

applySettings(settings, target=None)
autoFillBackground(self) → bool
backgroundRole(self) → QPalette.ColorRole
baseSize(self) → QSize
blockSignals(self, bool) → bool
buildCallbackDicts()

Create a dictionary of all methods that have a maestro_callback decorator.

changeEvent(self, QEvent)
childAt(self, QPoint) → QWidget

childAt(self, int, int) -> QWidget

childEvent(self, QChildEvent)
children(self) → List[QObject]
childrenRect(self) → QRect
childrenRegion(self) → QRegion
cleanup()
clearFocus(self)
clearMask(self)
close(self) → bool
closeEvent(event)

Receives the close event and calls the panel’s ‘close’-decorated appmethod. If the appmethod specifically returns False, the close event will be ignored and the panel will remain open. All other return values (including None) will allow the panel to proceed with closing.

This is a PyQT slot method and should not be explicitly called.

colorCount(self) → int
configDialogSettings()
connectNotify(self, QMetaMethod)
contentsMargins(self) → QMargins
contentsRect(self) → QRect
contextMenuEvent(self, QContextMenuEvent)
contextMenuPolicy(self) → Qt.ContextMenuPolicy
create(self, window: sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)
createBottomBar()
createInputSelector()
createJobDir()
createWindowContainer(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget
currentTaskRunner()
cursor(self) → QCursor
customContextMenuRequested

customContextMenuRequested(self, QPoint) [signal]

customEvent(self, QEvent)
customOPLSDirForModel(job_num)

Get the custom OPLS directory (if any) for the model corresponding to job_num

Parameters

job_num (int) – The index of the job number

Return type

str or None

Returns

The opls directory to use, or None if this model does not use it

definePanelSettings()

Override this method to define the settings for the panel. The aliased settings provide an interface for saving/restoring panel state as well as for interacting with task/job runners that need to access the panel state in a way that is agnostic to the specifics of widget names and types.

Each panel setting is defined by a tuple that specifies the mapping of alias to panel setting. An optional third element in the tuple can be used to group settings by category. This allows multiple settings to share the same alias.

Each setting can either point to a specific object (usually a qt widget), or a pair of setter/getter functions.

If the mapped object is a string, this will be interpreted by af2 as referring to an attribute on the panel, and a AttributeSettingWrapper instance will automatically be created. For example, specifying the string ‘num_atoms’ will create a mapping to self.num_atoms which will simply get and set the value of that instance member.

Custom setter and getter functions should take the form getter(), returning a value that can be encoded/decoded by JSON, and setter(value), where the type of value is the same as the return type of the getter.

Commonly used objects/widgets should be handled automatically in settings.py. It’s worth considering whether it makes more sense to use a custom setter/getter here or add support for the widget in settings.py.

Returns

a list of tuples defining the custom settings.

Return type

list of tuples. Each tuple can be of type (str, object, str) or (str, (callable, callable), str) where the final str is optional.

Custom settings tuples consists of up to three elements:

  1. alias - a string identier for the setting. Ex. “box_centroid”

  2. either:

    1. an object of a type that is supported by settings.py or

    2. the string name of an existing panel attribute (i.e. member variable), or

    3. a (getter, setter) tuple. The getter should take no arguments, and the setter should take a single value.

  3. optionally, a group identifier. This can be useful if the panel runs two different jobs that both have a parameter with the same name but that needs to map to different widgets. If a setting has a group name, it will be ignored by runners unless the runner name matches the group name.

deleteLater(self)
depth(self) → int
destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)
destroyed

destroyed(self, object: QObject = None) [signal]

devType(self) → int
devicePixelRatio(self) → int
devicePixelRatioF(self) → float
devicePixelRatioFScale() → float
disconnect(self)
disconnectNotify(self, QMetaMethod)
dragEnterEvent(self, QDragEnterEvent)
dragLeaveEvent(self, QDragLeaveEvent)
dragMoveEvent(self, QDragMoveEvent)
dropEvent(self, QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
effectiveWinId(self) → sip.voidptr
ensurePolished(self)
enterEvent(self, QEvent)
error(text, preferences=None, key='')

Display an error dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
find(sip.voidptr) → QWidget
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

focusInEvent(self, QFocusEvent)
focusNextChild(self) → bool
focusNextPrevChild(self, bool) → bool
focusOutEvent(self, QFocusEvent)
focusPolicy(self) → Qt.FocusPolicy
focusPreviousChild(self) → bool
focusProxy(self) → QWidget
focusWidget(self) → QWidget
font(self) → QFont
fontInfo(self) → QFontInfo
fontMetrics(self) → QFontMetrics
foregroundRole(self) → QPalette.ColorRole
frameGeometry(self) → QRect
frameSize(self) → QSize
generateStatus()

Generate the text to put into the status bar

Returns

The text to put into the status bar

Return type

str

geometry(self) → QRect
getAliasedSettings()
getAliasedValue(alias)
getAllJaguarMarkers()

Get all markers._BaseMarker currently loaded into the panel

Returns

An iterator of markers._BaseMarker

Return type

iterator

getAllMarkers()

Get all markers.Marker loaded into the panel

Returns

list(markers.Marker)

Return type

list

getCmdListArgValue(cmdlist, arg)
getConfigDialog()
getContentsMargins(self) → Tuple[int, int, int, int]
getJaguarMarker(atoms)

Retrieve a marker for the specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Returns

The requested marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If no marker exists for the specified atoms

Note

As indicated by the return type, this function only returns schrodinger.maestro.markers._BaseMarker derived markers. Multi atom schrodinger.maestro.markers.Marker type markers are not accessible in this way.

getJobCount()

Return the number of jobs that the user would like to run.

Returns

Number of jobs to run

Return type

int

getJobSpec()
getModel(index)

Return the model system at the specified index.

Parameters

index (int) – Index of the system to return

Returns

Model system at the specified job index

Return type

cms.Cms

getObjValue(obj)
getPanelState()

Gets the current state of the panel in the form of a serializable dict. The state consists of the settings specified in definePanelSettings() as well as the automatically harvested settings.

getPersistenceKey(alias)

Return a unique identifier for saving/restoring a setting in the preferences. Override this method to change the key scheme (this is necessary if creating a common resource which is shared by multiple panels).

Parameters

alias (str) – the alias for which we are generating a key

getSettings(target=None, ignore_list=None)
getStructFromPtEntry()

Get the first included entry in the Workspace if that entry is one of the chosen entries, or the first selected entry if no included entry is chosen.

Return type

(schrodinger.structure.Structure, string) or (None, None)

Returns

one structure from selected or included entries, the structure entry id

getValidatedOPLSDir(oplsdir=None)

Validate the existing oplsdir or get a requested oplsdir from the user’s selection in the force field selector widget

Parameters

oplsdir (str) – The currently requested oplsdir

Return type

False, None or str

Returns

False if no valid oplsdir can be found, None if there is no custom dir requested, or the path to the custom directory

getWorkspaceStructure()

If panel is open in Maestro session, returns the current workspace schrodinger.strucutre.Structure.

If panel is open from outside of Maestro, returns the self.workspace_st if self.workspace_st_file is available. Used while running from command line or starting the panel from KNIME.

Returns None otherwise.

Return type

schrodinger.structure.Structure or None

Returns

Maestro workspace structure or None

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap
grabGesture(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())
grabKeyboard(self)
grabMouse(self)

grabMouse(self, Union[QCursor, Qt.CursorShape])

grabShortcut(self, Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int
graphicsEffect(self) → QGraphicsEffect
graphicsProxyWidget(self) → QGraphicsProxyWidget
gui_closed
hasFocus(self) → bool
hasHeightForWidth(self) → bool
hasMouseTracking(self) → bool
hasTabletTracking(self) → bool
height(self) → int
heightForWidth(self, int) → int
heightMM(self) → int
hide(self)
hideAllJaguarMarkers()

Hide all schrodinger.maestro.markers._BaseMarker markers for this panel

hideAllMarkers()

Hide all schrodinger.maestro.markers.Marker markers for this panel.

hideEvent(self, QHideEvent)
hideLayoutElements(layout)

Hide all elements from the given layout. Used for customizing KNIME panel wrappers.

ignoreMaestroCallbacks()

A context manager for temporarily disabling Maestro callbacks created using the decorators above. (Note that callbacks that have been manually added using maestro.*_callback_add() will not be disabled.)

Example:

def includeEntry(self, entry_id):
    proj = maestro.project_table_get()
    with self.ignoreMaestroCallbacks():
        proj[entry_id].in_workspace = project.IN_WORKSPACE

@maestro_callback.project_changed
def onProjectChanged(self):
    print "This method will not be called during includeEntry."

@maestro_callback.workspace_changed
def onWorkspaceChanged(self):
    print "Neither will this one."
info(text, preferences=None, key='')

Display an information dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

inherits(self, str) → bool
initPainter(self, QPainter)
inputMethodEvent(self, QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHints
inputMethodQuery(self, Qt.InputMethodQuery) → Any
MultiCmdJobApp.insertAction(self, QAction, QAction)
insertActions(self, QAction, Iterable[QAction])
installEventFilter(self, QObject)
isActiveWindow(self) → bool
isAncestorOf(self, QWidget) → bool
isEnabled(self) → bool
isEnabledTo(self, QWidget) → bool
isFullScreen(self) → bool
isHidden(self) → bool
isLeftToRight(self) → bool
isMaximized(self) → bool
isMinimized(self) → bool
isModal(self) → bool
isRightToLeft(self) → bool
isSignalConnected(self, QMetaMethod) → bool
isVisible(self) → bool
isVisibleTo(self, QWidget) → bool
isWidgetType(self) → bool
isWindow(self) → bool
isWindowModified(self) → bool
isWindowType(self) → bool
jobCompleted
jobDir()
jobname()

Return the job name currently set for the current task.

jobnameData()

Provides panel settings that are to be incorporated into job names. If self.default_jobname includes string formatting characters (i.e. %s, {0}, etc.), then this method must be implemented. It should return a tuple or a dictionary to be interpolated into the job name.

jobnameDataChanged()

If the job name includes panel settings, then this method should be called whenever the relevant panel settings are modified

keyPressEvent(self, QKeyEvent)
keyReleaseEvent(self, QKeyEvent)
keyboardGrabber() → QWidget
killTimer(self, int)
lastJobCompleted
launchFromJobSpec(sub_jobname, job_num, oplsdir=None)

See parent class for documentation. Here mainly OPLS directory is obtained from structure properties.

launchJobCmd(cmdlist, show_progress_bar=False, auto_add_host=True, use_parallel_flag=True, jobdir=None)

Launches a job control command. Use this to launch scripts that accept the standard job control options arguments like -HOST, -DISP, etc. By default, automatically populates standard arguments from the config dialog, but will not overwrite if they are already found in cmdlist. For example, if -HOST is found in cmdlist, launchJobCmd will ignore the host specified in the config dialog.

