schrodinger.ui.qt.appframework2.af2_template module

class schrodinger.ui.qt.appframework2.af2_template.AppTemplate(**kwargs)

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

__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.
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.

getConfigDialog()
setup()
setDefaults()
layOut()
defineCustomSettings()
startJob()
resetPanel()
closePanel()
onProjectChanged(proj)
onProjectClosed()
onWorkspaceChanged(what_changed)
onWorkspaceChangedWithActiveProj(what_changed, proj)
validatePanel(**kwargs)
DrawChildren = 2
DrawWindowBackground = 1
IGNORE_DELAYED_CALLBACKS = False
IgnoreMask = 4
NO_PROGRESS_BAR = 0
PROGRESS_BAR_NO_TEXT = 2
PROGRESS_BAR_WITH_TEXT = 1
class PaintDeviceMetric

Bases: int

__init__

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

bit_length() → int

Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6

conjugate()

Returns self, the complex conjugate of any int.

denominator

the denominator of a rational number in lowest terms

from_bytes(bytes, byteorder, *, signed=False) → int

Return the integer represented by the given array of bytes.

The bytes argument must be a bytes-like object (e.g. bytes or bytearray).

The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.

The signed keyword-only argument indicates whether two’s complement is used to represent the integer.

imag

the imaginary part of a complex number

numerator

the numerator of a rational number in lowest terms

real

the real part of a complex number

to_bytes(length, byteorder, *, signed=False) → bytes

Return an array of bytes representing an integer.

The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.

The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.

The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.

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

__init__

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

bit_length() → int

Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6

conjugate()

Returns self, the complex conjugate of any int.

denominator

the denominator of a rational number in lowest terms

from_bytes(bytes, byteorder, *, signed=False) → int

Return the integer represented by the given array of bytes.

The bytes argument must be a bytes-like object (e.g. bytes or bytearray).

The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.

The signed keyword-only argument indicates whether two’s complement is used to represent the integer.

imag

the imaginary part of a complex number

numerator

the numerator of a rational number in lowest terms

real

the real part of a complex number

to_bytes(length, byteorder, *, signed=False) → bytes

Return an array of bytes representing an integer.

The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.

The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.

The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.

class RenderFlags

Bases: sip.simplewrapper

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

__init__

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

acceptDrops(self) → bool
accessibleDescription(self) → str
accessibleName(self) → str
actionEvent(self, QActionEvent)
actions(self) → List[QAction]
activateWindow(self)
addAction(self, QAction)
addActions(self, object)
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) → object
childrenRect(self) → QRect
childrenRegion(self) → QRegion
cleanup()
cleanupWriteCmd(cmdlist)

Removes options from the command that only work within Maestro. :param cmdlist: the job invocation command :type cmdlist: list

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.

cmdListToCmd(cmdlist)

Converts a command list to a command string.

Parameters:cmdlist (list) – a list of commands
Returns:a command string with all arguments wrapped in double quotes
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, 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) → object
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 (schrodinger.utils.preferences.Preferences object) – The Preferences class to use to store the show/don’t show preference for this dialog. Note that the Preferences object must currently be set to the preference group containing key.
  • key (str) – The key to store the preference under
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)
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(event)
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 (schrodinger.utils.preferences.Preferences object) – The Preferences class to use to store the show/don’t show preference for this dialog. Note that the Preferences object must currently be set to the preference group containing key.
  • key (str) – The key to store the preference under
Return type:

None

inherits(self, str) → bool
initPainter(self, QPainter)
inputMethodEvent(self, QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHints
inputMethodQuery(self, Qt.InputMethodQuery) → Any
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
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(oplsdir=None)

Call this function in start method if the calling script implements the launch api. This function requires implementation of getJobSpec to return the job specification.

Parameters:oplsdir (None, False or str) – If None (default), search widgets on the panel for a schrodinger.ui.qt.forcefield.ForceFieldSelector (or subclass thereof) and get any custom OPLS directory information from that widget. If False, do not use a custom OPLS directory. If a str, this is the path to use for the custom OPLS directory. Note that the OPLSDIR setting found by oplsdir=None is ambiguous if there is more than one ForceFieldSelector child widget, and that ForceFieldSelector widgets that are NOT child widgets of this panel - such as a widget on a dialog - will not be found. Setting this parameter to False for a panel that does not use a ForceFieldSelector widget avoids the widget search but will only shave a few thousandths of a second off job startup time even for very complex panels.
launchJobCmd(cmdlist, show_progress_bar=0, 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 (int) – Whether or not to show a progress bar tracking the job’s status. If NO_PROGRESS_BAR, no progress bar will be shown. If PROGRESS_BAR_NO_TEXT, a progress bar will be shown. If PROGRESS_BAR_WITH_TEXT, a progress bar will be shown and will also display the job progress text description.
  • 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=0)

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. If NO_PROGRESS_BAR, no progress bar will be shown. If PROGRESS_BAR_NO_TEXT, a progress bar will be shown. If PROGRESS_BAR_WITH_TEXT, a progress bar will be shown and will also display the job progress text description.
launchScript(script, script_args=None, input_files=[], structure_output_file=None, output_files=[], aux_modules=[], show_progress_bar=0, **kwargs)

DEPRECATED for 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 (int) – Whether or not to show a progress bar tracking the job’s status. If NO_PROGRESS_BAR, no progress bar will be shown. If PROGRESS_BAR_NO_TEXT, a progress bar will be shown. If PROGRESS_BAR_WITH_TEXT, a progress bar will be shown and will also display the job