This method honors self.start_mode; it can either launch the script or write out a job file to the job directory.

Parameters
  • cmdlist (list) – the command list

  • show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

  • auto_add_host (bool) – Whether or not to automatically add -HOST flag to command when it is not already included.

  • use_parallel_flag (bool) – Whether requesting CPUs > 1 without specifying threads > 1 should be represented by the use of the -PARALLEL X flag (True, default) or -HOST host:X (False). -PARALLEL is a Jaguar flag and may not be appropriate for other programs.

  • jobdir (str) – launch the job from this dir, if provided.

Returns

Job object for started job, or None if job start failed or if writing instead of starting. Panels should in general ignore the return value.

launchLauncher(slauncher, show_progress_bar=False)

Either launches a launcher instance or writes the job invocation command, depending on the state of self.start_mode. This allows the panel’s start method to double as a write method.

Calling launchLauncher() is only necessary if creating a customized launcher using makeLauncher().

Parameters

show_progress_bar (int) – Whether or not to show a progress bar tracking the job’s status.

launchScript(script, script_args=None, input_files=[], structure_output_file=None, output_files=[], aux_modules=[], show_progress_bar=False, **kwargs)

DEPRECATED, add get_job_spec_from_args() to the backend script and launch it using launchJobCmd() or also add getJobSpec() to the panel and launch using launchFromJobSpec().

Creates and launches a script using makeLauncher. For documentation on method parameters, see makeLauncher below. Use this method for scripts that do not themselves integrate with job control.

This method honors self.start_mode; it can either launch the script or write out a job file to the job directory.

Parameters

show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

launcherToCmdList(slauncher)
layOut()
layout(self) → QLayout
layoutDirection(self) → Qt.LayoutDirection
leaveEvent(self, QEvent)
loadPanelState(filename=None)

Load the panel state from a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

loadPersistentOptions()

Load all persistent options from the preferences.

loadSettings(jobname)

Load the GUI state for the job in the CWD with the given name. Default implementation will return False. Each KNIME panel will need to implement a custom version. For example, the panel may want to read the <jobname.sh> file, parse the list of command-line options, and populate the GUI accordintly. If a panel writes key/value file, then it would need to read it here.

Returns

True if panel state was restored, False if saved state was not found.

Return type

bool

locale(self) → QLocale
logicalDpiX(self) → int
logicalDpiY(self) → int
lower(self)
makeLauncher(script, script_args=[], input_files=[], structure_output_file=None, output_files=[], aux_modules=[], **kwargs)

DEPRECATED, add get_job_spec_from_args() to the backend script and launch it using launchJobCmd() or also add getJobSpec() to the panel and launch using launchFromJobSpec().

Create a launcher.Launcher instance using the settings defined by the panel, its config dialog, and specified arguments. Returns a launcher instance ready to be launched or further modified. Use this method for scripts that do not themselves integrate with job control.

Only use this method if you need to modify the launcher before launching it. Otherwise, the method launchScript() is preferred to create the launcher and launch it.

Parameters
  • script (str) – Remote path to the script to be launched. See Launcher documentation for more info. If only launching to localhost is desired, then a local path can be specified.

  • script_args (list of str) – arguments to be added to the script’s command line

  • input_files (list of str) – input files that will be copied to the temporary job directory.

  • structure_output_file (str) – this is the file that will be registered with job control to incorporate at the end of the job

  • output_files (list of str) – additional output files to be copied back from the temporary job directory

  • aux_modules (list of modules) – Additional modules required by the script

Returns

A prepped launcher

Return type

Launcher

mapFrom(self, QWidget, QPoint) → QPoint
mapFromGlobal(self, QPoint) → QPoint
mapFromParent(self, QPoint) → QPoint
mapTo(self, QWidget, QPoint) → QPoint
mapToGlobal(self, QPoint) → QPoint
mapToParent(self, QPoint) → QPoint
mask(self) → QRegion
maximumHeight(self) → int
maximumSize(self) → QSize
maximumWidth(self) → int
metaObject(self) → QMetaObject
metric(self, QPaintDevice.PaintDeviceMetric) → int
minimumHeight(self) → int
minimumSize(self) → QSize
minimumSizeHint(self) → QSize
minimumWidth(self) → int
mouseDoubleClickEvent(self, QMouseEvent)
mouseGrabber() → QWidget
mouseMoveEvent(self, QMouseEvent)
mousePressEvent(self, QMouseEvent)
mouseReleaseEvent(self, QMouseEvent)
move(self, QPoint)

move(self, int, int)

moveEvent(self, QMoveEvent)
moveToThread(self, QThread)
nativeEvent(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]
nativeParentWidget(self) → QWidget
nextInFocusChain(self) → QWidget
normalGeometry(self) → QRect
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

overrideWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
overrideWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
paintEngine(self) → QPaintEngine
paintEvent(self, QPaintEvent)
paintingActive(self) → bool
palette(self) → QPalette
classmethod panel(run=True)

Launch a singleton instance of this class. If the panel has already been instantiated, the existing panel instance will be re-opened and brought to the front.

Parameters

run (bool) – Whether to launch the panel

Returns

The singleton panel instance

Return type

App

parent(self) → QObject
parentWidget(self) → QWidget
physicalDpiX(self) → int
physicalDpiY(self) → int
pos(self) → QPoint
previousInFocusChain(self) → QWidget
processSettings(settings=None, runner=None)

This method is meant to be used as a callback to a task runner. If it is called with no arguments, it returns a dictionary of all the alieased settings. If settings are passed, the settings are first applied to self, and then the newly modified settings are returned.

Parameters
  • settings (dict or None) – a settings dictionary to apply to this object

  • runner (tasks.AbstractTaskRuner) – the task runner that is invoking this callback. This optional argument is necessary for per-runner grouping of settings

processTaskMessage(message_type, text, options=None, runner=None)

This method is meant to be used as a callback to a task runner, and provides a single point of interaction from the runner to the user.

Parameters
  • message_type (int) – the type of message being sent

  • text (str) – the main text to show the user

  • options – extra options

property(self, str) → Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

question(msg, button1='OK', button2='Cancel', title='Question')

Display a prompt dialog window with specified text. Returns True if first button (default OK) is pressed, False otherwise.

raise_(self)
readShFile(jobname)

Reads the jobname.sh file (written by _write()) and returns the list of command line arguments

receivers(self, PYQT_SIGNAL) → int
rect(self) → QRect
registerJob(job, show_progress_bar=False)

Registers a job with the periodic job check callback and starts timer.

Parameters
  • job (jobcontrol.Job) – job to register

  • show_progress_bar (bool) – Whether or not to show a progress bar tracking the job’s status.

releaseKeyboard(self)
releaseMouse(self)
releaseShortcut(self, int)
removeAction(self, QAction)
removeAllJaguarMarkers()

Remove all markers schrodinger.maestro.markers._BaseMarker markers from this panel

removeAllJaguarMarkersForEntry(eid)

Remove all markers for the specified entry id from this panel

Parameters

eid (str) – The entry id to remove markers for

removeAllMarkers()

Remove all schrodinger.maestro.markers.Marker markers from this panel.

removeEventFilter(self, QObject)
removeJaguarMarker(marker)

Removes the specified marker

Parameters

marker (schrodinger.maestro.markers._BaseMarker) – The marker to remove

Raises

ValueError – If there is no marker on the specified atoms

removeJaguarMarkerForAtoms(atoms)

Removes the marker for specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Raises

ValueError – If no marker exists for the specified atoms

removeMarker(marker)

Remove the schrodinger.maestro.markers.Marker

Parameters

marker (schrodinger.maestro.markers.Marker) – Marker to remove

Raises

ValueError – If marker is the wrong type or is not associated with the panel.

render(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))

render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))

repaint(self)

repaint(self, int, int, int, int) repaint(self, QRect) repaint(self, QRegion)

reportValidation(results)

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters

results (validation.ValidationResults) – Set of validation results generated by validate

Returns

if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

resetAllRunners()

Resets all task runners associated with this panel (main tasks and other tasks added via setupTaskRunner). This is called from _reset() and normally does not need to be called directly.

resize(self, QSize)

resize(self, int, int)

resizeEvent(self, QResizeEvent)
restoreCursor(app_wide=True)

Restore the application level cursor to the default. If ‘app_wide’ is True then if will be restored for the entire application, if it’s False, it will be just for this panel.

Parameters

app_wide (bool) – If True then this will restore the cursor for the entire application (including Maestro if running there). If False then this will apply only to this panel.

restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool
run()
runCanvas()

This handles Canvas-specific logic

classmethod runKnime(input_selector_file=None, workspace_st_file=None, jobname=None, run=True, load_settings=True, panel_state_file=None)

Call this static method to instantiate this panel in KNIME mode - where OK & Cancel buttons are shown at the bottom. Pressing OK button cases the job files to be written to the CWD.

Parameters
  • input_selector_file (str) – the filename to be fed into the input selector, replacing interactive input from the user. Required if the panel contains an input selector.

  • workspace_st_file (str) – the filename containing the schrodinger.structure.Structure that replaces the workspace structure in a Maestro session.

  • jobname (str) – Jobname for the panel

  • run (bool) – Whether to launch the panel. If False, just returns the panel instance without starting the event loop.

  • load_settings (bool) – Whether to load previous settings for the given jobname from the CWD.

  • panel_state_file – Unused (added for backwards compatability)

runMaestro()

This can be extended in derived classes to perform maestro-only tasks such as setting up the mini-monitor or connecting maestro callbacks

runMode()
runStandalone()
runSubpanel()
runValidation(silent=False, validate_children=True, stop_on_fail=True)

Runs validation and reports the results (unless run silently).

Parameters
  • silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.

  • validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.

  • stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

sanitizeJobnameText(text)

Modify the given text so it can be used in a job name. White space is replaced with underscores and all other disallowed characters are removed.

Parameters

text (basestring) – The text to sanitize

Returns

The sanitized text

Return type

basestring

saveGeometry(self) → QByteArray
savePersistentOptions()

Store all persistent options to the preferences.

MultiCmdJobApp.scroll(self, int, int)

scroll(self, int, int, QRect)

sender(self) → QObject
senderSignalIndex(self) → int
setAcceptDrops(self, bool)
setAccessibleDescription(self, str)
setAccessibleName(self, str)
setAlias(alias, obj, persistent=False)

Sets an alias to conveniently access an object.

Parameters
  • alias (hashable) – any hashable, but typically a string name

  • obj (object) – the actual object to be referenced

  • persistent (bool) – whether to make the setting persistent

setAliasedValue(alias, value)
setAliases(alias_dict, persistent=False)

Sets multiple aliases at once. Already used aliases are overwritten; other existing aliases are not affected.

Parameters
  • alias_dict (dict) – map of aliases to objects

  • persistent (bool) – whether to make the settings persistent

setAttribute(self, Qt.WidgetAttribute, on: bool = True)
setAutoFillBackground(self, bool)
setBackgroundRole(self, QPalette.ColorRole)
MultiCmdJobApp.setBaseSize(self, int, int)

setBaseSize(self, QSize)

setConfigDialogSettings(new_values)
MultiCmdJobApp.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins)

setContextMenuPolicy(self, Qt.ContextMenuPolicy)
setCurrentTask(index)

Selects the current main task for the panel. Switching to a new task involves several steps. These are 1) saving the current panel state to the task runner, 2) hiding the current task widget (and all others), 3) showing the widget for the new task, and 4) setting the panel state to correspond to the new task runner’s settings.

Parameters

index (int) – the index of the task to be selected. The index for each main task is set sequentially from 0 as each task as added using self.addMainTaskRunner()

setCursor(self, Union[QCursor, Qt.CursorShape])
setDefaults()
setDisabled(self, bool)
setEnabled(self, bool)
setFixedHeight(self, int)
setFixedSize(self, QSize)

setFixedSize(self, int, int)

setFixedWidth(self, int)
setFocus(self)

setFocus(self, Qt.FocusReason)

setFocusPolicy(self, Qt.FocusPolicy)
setFocusProxy(self, QWidget)
setFont(self, QFont)
setForegroundRole(self, QPalette.ColorRole)
setGeometry(self, QRect)

setGeometry(self, int, int, int, int)

setGraphicsEffect(self, QGraphicsEffect)
setHidden(self, bool)
setInputMethodHints(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])
setJobname(jobname)

Set the job name for the current task.

setLayout(self, QLayout)
setLayoutDirection(self, Qt.LayoutDirection)
setLocale(self, QLocale)
setMask(self, QBitmap)

setMask(self, QRegion)

setMaximumHeight(self, int)
MultiCmdJobApp.setMaximumSize(self, int, int)

setMaximumSize(self, QSize)

setMaximumWidth(self, int)
setMinimumHeight(self, int)
MultiCmdJobApp.setMinimumSize(self, int, int)

setMinimumSize(self, QSize)

setMinimumWidth(self, int)
setMouseTracking(self, bool)
setObjValue(obj, value)
setObjectName(self, str)
setPalette(self, QPalette)
setPanelOptions()

See parent class for more options.

self.use_mini_jobbar - whether this panel use the narrow version of the bottom job bar. This is useful for narrow panels where the regular job bar is too wide to fit. Default: False

self.viewname - this identifier is used by the mini-monitor so that it knows which jobs belong to this panel. This is automatically generated from the module and class name of the panel and so it does not need to be set unless the module/class names are generic.

self.program_name - a human-readable text name for the job this panel launches. This shows up in the main job monitor to help the user identify the job. Example: “Glide grid generation”. Default: “Job”

self.omit_one_from_standard_jobname - see documentation in jobnames.py

add_driverhost - If True, the backend supports running -DRIVERHOST to specify a different host for the driver job than subjobs. Only certain workflows support this option.

setPanelState(state)

Resets the panel and then sets the panel to the specified state

Parameters

state (PanelState) – the panel state to set. This object should originate from a call to getPanelState()

setParent(self, QWidget)

setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType])

setPersistent(alias=None)

Set options to be persistent. Any options to be made persistent must be aliased, since the alias is used to form the preference key. If no alias is specified, all aliased settings will be made persistent.

Parameters

alias (str or None) – the alias to save, or None

setProperty(self, str, Any) → bool
setShortcutAutoRepeat(self, int, enabled: bool = True)
setShortcutEnabled(self, int, enabled: bool = True)
MultiCmdJobApp.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize)

setSizePolicy(self, QSizePolicy)

setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy)

setStatusTip(self, str)
setStyle(self, QStyle)
setStyleSheet(self, str)
MultiCmdJobApp.setTabOrder(QWidget, QWidget)
setTabletTracking(self, bool)
setToolTip(self, str)
setToolTipDuration(self, int)
setUpdatesEnabled(self, bool)
setVisible(self, bool)
setWaitCursor(app_wide=True)

Set the cursor to the wait cursor. This will be an hourglass, clock or similar. Call restoreCursor() to return to the default cursor.

Parameters

app_wide (bool) – If True then this will apply to the entire application (including Maestro if running there). If False then this will apply only to this panel.

setWhatsThis(self, str)
setWindowFilePath(self, str)
setWindowFlag(self, Qt.WindowType, on: bool = True)
setWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
setWindowIcon(self, QIcon)
setWindowIconText(self, str)
setWindowModality(self, Qt.WindowModality)
setWindowModified(self, bool)
setWindowOpacity(self, float)
setWindowRole(self, str)
setWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
setWindowTitle(self, str)
setup()
setupTaskRunner(runner, taskwidget)

Connects a task widget to a task runner and associates the runner with this af2 panel via the panel callbacks.

This method is called by self.addMainTaskRunner() and does not need to be called for main tasks; however, it is useful for setting up other tasks that are not main tasks - for example, if there is a smaller job that gets launched from a button in the middle of the panel somewhere.

Parameters
  • runner (tasks.AbstractTaskRuner) – the task runner

  • taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

sharedPainter(self) → QPainter
show()

Re-show all panel markers when the panel is re-shown. This separate method is needed for QDialog instances.

showAllJaguarMarkers()

Show all schrodinger.maestro.markers._BaseMarker markers for which all marked atoms are in the workspace. Hide all other markers.

showAllMarkers()

Set all schrodinger.maestro.markers.Marker markers to be shown if the relevant atoms are in the workspace. These markers are hidden automatically by Maestro when atoms are excluded.

showEvent(event)

When the panel is shown, call the panel’s ‘show’-decorated methods. Note that restoring a minimized panel will not trigger the ‘show’ methods.

showFullScreen(self)
showLaunchStatus(num_succeeded, njobs)

Show a label at the bottom of the panel with status of the launch.

showMaximized(self)
showMinimized(self)
showNormal(self)
showProgressBarForJob(job, show_lbl=True, start_timer=True)

Show a progress bar that tracks the progress of the specified job

Parameters
  • job (schrodinger.job.jobcontrol.Job) – The job to track

  • show_lbl (bool) – If True, the job progress text description will be shown above the progress bar. If False, the text description will not be shown.

  • start_timer (bool) – If True, the progress bar will automatically be updated and removed when the job is complete. If False, it is the caller’s responsibility to periodically call self.progress_bar.readJobAndUpdateProgress() and to call self.status_bar.hideProgress() when the job is complete.

showSTUDialog(sh_txt, jobname)

Shows dialog with information necessary to start a STU test, including a label that links to the test suite.

Parameters

sh_txt (str) – Text contained within the .sh file

signalsBlocked(self) → bool
size(self) → QSize
sizeHint(self) → QSize
sizeIncrement(self) → QSize
sizePolicy(self) → QSizePolicy
stackUnder(self, QWidget)
startDebug()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
startUp()
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
statusTip(self) → str
style(self) → QStyle
styleSheet(self) → str
syncConfigDialog()
tabletEvent(self, QTabletEvent)
testAttribute(self, Qt.WidgetAttribute) → bool
thread(self) → QThread
timerEvent(self, QTimerEvent)
property title
toolTip(self) → str
toolTipDuration(self) → int
tr(self, str, disambiguation: str = None, n: int = - 1) → str
underMouse(self) → bool
ungrabGesture(self, Qt.GestureType)
unsetCursor(self)
unsetLayoutDirection(self)
unsetLocale(self)
update(self)

update(self, QRect) update(self, QRegion) update(self, int, int, int, int)

updateGeometry(self)
updateJobname(uniquify_custom=True)

Generate a new job name based on the current panel settings

Parameters

uniquify_custom (bool) – Whether we should uniquify custom job name by adding integers to the end. If False, only standard and modified job names will be uniquified. (See JobnameType for an explanation of job name types.)

updateMicroFocus(self)
updateStatusBar()

Updates the status bar.

updatesEnabled(self) → bool
validForceFieldSelectorCustomOPLSDir()

Check whether a force field selector exists and if so whether it is set to use a custom OPLS directory that is valid. :return: whether OPLS directory has issues :rtype: bool

validateJobCount(**kwargs)
validateModelLoaded(**kwargs)
validateOPLSDir(opls_dir=None)

See forcefield.validate_opls_dir()

Parameters

opls_dir (str or None) – the opls dir to validate

Returns

the validation result

Return type

forcefield.OPLSDirResult

visibleRegion(self) → QRegion
warning(text, preferences=None, key='')

Display a warning dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

whatsThis(self) → str
wheelEvent(self, QWheelEvent)
width(self) → int
widthMM(self) → int
winId(self) → sip.voidptr
window(self) → QWidget
windowFilePath(self) → str
windowFlags(self) → Qt.WindowFlags
windowHandle(self) → QWindow
windowIcon(self) → QIcon
windowIconChanged

windowIconChanged(self, QIcon) [signal]

windowIconText(self) → str
windowIconTextChanged

windowIconTextChanged(self, str) [signal]

windowModality(self) → Qt.WindowModality
windowOpacity(self) → float
windowRole(self) → str
windowState(self) → Qt.WindowStates
windowTitle(self) → str
windowTitleChanged

windowTitleChanged(self, str) [signal]

windowType(self) → Qt.WindowType
writeJobCmd(cmdlist)

Writes the job invocation command to a file named “<jobname>.sh” Removes options from the command that are maestro-specific.

Note this may modify the contents of cmdlist

writePanelState(filename=None)

Write the panel state to a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

writeStateAndClose()

Will “write” the job files and close the panel.

x(self) → int
y(self) → int
class schrodinger.application.matsci.guibase.PerStrucConfigDialog(parent, title='', jobname='', checkcommand=None, multi_gpgpu_allowed=True, no_cpu=True, **kw)

Bases: schrodinger.application.desmond.gui.DesmondGuiConfigDialog

Dialog for configuring jobs that can have CPUs/GPUs per input structure specified.

CPU_UNIT_LABEL = 'processors per structure'
GPU_UNIT_LABEL = 'GPUs per structure'
CANCEL = 'Cancel'
HELP = 'Help'
HOST_LABEL_TEXT = 'Host:'
SAVE = 'OK'
START = 'Run'
WRITE = 'Write'
__init__(parent, title='', jobname='', checkcommand=None, multi_gpgpu_allowed=True, no_cpu=True, **kw)

See class docstring. Raises an Exception if the disposition specified as the default is not recognized.

If pre_close_command is specified, it will be run when the user presses the Start button. The dialog is only closed if that function returns 0.

activate()

Display the dialog and return the dialog parameters as as StartDialogParam object. If the dialog was cancelled then return None and restore the prior state.

applySettings(settings)

See parent class docstring

cpus3Edited(ignored=None)
currentHost(menu=None)

Returns the host currently selected in the menu parameter. If none is given, use self.host_menu. currentHost() can be overridden to use a different menu by default.

Parameters

menu (QtWidgets.QComboBox) – Menu to check for current host

getHostPref()

Get the stored host preference if available

Returns

Stored host preference if available or None

Return type

str or None

getHostType()
getHosts(_1=True, _2=False)

Get the hosts based on current CPU/GPU setting.

Returns

List of current hosts

Return type

config_dialog.Host

getSettings(extra_kws=None)

Return dialog state by saving the state of the checkbox and then calling the base class

getTotalOpenMPCPUs()

Compute the total number of Open MP CPUs to use based on the number of threads and subjobs the user entered

Return type

int

Returns

total number of CPUs

isCPUHost()
isGPUHost()
onProcUnitComboIndexChanged(use_host=None)

Update the available hosts based on the current processor unit type. Will also hide/show widgets based on whether GPU is selected but no GPU hosts are available or not.

Parameters

use_host (str) – Host to be set in the host combo

onWriteRequested()

Slot for Write button.

savePressed()

Slot for Save button

setUpButtonBox(can_start=True)

Set up the dialog’s button box and add ‘Write’ button.

setupHostCombo(combo, use_host=None, hosts=None)
setupHostLayout()

Setup the host layout, including hostlist/table and numbers of cpus (including cpus3).

Returns

Whether the dialog should add a start button.

Return type

bool

showHelp()
startPressed()

Slot for OK and Run button

updateCPULimits()

This method is called whenever host selection is changed. It updates maximum number of allowed CPUs.

updateOpenMPInfo()

Show/Hide the proper frames and update the processors label

updateOpenMPLabel()

Update the Open MP label with the current number of processors requested

updateQueueResources()

This updates the queue resources display when the host has changed.

validate()

Checks the panel to make sure settings are valid. Return False if any validation test fails, otherwise return True.

validateAndAccept()

Validate the settings, and if no errors are found, close the dialog.

validateNumCpus(host, editfield, silent=False)

Validate number of CPUs :type host: Host :param host: the host on which the CPUs reside :type editfield: QWidget :param editfield: widget specifying the number of CPUs :type silent: bool :param silent: suppresses warning dialogs when set to True

validateNumGpus(host, editfield, silent=False)

Validate number of GPUs :type host: Host :param host: the host on which the GPUs reside :type editfield: QWidget :param editfield: widget specifying the number of GPUs :type silent: bool :param silent: suppresses warning dialogs when set to True

validateNumOpenMP(host, silent=False)

Checks to make sure the number of requested processors and threads is consistent with what we know of the host capabilities.

Parameters
  • host (Host) – The host on which the CPUs reside

  • silent (bool) – suppresses warning dialogs when set to True

Return type

bool

Returns

True if number of processors & threads is allowed, False if not

validateNumProcs(silent=False)

See ConfigDialog.validateNumProcs docstring.

warning(text)

Display a warning window with the specified text.

writePressed()

Slot for Write button

class schrodinger.application.matsci.guibase.PerStrucSingleGpuConfigDialog(*args, **kwargs)

Bases: schrodinger.application.desmond.gui.SingleGpuDesmondGuiConfigDialog

Class to configure jobs that can use a single GPU per input structure.

CPU_UNIT_LABEL = 'processors per structure'
GPU_UNIT_LABEL = 'GPUs per structure'
CANCEL = 'Cancel'
HELP = 'Help'
HOST_LABEL_TEXT = 'Host:'
SAVE = 'OK'
START = 'Run'
WRITE = 'Write'
__init__(*args, **kwargs)

See class docstring. Raises an Exception if the disposition specified as the default is not recognized.

If pre_close_command is specified, it will be run when the user presses the Start button. The dialog is only closed if that function returns 0.

activate()

Display the dialog and return the dialog parameters as as StartDialogParam object. If the dialog was cancelled then return None and restore the prior state.

applySettings(settings)

See parent class docstring

cpus3Edited(ignored=None)
currentHost(menu=None)

Returns the host currently selected in the menu parameter. If none is given, use self.host_menu. currentHost() can be overridden to use a different menu by default.

Parameters

menu (QtWidgets.QComboBox) – Menu to check for current host

getHostPref()

Get the stored host preference if available

Returns

Stored host preference if available or None

Return type

str or None

getHostType()
getHosts(_1=True, _2=False)

Get the hosts based on current CPU/GPU setting.

Returns

List of current hosts

Return type

config_dialog.Host

getSettings(extra_kws=None)

Return dialog state by saving the state of the checkbox and then calling the base class

getTotalOpenMPCPUs()

Compute the total number of Open MP CPUs to use based on the number of threads and subjobs the user entered

Return type

int

Returns

total number of CPUs

isCPUHost()
isGPUHost()
onProcUnitComboIndexChanged(use_host=None)

Update the available hosts based on the current processor unit type. Will also hide/show widgets based on whether GPU is selected but no GPU hosts are available or not.

Parameters

use_host (str) – Host to be set in the host combo

onWriteRequested()

Slot for Write button.

savePressed()

Slot for Save button

setUpButtonBox(can_start=True)

Set up the dialog’s button box and add ‘Write’ button.

setupHostCombo(combo, use_host=None, hosts=None)
setupHostLayout()

Setup the host layout, including hostlist/table and numbers of cpus (including cpus3).

Returns

Whether the dialog should add a start button.

Return type

bool

showHelp()
startPressed()

Slot for OK and Run button

updateCPULimits()

This method is called whenever host selection is changed. It updates maximum number of allowed CPUs.

updateOpenMPInfo()

Show/Hide the proper frames and update the processors label

updateOpenMPLabel()

Update the Open MP label with the current number of processors requested

updateQueueResources()

This updates the queue resources display when the host has changed.

validate()

Checks the panel to make sure settings are valid. Return False if any validation test fails, otherwise return True.

validateAndAccept()

Validate the settings, and if no errors are found, close the dialog.

validateNumCpus(host, editfield, silent=False)

Validate number of CPUs :type host: Host :param host: the host on which the CPUs reside :type editfield: QWidget :param editfield: widget specifying the number of CPUs :type silent: bool :param silent: suppresses warning dialogs when set to True

validateNumGpus(host, editfield, silent=False)

Validate number of GPUs :type host: Host :param host: the host on which the GPUs reside :type editfield: QWidget :param editfield: widget specifying the number of GPUs :type silent: bool :param silent: suppresses warning dialogs when set to True

validateNumOpenMP(host, silent=False)

Checks to make sure the number of requested processors and threads is consistent with what we know of the host capabilities.

Parameters
  • host (Host) – The host on which the CPUs reside

  • silent (bool) – suppresses warning dialogs when set to True

Return type

bool

Returns

True if number of processors & threads is allowed, False if not

validateNumProcs(silent=False)

See ConfigDialog.validateNumProcs docstring.

warning(text)

Display a warning window with the specified text.

writePressed()

Slot for Write button

class schrodinger.application.matsci.guibase.PerStructDesmondSubhostConfigDialog(*arg, gpu_num=None, cpu_num=None, sim_jobnum=None, sim_job_sb=None, allow_cpu=False, has_subjobs_func=None, **kwargs)

Bases: schrodinger.application.desmond.fep_dialog.FEPConfigDialog

Subclass fep_dialog.FEPConfigDialog dialog, and customize it for panels that run multiple desmond subjobs.

__init__(*arg, gpu_num=None, cpu_num=None, sim_jobnum=None, sim_job_sb=None, allow_cpu=False, has_subjobs_func=None, **kwargs)

See parent class for additional documentation string.

Parameters
  • gpu_num (int) – Fix the gpu processor number per subjob, if provided.

  • cpu_num (int) – Fix the cpu processor number per subjob, if provided.

  • sim_jobnum (int) – The default simultaneous subjob number.

  • sim_job_sb (str) – the attribute name of the parent to define the number of simultaneous subjob.

  • allow_cpu (bool) – whether to allow subjob submission to cpu master host.

  • has_subjobs_func – Function that takes no arguments and returns a boolean indicating whether subjobs will be run. If not supplied, validation will always assume subjobs are run.

Type

callable

updateMaxjobsDefault()

Overwrite the parent class method to set the upper limit of max simultaneous subjobs.

validateSubHost()

Overwritten the parent method.

validate()

Overwritten the parent method to allow cpu hosts for master jobs.

CANCEL = 'Cancel'
CPU_UNIT_LABEL = 'processors'
GPU_UNIT_LABEL = 'GPUs'
HELP = 'Help'
HOST_LABEL_TEXT = 'CPU Host:'
SAVE = 'OK'
START = 'Run'
WRITE = 'Write'
activate()

Display the dialog and return the dialog parameters as as StartDialogParam object. If the dialog was cancelled then return None and restore the prior state.

addNumericLineEdit(layout, value=1, prelabel=None, postlabel=None)

Creates a standard line edit used for input, adds it to the provided layout, and then returns the line edit so that it can be stored and its value accessed later.

Parameters

value (int) – the initial value for the line edit

:type prelabel string or QLabel :type postlabel string or QLabel

If prelabel or postlabel are strings, QLabels with the textual value will be created.

addSubprocessStackedWidget(layout, prelabel, postlabel)

Add a stacked widget to the given layout with one widget being a lineedit with labels, and the other a combo box with labels.

Parameters
  • layout (QtWidgets.QLayout) – layout to which the stacked widget should be added.

  • prelabel (str or QLabel) – text preceding the widgets added to the stacked widget.

  • postlabel (str or QLabel) – text following the widgets added to the stacked widget.

Returns

the stacked widget containing the lineedit and combobox

Return type

QtWidgets.QStackedWidget

applySettings(settings)

See parent class docstring

buildComboBox()

Build a QComboBox with specific included options.

buildLabel(layout, label)

Build a new QLabel if label is a str, and add the widget to the given layout.

Parameters
  • layout (QtWidgets.QLayout) – layout to which the stacked widget should be added.

  • label (string or QLabel) – the text or widget to add to layout.

buildLineEdit(value=1)

Build a QLineEdit with specific width and validator.

cpus3Edited(ignored=None)
currentHost(menu=None)

See ConfigDialog.currentHost() docstring.

getHostPref()

Get the stored host preference if available

Returns

Stored host preference if available or None

Return type

str or None

getHostType()
getHosts(ncpus=True, excludeGPGPUs=True)

Returns list of host entries from appropriate schrodinger.hosts file, with parenthetical entry of the number of available processors (if ‘ncpus’ is True). If excludeGPGPUs is True, hosts with GPGPUs will be excluded from the list

getSettings(extra_kws=None)
getTotalOpenMPCPUs()

Compute the total number of Open MP CPUs to use based on the number of threads and subjobs the user entered

Return type

int

Returns

total number of CPUs

isCPUHost()
isGPUHost()
onHostMenuChanged(index)
savePressed()

Slot for Save button

setUpButtonBox(can_start=True)

Set up the button box items for the dialog.

Parameters

can_start – If True, add a Start button. Otherwise add a Write button.

setupHostCombo(combo, use_host=None, hosts=None)
setupHostLayout()

Setup the host layout, including hostlist/table and numbers of cpus (including cpus3).

Returns

Whether the dialog should add a start button.

Return type

bool

setupSubHostCombo(combo)

Add only GPU Hosts to the combo box input. The combo box menu will be cleared first.

Parameters

combo (QtWidgets.QComboBox) – combo box to append to.

setupSubHostLayout()
showHelp()
startPressed()

Slot for OK and Run button

updateCPULimits()

This method is called whenever host selection is changed. It updates maximum number of allowed CPUs as well as GPUs.

updateNumCPUsLabel()

We update the label here, if present.

updateOpenMPInfo()

Show/Hide the proper frames and update the processors label

updateOpenMPLabel()

Update the Open MP label with the current number of processors requested

updateQueueResources()

This updates the queue resources display when the host has changed.

validateAndAccept()

Validate the settings, and if no errors are found, close the dialog.

validateNumCpus(host, editfield, silent=False)

Validate number of CPUs :type host: Host :param host: the host on which the CPUs reside :type editfield: QWidget :param editfield: widget specifying the number of CPUs :type silent: bool :param silent: suppresses warning dialogs when set to True

validateNumGpus(host, editfield, silent=False)

Validate number of GPUs :type host: Host :param host: the host on which the GPUs reside :type editfield: QWidget :param editfield: widget specifying the number of GPUs :type silent: bool :param silent: suppresses warning dialogs when set to True

validateNumOpenMP(host, silent=False)

Checks to make sure the number of requested processors and threads is consistent with what we know of the host capabilities.

Parameters
  • host (Host) – The host on which the CPUs reside

  • silent (bool) – suppresses warning dialogs when set to True

Return type

bool

Returns

True if number of processors & threads is allowed, False if not

validateNumProcs(silent=False)

Checks that the number of processors requested is reasonable. Here the validation is conditional on the ‘cpus’ option. In derived classes this may not be valid (i.e. the validation should be run regardless of the ncpus options.

Parameters
  • menu (QComboBox) – The menu specifying the host selection to be validated

  • numfield (QLineEdit) – The widget specifying the requested # of processors

  • silent (bool) – suppresses warning dialogs when set to True

validatePlatform()

Verify that the current platform is acceptible for the requested action.

Returns

True if the platform is valid, False otherwise

Return type

bool

validateSubjobs()

Validates subjob field is populated with a value that can be cast into an int

warning(text)

Display a warning window with the specified text.

writePressed()

Slot for Write button

class schrodinger.application.matsci.guibase.ConfigDialogWithPlatformValidation(*args, incompatible_platforms=(), platform_warning='', **kwargs)

Bases: schrodinger.ui.qt.config_dialog.ConfigDialog

Adds a platform check to ConfigDialog for localhost jobs.

__init__(*args, incompatible_platforms=(), platform_warning='', **kwargs)
Parameters
  • incompatible_platforms (tuple) – Incompatible platforms for the job.

  • platform_warning (str) – The warning to be displayed if the platform is incompatible.

validateHost(host)

Validates whether or not a launch host is valid for the job. Currently only validates localhost.

Parameters

host (schrodinger.job.jobcontrol.Host object) – Launch host to validate

Return type

bool

Returns

True if the selected host is valid for the job, False otherwise.

validate()

Checks the panel to make sure settings are valid. Return False if any validation test fails, otherwise return True.

Return type

bool

Returns

True if all checks pass, False otherwise

CANCEL = 'Cancel'
CPU_UNIT_LABEL = 'processors'
GPU_UNIT_LABEL = 'GPUs'
HELP = 'Help'
HOST_LABEL_TEXT = 'Host:'
SAVE = 'OK'
START = 'Run'
WRITE = 'Write'
activate()

Display the dialog and return the dialog parameters as as StartDialogParam object. If the dialog was cancelled then return None and restore the prior state.

applySettings(settings)

Set dialog state using previously-saved parameters

Parameters

settings (StartDialogParams) – saved dialog settings

cpus3Edited(ignored=None)
currentHost(menu=None)

Returns the host currently selected in the menu parameter. If none is given, use self.host_menu. currentHost() can be overridden to use a different menu by default.

Parameters

menu (QtWidgets.QComboBox) – Menu to check for current host

getHostPref()

Get the stored host preference if available

Returns

Stored host preference if available or None

Return type

str or None

getHostType()
getHosts(ncpus=True, excludeGPGPUs=True)

Returns list of host entries from appropriate schrodinger.hosts file, with parenthetical entry of the number of available processors (if ‘ncpus’ is True). If excludeGPGPUs is True, hosts with GPGPUs will be excluded from the list

getSettings(extra_kws=None)
getTotalOpenMPCPUs()

Compute the total number of Open MP CPUs to use based on the number of threads and subjobs the user entered

Return type

int

Returns

total number of CPUs

isCPUHost()
isGPUHost()
savePressed()

Slot for Save button

setUpButtonBox(can_start=True)

Set up the button box items for the dialog.

Parameters

can_start – If True, add a Start button. Otherwise add a Write button.

setupHostCombo(combo, use_host=None, hosts=None)
setupHostLayout()

Setup the host layout, including hostlist/table and numbers of cpus (including cpus3).

Returns

Whether the dialog should add a start button.

Return type

bool

showHelp()
startPressed()

Slot for OK and Run button

updateCPULimits()

This method is called whenever host selection is changed. It updates maximum number of allowed CPUs.

updateOpenMPInfo()

Show/Hide the proper frames and update the processors label

updateOpenMPLabel()

Update the Open MP label with the current number of processors requested

updateQueueResources()

This updates the queue resources display when the host has changed.

validateAndAccept()

Validate the settings, and if no errors are found, close the dialog.

validateNumCpus(host, editfield, silent=False)

Validate number of CPUs :type host: Host :param host: the host on which the CPUs reside :type editfield: QWidget :param editfield: widget specifying the number of CPUs :type silent: bool :param silent: suppresses warning dialogs when set to True

validateNumGpus(host, editfield, silent=False)

Validate number of GPUs :type host: Host :param host: the host on which the GPUs reside :type editfield: QWidget :param editfield: widget specifying the number of GPUs :type silent: bool :param silent: suppresses warning dialogs when set to True

validateNumOpenMP(host, silent=False)

Checks to make sure the number of requested processors and threads is consistent with what we know of the host capabilities.

Parameters
  • host (Host) – The host on which the CPUs reside

  • silent (bool) – suppresses warning dialogs when set to True

Return type

bool

Returns

True if number of processors & threads is allowed, False if not

validateNumProcs(silent=False)

Checks that the number of processors requested is reasonable. Here the validation is conditional on the ‘cpus’ option. In derived classes this may not be valid (i.e. the validation should be run regardless of the ncpus options.

Parameters
  • menu (QComboBox) – The menu specifying the host selection to be validated

  • numfield (QLineEdit) – The widget specifying the requested # of processors

  • silent (bool) – suppresses warning dialogs when set to True

warning(text)

Display a warning window with the specified text.

writePressed()

Slot for Write button

schrodinger.application.matsci.guibase.validate_child_widgets(child_widgets)

Runs each widget’s validators while respecting the validation_order across all other widgets.

Rather than running validators one widget at a time, ensures that the validator with smallest validation_order across widgets is run first, and so on.

Validation methods that call this function and return its value should be decorated with @validation.multi_validator()

Parameters

child_widgets (list) – The widgets to run validations for

Return type

validation.ValidationResults

Returns

The results of validations, or the results up to and including the first failed validation.

class schrodinger.application.matsci.guibase.ProcessPtStructuresApp(**kwargs)

Bases: schrodinger.ui.qt.appframework2.af2.App

Base class for panels that process pt structures and either replace them or creates new entries

REPLACE_ENTRIES = 'Replace current entries'
NEW_ENTRIES = 'Create new entries'
RUN_BUTTON_TEXT = 'Run'
TEMP_DIR = '/scr/buildbot'
DEFAULT_GROUP_NAME = 'new_structures'
setPanelOptions()

Override the generic parent class to set panel options

layOut()

Lay out the widgets for the panel

outputTypeChanged()

React to a change in output type

myStartMethod()

Process the selected or included rows’ structures

setUp()

Make any preparations required for processing structures

processStructure(struct)

Process each structure. Should be implemented in derived classes.

Parameters

struct (structure.Structure) – The structure to process

wrapUp()

Wrap up processing the structures

reset()

Reset the panel

DrawChildren = 2
DrawWindowBackground = 1
IGNORE_DELAYED_CALLBACKS = False
IgnoreMask = 4
class PaintDeviceMetric

Bases: int

PdmDepth = 6
PdmDevicePixelRatio = 11
PdmDevicePixelRatioScaled = 12
PdmDpiX = 7
PdmDpiY = 8
PdmHeight = 2
PdmHeightMM = 4
PdmNumColors = 5
PdmPhysicalDpiX = 9
PdmPhysicalDpiY = 10
PdmWidth = 1
PdmWidthMM = 3
class RenderFlag

Bases: int

class RenderFlags

Bases: sip.simplewrapper

QWidget.RenderFlags(Union[QWidget.RenderFlags, QWidget.RenderFlag]) QWidget.RenderFlags(QWidget.RenderFlags)

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__init__(**kwargs)
Parameters
  • stop_before (int) – Exit the constructor before specified step.

  • parent (QWidget) – Parent widget, if any.

  • in_knime (bool) – Whether we are currently running under KNIME - a mode in which input selector is hidden, optionally a custom Workspace Structure is specified, and buttom bar has OK & Cancel buttons.

  • workspace_st_file (bool) – Structure to be returned by getWorkspaceStructure() when in_knime is True.

acceptDrops(self) → bool
accessibleDescription(self) → str
accessibleName(self) → str
actionEvent(self, QActionEvent)
actions(self) → List[QAction]
activateWindow(self)
addAction(self, QAction)
addActions(self, Iterable[QAction])
addJaguarMarker(atoms, color=None, icon=None, text='', alt_color=None, highlight=False)

Add a marker to the specified atom(s)

Parameters
  • atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to mark. A list may contain between one and four atoms (inclusive).

  • color (tuple, str, int, or schrodinger.structutils.color) – The color of the marker and icon. May be an RGB tuple, color name, color index, or schrodinger.structutils.color instance. If not given, white will be used.

  • icon (int) – The icon to draw next to the marker. Should be one the self.MARKER_ICONS constants. If not given, no icon will be drawn.

  • text (str) – The text to display next to the marker. If not given, no text will be displayed. Note that this argument will be ignored when marking a single atom.

  • alt_color (tuple, str, int, or schrodinger.structutils.color) – The alternate marker color. This color is always used for text, and is used for the marker and icon when highlight is True. If not given, color will be used.

  • highlight (bool) – Whether the marker should be highlighted. A highlighted marker is indicated with thicker lines and is colored using alt_color instead of color.

Returns

The newly created marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If a marker already exists for the specified atoms

Note

Either an icon or text may be displayed on a marker, but not both. If both are given, only the text will be shown.

addMainTaskRunner(runner, taskwidget)

A “main” task runner is a runner that is operated by a task widget (generally a job bar) at the very bottom of the panel. A panel may have more than one main task, but there is always one that is the “current” task. This is useful for panels that have multiple modes, with each mode launching a different job.

The related method, self.setCurrentTask(), is used to switch between main runners that have been added via this function.

Parameters
  • runner (tasks.AbstractTaskRuner) – the task runner

  • taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

addMarker(atoms, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for a group of atoms.

Parameters
  • atoms (list or schrodinger.structure._StructureAtom) – List of atoms to be marked

  • color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

addMarkerFromAsl(asl, color=(1.0, 1.0, 1.0), group_name=None)

Generates a set of simple, dot-styled markers for group of Workspace atoms that match the given ASL. Same atoms continue to be marked even if the Workspace is later modified such that ASL matching changes.

Parameters
  • asl – ASL for the atoms to mark.

  • color (tuple of 3 floats) – The amount of red, green and blue to use, each ranging from 0.0 to 1.0. Default is white (1., 1., 1.).

@group_name: Optional string to set as the name of this group of markers in Maestro. If not set, a unique identifier will be generated.

Returns

Marker object

Return type

markers.Marker

adjustSize(self)
applyAliasedSettings(settings)

Applies any aliased settings with new values from the dictionary. Any aliases not present in the settings dictionary will be left unchanged.

Parameters

settings (dict) – a dictionary mapping aliases to new values to apply

applySettings(settings, target=None)
autoFillBackground(self) → bool
backgroundRole(self) → QPalette.ColorRole
baseSize(self) → QSize
blockSignals(self, bool) → bool
buildCallbackDicts()

Create a dictionary of all methods that have a maestro_callback decorator.

changeEvent(self, QEvent)
childAt(self, QPoint) → QWidget

childAt(self, int, int) -> QWidget

childEvent(self, QChildEvent)
children(self) → List[QObject]
childrenRect(self) → QRect
childrenRegion(self) → QRegion
cleanup()
clearFocus(self)
clearMask(self)
close(self) → bool
closeEvent(event)

Receives the close event and calls the panel’s ‘close’-decorated appmethod. If the appmethod specifically returns False, the close event will be ignored and the panel will remain open. All other return values (including None) will allow the panel to proceed with closing.

This is a PyQT slot method and should not be explicitly called.

colorCount(self) → int
connectNotify(self, QMetaMethod)
contentsMargins(self) → QMargins
contentsRect(self) → QRect
contextMenuEvent(self, QContextMenuEvent)
contextMenuPolicy(self) → Qt.ContextMenuPolicy
create(self, window: sip.voidptr = 0, initializeWindow: bool = True, destroyOldWindow: bool = True)
createBottomBar()
createInputSelector()
createWindowContainer(QWindow, parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = 0) → QWidget
currentTaskRunner()
cursor(self) → QCursor
customContextMenuRequested

customContextMenuRequested(self, QPoint) [signal]

customEvent(self, QEvent)
definePanelSettings()

Override this method to define the settings for the panel. The aliased settings provide an interface for saving/restoring panel state as well as for interacting with task/job runners that need to access the panel state in a way that is agnostic to the specifics of widget names and types.

Each panel setting is defined by a tuple that specifies the mapping of alias to panel setting. An optional third element in the tuple can be used to group settings by category. This allows multiple settings to share the same alias.

Each setting can either point to a specific object (usually a qt widget), or a pair of setter/getter functions.

If the mapped object is a string, this will be interpreted by af2 as referring to an attribute on the panel, and a AttributeSettingWrapper instance will automatically be created. For example, specifying the string ‘num_atoms’ will create a mapping to self.num_atoms which will simply get and set the value of that instance member.

Custom setter and getter functions should take the form getter(), returning a value that can be encoded/decoded by JSON, and setter(value), where the type of value is the same as the return type of the getter.

Commonly used objects/widgets should be handled automatically in settings.py. It’s worth considering whether it makes more sense to use a custom setter/getter here or add support for the widget in settings.py.

Returns

a list of tuples defining the custom settings.

Return type

list of tuples. Each tuple can be of type (str, object, str) or (str, (callable, callable), str) where the final str is optional.

Custom settings tuples consists of up to three elements:

  1. alias - a string identier for the setting. Ex. “box_centroid”

  2. either:

    1. an object of a type that is supported by settings.py or

    2. the string name of an existing panel attribute (i.e. member variable), or

    3. a (getter, setter) tuple. The getter should take no arguments, and the setter should take a single value.

  3. optionally, a group identifier. This can be useful if the panel runs two different jobs that both have a parameter with the same name but that needs to map to different widgets. If a setting has a group name, it will be ignored by runners unless the runner name matches the group name.

deleteLater(self)
depth(self) → int
destroy(self, destroyWindow: bool = True, destroySubWindows: bool = True)
destroyed

destroyed(self, object: QObject = None) [signal]

devType(self) → int
devicePixelRatio(self) → int
devicePixelRatioF(self) → float
devicePixelRatioFScale() → float
disconnect(self)
disconnectNotify(self, QMetaMethod)
dragEnterEvent(self, QDragEnterEvent)
dragLeaveEvent(self, QDragLeaveEvent)
dragMoveEvent(self, QDragMoveEvent)
dropEvent(self, QDropEvent)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
effectiveWinId(self) → sip.voidptr
ensurePolished(self)
enterEvent(self, QEvent)
error(text, preferences=None, key='')

Display an error dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
find(sip.voidptr) → QWidget
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

focusInEvent(self, QFocusEvent)
focusNextChild(self) → bool
focusNextPrevChild(self, bool) → bool
focusOutEvent(self, QFocusEvent)
focusPolicy(self) → Qt.FocusPolicy
focusPreviousChild(self) → bool
focusProxy(self) → QWidget
focusWidget(self) → QWidget
font(self) → QFont
fontInfo(self) → QFontInfo
fontMetrics(self) → QFontMetrics
foregroundRole(self) → QPalette.ColorRole
frameGeometry(self) → QRect
frameSize(self) → QSize
geometry(self) → QRect
getAliasedSettings()
getAliasedValue(alias)
getAllJaguarMarkers()

Get all markers._BaseMarker currently loaded into the panel

Returns

An iterator of markers._BaseMarker

Return type

iterator

getAllMarkers()

Get all markers.Marker loaded into the panel

Returns

list(markers.Marker)

Return type

list

getContentsMargins(self) → Tuple[int, int, int, int]
getJaguarMarker(atoms)

Retrieve a marker for the specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Returns

The requested marker

Return type

schrodinger.maestro.markers._BaseMarker

Raises

ValueError – If no marker exists for the specified atoms

Note

As indicated by the return type, this function only returns schrodinger.maestro.markers._BaseMarker derived markers. Multi atom schrodinger.maestro.markers.Marker type markers are not accessible in this way.

getObjValue(obj)
getPanelState()

Gets the current state of the panel in the form of a serializable dict. The state consists of the settings specified in definePanelSettings() as well as the automatically harvested settings.

getPersistenceKey(alias)

Return a unique identifier for saving/restoring a setting in the preferences. Override this method to change the key scheme (this is necessary if creating a common resource which is shared by multiple panels).

Parameters

alias (str) – the alias for which we are generating a key

getSettings(target=None, ignore_list=None)
getWorkspaceStructure()

If panel is open in Maestro session, returns the current workspace schrodinger.strucutre.Structure.

If panel is open from outside of Maestro, returns the self.workspace_st if self.workspace_st_file is available. Used while running from command line or starting the panel from KNIME.

Returns None otherwise.

Return type

schrodinger.structure.Structure or None

Returns

Maestro workspace structure or None

grab(self, rectangle: QRect = QRect(QPoint(0, 0), QSize(- 1, - 1))) → QPixmap
grabGesture(self, Qt.GestureType, flags: Union[Qt.GestureFlags, Qt.GestureFlag] = Qt.GestureFlags())
grabKeyboard(self)
grabMouse(self)

grabMouse(self, Union[QCursor, Qt.CursorShape])

grabShortcut(self, Union[QKeySequence, QKeySequence.StandardKey, str, int], context: Qt.ShortcutContext = Qt.WindowShortcut) → int
graphicsEffect(self) → QGraphicsEffect
graphicsProxyWidget(self) → QGraphicsProxyWidget
gui_closed
hasFocus(self) → bool
hasHeightForWidth(self) → bool
hasMouseTracking(self) → bool
hasTabletTracking(self) → bool
height(self) → int
heightForWidth(self, int) → int
heightMM(self) → int
hide(self)
hideAllJaguarMarkers()

Hide all schrodinger.maestro.markers._BaseMarker markers for this panel

hideAllMarkers()

Hide all schrodinger.maestro.markers.Marker markers for this panel.

hideEvent(self, QHideEvent)
hideLayoutElements(layout)

Hide all elements from the given layout. Used for customizing KNIME panel wrappers.

ignoreMaestroCallbacks()

A context manager for temporarily disabling Maestro callbacks created using the decorators above. (Note that callbacks that have been manually added using maestro.*_callback_add() will not be disabled.)

Example:

def includeEntry(self, entry_id):
    proj = maestro.project_table_get()
    with self.ignoreMaestroCallbacks():
        proj[entry_id].in_workspace = project.IN_WORKSPACE

@maestro_callback.project_changed
def onProjectChanged(self):
    print "This method will not be called during includeEntry."

@maestro_callback.workspace_changed
def onWorkspaceChanged(self):
    print "Neither will this one."
info(text, preferences=None, key='')

Display an information dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

inherits(self, str) → bool
initPainter(self, QPainter)
inputMethodEvent(self, QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHints
inputMethodQuery(self, Qt.InputMethodQuery) → Any
ProcessPtStructuresApp.insertAction(self, QAction, QAction)
insertActions(self, QAction, Iterable[QAction])
installEventFilter(self, QObject)
isActiveWindow(self) → bool
isAncestorOf(self, QWidget) → bool
isEnabled(self) → bool
isEnabledTo(self, QWidget) → bool
isFullScreen(self) → bool
isHidden(self) → bool
isLeftToRight(self) → bool
isMaximized(self) → bool
isMinimized(self) → bool
isModal(self) → bool
isRightToLeft(self) → bool
isSignalConnected(self, QMetaMethod) → bool
isVisible(self) → bool
isVisibleTo(self, QWidget) → bool
isWidgetType(self) → bool
isWindow(self) → bool
isWindowModified(self) → bool
isWindowType(self) → bool
jobname()

Return the job name currently set for the current task.

keyPressEvent(self, QKeyEvent)
keyReleaseEvent(self, QKeyEvent)
keyboardGrabber() → QWidget
killTimer(self, int)
layout(self) → QLayout
layoutDirection(self) → Qt.LayoutDirection
leaveEvent(self, QEvent)
loadPanelState(filename=None)

Load the panel state from a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

loadPersistentOptions()

Load all persistent options from the preferences.

loadSettings(jobname)

Load the GUI state for the job in the CWD with the given name. Default implementation will return False. Each KNIME panel will need to implement a custom version. For example, the panel may want to read the <jobname.sh> file, parse the list of command-line options, and populate the GUI accordintly. If a panel writes key/value file, then it would need to read it here.

Returns

True if panel state was restored, False if saved state was not found.

Return type

bool

locale(self) → QLocale
logicalDpiX(self) → int
logicalDpiY(self) → int
lower(self)
mapFrom(self, QWidget, QPoint) → QPoint
mapFromGlobal(self, QPoint) → QPoint
mapFromParent(self, QPoint) → QPoint
mapTo(self, QWidget, QPoint) → QPoint
mapToGlobal(self, QPoint) → QPoint
mapToParent(self, QPoint) → QPoint
mask(self) → QRegion
maximumHeight(self) → int
maximumSize(self) → QSize
maximumWidth(self) → int
metaObject(self) → QMetaObject
metric(self, QPaintDevice.PaintDeviceMetric) → int
minimumHeight(self) → int
minimumSize(self) → QSize
minimumSizeHint(self) → QSize
minimumWidth(self) → int
mouseDoubleClickEvent(self, QMouseEvent)
mouseGrabber() → QWidget
mouseMoveEvent(self, QMouseEvent)
mousePressEvent(self, QMouseEvent)
mouseReleaseEvent(self, QMouseEvent)
move(self, QPoint)

move(self, int, int)

moveEvent(self, QMoveEvent)
moveToThread(self, QThread)
nativeEvent(self, Union[QByteArray, bytes, bytearray], sip.voidptr) → Tuple[bool, int]
nativeParentWidget(self) → QWidget
nextInFocusChain(self) → QWidget
normalGeometry(self) → QRect
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

overrideWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
overrideWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
paintEngine(self) → QPaintEngine
paintEvent(self, QPaintEvent)
paintingActive(self) → bool
palette(self) → QPalette
classmethod panel(run=True)

Launch a singleton instance of this class. If the panel has already been instantiated, the existing panel instance will be re-opened and brought to the front.

Parameters

run (bool) – Whether to launch the panel

Returns

The singleton panel instance

Return type

App

parent(self) → QObject
parentWidget(self) → QWidget
physicalDpiX(self) → int
physicalDpiY(self) → int
pos(self) → QPoint
previousInFocusChain(self) → QWidget
processSettings(settings=None, runner=None)

This method is meant to be used as a callback to a task runner. If it is called with no arguments, it returns a dictionary of all the alieased settings. If settings are passed, the settings are first applied to self, and then the newly modified settings are returned.

Parameters
  • settings (dict or None) – a settings dictionary to apply to this object

  • runner (tasks.AbstractTaskRuner) – the task runner that is invoking this callback. This optional argument is necessary for per-runner grouping of settings

processTaskMessage(message_type, text, options=None, runner=None)

This method is meant to be used as a callback to a task runner, and provides a single point of interaction from the runner to the user.

Parameters
  • message_type (int) – the type of message being sent

  • text (str) – the main text to show the user

  • options – extra options

property(self, str) → Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

question(msg, button1='OK', button2='Cancel', title='Question')

Display a prompt dialog window with specified text. Returns True if first button (default OK) is pressed, False otherwise.

raise_(self)
readShFile(jobname)

Reads the jobname.sh file (written by _write()) and returns the list of command line arguments

receivers(self, PYQT_SIGNAL) → int
rect(self) → QRect
releaseKeyboard(self)
releaseMouse(self)
releaseShortcut(self, int)
removeAction(self, QAction)
removeAllJaguarMarkers()

Remove all markers schrodinger.maestro.markers._BaseMarker markers from this panel

removeAllJaguarMarkersForEntry(eid)

Remove all markers for the specified entry id from this panel

Parameters

eid (str) – The entry id to remove markers for

removeAllMarkers()

Remove all schrodinger.maestro.markers.Marker markers from this panel.

removeEventFilter(self, QObject)
removeJaguarMarker(marker)

Removes the specified marker

Parameters

marker (schrodinger.maestro.markers._BaseMarker) – The marker to remove

Raises

ValueError – If there is no marker on the specified atoms

removeJaguarMarkerForAtoms(atoms)

Removes the marker for specified atom(s)

Parameters

atoms (list or schrodinger.structure._StructureAtom) – The atom or list of atoms to retrieve the marker for. A list may contain between one and four atoms (inclusive).

Raises

ValueError – If no marker exists for the specified atoms

removeMarker(marker)

Remove the schrodinger.maestro.markers.Marker

Parameters

marker (schrodinger.maestro.markers.Marker) – Marker to remove

Raises

ValueError – If marker is the wrong type or is not associated with the panel.

render(self, QPaintDevice, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground | QWidget.DrawChildren))

render(self, QPainter, targetOffset: QPoint = QPoint(), sourceRegion: QRegion = QRegion(), flags: Union[QWidget.RenderFlags, QWidget.RenderFlag] = QWidget.RenderFlags(QWidget.DrawWindowBackground|QWidget.DrawChildren))

repaint(self)

repaint(self, int, int, int, int) repaint(self, QRect) repaint(self, QRegion)

reportValidation(results)

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters

results (validation.ValidationResults) – Set of validation results generated by validate

Returns

if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

resetAllRunners()

Resets all task runners associated with this panel (main tasks and other tasks added via setupTaskRunner). This is called from _reset() and normally does not need to be called directly.

resize(self, QSize)

resize(self, int, int)

resizeEvent(self, QResizeEvent)
restoreCursor(app_wide=True)

Restore the application level cursor to the default. If ‘app_wide’ is True then if will be restored for the entire application, if it’s False, it will be just for this panel.

Parameters

app_wide (bool) – If True then this will restore the cursor for the entire application (including Maestro if running there). If False then this will apply only to this panel.

restoreGeometry(self, Union[QByteArray, bytes, bytearray]) → bool
run()
runCanvas()

This handles Canvas-specific logic

classmethod runKnime(input_selector_file=None, workspace_st_file=None, jobname=None, run=True, load_settings=True, panel_state_file=None)

Call this static method to instantiate this panel in KNIME mode - where OK & Cancel buttons are shown at the bottom. Pressing OK button cases the job files to be written to the CWD.

Parameters
  • input_selector_file (str) – the filename to be fed into the input selector, replacing interactive input from the user. Required if the panel contains an input selector.

  • workspace_st_file (str) – the filename containing the schrodinger.structure.Structure that replaces the workspace structure in a Maestro session.

  • jobname (str) – Jobname for the panel

  • run (bool) – Whether to launch the panel. If False, just returns the panel instance without starting the event loop.

  • load_settings (bool) – Whether to load previous settings for the given jobname from the CWD.

  • panel_state_file – Unused (added for backwards compatability)

runMaestro()

This can be extended in derived classes to perform maestro-only tasks such as setting up the mini-monitor or connecting maestro callbacks

runMode()
runStandalone()
runSubpanel()
runValidation(silent=False, validate_children=True, stop_on_fail=True)

Runs validation and reports the results (unless run silently).

Parameters
  • silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.

  • validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.

  • stop_on_fail (bool) – stop validation when first failure is encountered

Returns

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type

ValidationResults or bool

saveGeometry(self) → QByteArray
savePersistentOptions()

Store all persistent options to the preferences.

ProcessPtStructuresApp.scroll(self, int, int)

scroll(self, int, int, QRect)

sender(self) → QObject
senderSignalIndex(self) → int
setAcceptDrops(self, bool)
setAccessibleDescription(self, str)
setAccessibleName(self, str)
setAlias(alias, obj, persistent=False)

Sets an alias to conveniently access an object.

Parameters
  • alias (hashable) – any hashable, but typically a string name

  • obj (object) – the actual object to be referenced

  • persistent (bool) – whether to make the setting persistent

setAliasedValue(alias, value)
setAliases(alias_dict, persistent=False)

Sets multiple aliases at once. Already used aliases are overwritten; other existing aliases are not affected.

Parameters
  • alias_dict (dict) – map of aliases to objects

  • persistent (bool) – whether to make the settings persistent

setAttribute(self, Qt.WidgetAttribute, on: bool = True)
setAutoFillBackground(self, bool)
setBackgroundRole(self, QPalette.ColorRole)
ProcessPtStructuresApp.setBaseSize(self, int, int)

setBaseSize(self, QSize)

ProcessPtStructuresApp.setContentsMargins(self, int, int, int, int)

setContentsMargins(self, QMargins)

setContextMenuPolicy(self, Qt.ContextMenuPolicy)
setCurrentTask(index)

Selects the current main task for the panel. Switching to a new task involves several steps. These are 1) saving the current panel state to the task runner, 2) hiding the current task widget (and all others), 3) showing the widget for the new task, and 4) setting the panel state to correspond to the new task runner’s settings.

Parameters

index (int) – the index of the task to be selected. The index for each main task is set sequentially from 0 as each task as added using self.addMainTaskRunner()

setCursor(self, Union[QCursor, Qt.CursorShape])
setDefaults()
setDisabled(self, bool)
setEnabled(self, bool)
setFixedHeight(self, int)
setFixedSize(self, QSize)

setFixedSize(self, int, int)

setFixedWidth(self, int)
setFocus(self)

setFocus(self, Qt.FocusReason)

setFocusPolicy(self, Qt.FocusPolicy)
setFocusProxy(self, QWidget)
setFont(self, QFont)
setForegroundRole(self, QPalette.ColorRole)
setGeometry(self, QRect)

setGeometry(self, int, int, int, int)

setGraphicsEffect(self, QGraphicsEffect)
setHidden(self, bool)
setInputMethodHints(self, Union[Qt.InputMethodHints, Qt.InputMethodHint])
setJobname(jobname)

Set the job name for the current task.

setLayout(self, QLayout)
setLayoutDirection(self, Qt.LayoutDirection)
setLocale(self, QLocale)
setMask(self, QBitmap)

setMask(self, QRegion)

setMaximumHeight(self, int)
ProcessPtStructuresApp.setMaximumSize(self, int, int)

setMaximumSize(self, QSize)

setMaximumWidth(self, int)
setMinimumHeight(self, int)
ProcessPtStructuresApp.setMinimumSize(self, int, int)

setMinimumSize(self, QSize)

setMinimumWidth(self, int)
setMouseTracking(self, bool)
setObjValue(obj, value)
setObjectName(self, str)
setPalette(self, QPalette)
setPanelState(state)

Resets the panel and then sets the panel to the specified state

Parameters

state (PanelState) – the panel state to set. This object should originate from a call to getPanelState()

setParent(self, QWidget)

setParent(self, QWidget, Union[Qt.WindowFlags, Qt.WindowType])

setPersistent(alias=None)

Set options to be persistent. Any options to be made persistent must be aliased, since the alias is used to form the preference key. If no alias is specified, all aliased settings will be made persistent.

Parameters

alias (str or None) – the alias to save, or None

setProperty(self, str, Any) → bool
setShortcutAutoRepeat(self, int, enabled: bool = True)
setShortcutEnabled(self, int, enabled: bool = True)
ProcessPtStructuresApp.setSizeIncrement(self, int, int)

setSizeIncrement(self, QSize)

setSizePolicy(self, QSizePolicy)

setSizePolicy(self, QSizePolicy.Policy, QSizePolicy.Policy)

setStatusTip(self, str)
setStyle(self, QStyle)
setStyleSheet(self, str)
ProcessPtStructuresApp.setTabOrder(QWidget, QWidget)
setTabletTracking(self, bool)
setToolTip(self, str)
setToolTipDuration(self, int)
setUpdatesEnabled(self, bool)
setVisible(self, bool)
setWaitCursor(app_wide=True)

Set the cursor to the wait cursor. This will be an hourglass, clock or similar. Call restoreCursor() to return to the default cursor.

Parameters

app_wide (bool) – If True then this will apply to the entire application (including Maestro if running there). If False then this will apply only to this panel.

setWhatsThis(self, str)
setWindowFilePath(self, str)
setWindowFlag(self, Qt.WindowType, on: bool = True)
setWindowFlags(self, Union[Qt.WindowFlags, Qt.WindowType])
setWindowIcon(self, QIcon)
setWindowIconText(self, str)
setWindowModality(self, Qt.WindowModality)
setWindowModified(self, bool)
setWindowOpacity(self, float)
setWindowRole(self, str)
setWindowState(self, Union[Qt.WindowStates, Qt.WindowState])
setWindowTitle(self, str)
setup()
setupTaskRunner(runner, taskwidget)

Connects a task widget to a task runner and associates the runner with this af2 panel via the panel callbacks.

This method is called by self.addMainTaskRunner() and does not need to be called for main tasks; however, it is useful for setting up other tasks that are not main tasks - for example, if there is a smaller job that gets launched from a button in the middle of the panel somewhere.

Parameters
  • runner (tasks.AbstractTaskRuner) – the task runner

  • taskwidget (taskwidgets.TaskUIMixin) – the associated task widget

sharedPainter(self) → QPainter
show()

Re-show all panel markers when the panel is re-shown. This separate method is needed for QDialog instances.

showAllJaguarMarkers()

Show all schrodinger.maestro.markers._BaseMarker markers for which all marked atoms are in the workspace. Hide all other markers.

showAllMarkers()

Set all schrodinger.maestro.markers.Marker markers to be shown if the relevant atoms are in the workspace. These markers are hidden automatically by Maestro when atoms are excluded.

showEvent(event)

When the panel is shown, call the panel’s ‘show’-decorated methods. Note that restoring a minimized panel will not trigger the ‘show’ methods.

showFullScreen(self)
showMaximized(self)
showMinimized(self)
showNormal(self)
showProgressBarForJob(job, show_lbl=True, start_timer=True)

Show a progress bar that tracks the progress of the specified job

Parameters
  • job (schrodinger.job.jobcontrol.Job) – The job to track

  • show_lbl (bool) – If True, the job progress text description will be shown above the progress bar. If False, the text description will not be shown.

  • start_timer (bool) – If True, the progress bar will automatically be updated and removed when the job is complete. If False, it is the caller’s responsibility to periodically call self.progress_bar.readJobAndUpdateProgress() and to call self.status_bar.hideProgress() when the job is complete.

signalsBlocked(self) → bool
size(self) → QSize
sizeHint(self) → QSize
sizeIncrement(self) → QSize
sizePolicy(self) → QSizePolicy
stackUnder(self, QWidget)
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
startUp()
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
statusTip(self) → str
style(self) → QStyle
styleSheet(self) → str
tabletEvent(self, QTabletEvent)
testAttribute(self, Qt.WidgetAttribute) → bool
thread(self) → QThread
timerEvent(self, QTimerEvent)
property title
toolTip(self) → str
toolTipDuration(self) → int
tr(self, str, disambiguation: str = None, n: int = - 1) → str
underMouse(self) → bool
ungrabGesture(self, Qt.GestureType)
unsetCursor(self)
unsetLayoutDirection(self)
unsetLocale(self)
update(self)

update(self, QRect) update(self, QRegion) update(self, int, int, int, int)

updateGeometry(self)
updateMicroFocus(self)
updatesEnabled(self) → bool
validateOPLSDir(opls_dir=None)

See forcefield.validate_opls_dir()

Parameters

opls_dir (str or None) – the opls dir to validate

Returns

the validation result

Return type

forcefield.OPLSDirResult

visibleRegion(self) → QRegion
warning(text, preferences=None, key='')

Display a warning dialog with the specified text. If preferences and key are both supplied, then the dialog will contain a “Don’t show this again” checkbox. Future invocations of this dialog with the same preferences and key values will obey the user’s show preference.

Parameters
  • text (str) – The information to display in the dialog

  • preferences – obsolete; ignored.

  • key (str) – The key to store the preference under. If specified, a “Do not show again” checkbox will be rendered in the dialog box.

Return type

None

whatsThis(self) → str
wheelEvent(self, QWheelEvent)
width(self) → int
widthMM(self) → int
winId(self) → sip.voidptr
window(self) → QWidget
windowFilePath(self) → str
windowFlags(self) → Qt.WindowFlags
windowHandle(self) → QWindow
windowIcon(self) → QIcon
windowIconChanged

windowIconChanged(self, QIcon) [signal]

windowIconText(self) → str
windowIconTextChanged

windowIconTextChanged(self, str) [signal]

windowModality(self) → Qt.WindowModality
windowOpacity(self) → float
windowRole(self) → str
windowState(self) → Qt.WindowStates
windowTitle(self) → str
windowTitleChanged

windowTitleChanged(self, str) [signal]

windowType(self) → Qt.WindowType
writePanelState(filename=None)

Write the panel state to a JSON file

Parameters

filename (str) – the JSON filename. Defaults to “panelstate.json”

writeStateAndClose()

Called when OK button button is pressed when running in KNIME mode. Will “write” the job files for current task, and close the panel.

x(self) → int
y(self) → int
exception schrodinger.application.matsci.guibase.WorkflowError

Bases: ValueError

Custom exception for when the workflow should be stopped

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.matsci.guibase.format_tooltip(tip, min_width=None)

Return a formatted tooltip.

Parameters
  • tip (str) – the tip text

  • min_width (int or None) – the minimum tip width, if None a default is used

Return type

str

Returns

the formatted tool tip

schrodinger.application.matsci.guibase.load_entries_for_panel(*entry_ids, panel=None, load_func=None, included_entry=False, selected_entries=False, load_job=False)
Parameters
  • entry_ids (tuple) – Entry ids to load into the panel

  • panel (af2.App) – The panel to populate

  • load_func (callable) – The panel method to call to load the entries

  • included_entry (bool) – Whether the group’s entries should be included for the panel

  • selected_entries (bool) – Whether the group’s entries should be selected for the panel

  • load_job (bool) – Whether the entry’s job should be loaded into the panel

Raises

RuntimeError – If neither included nor selected entries is being used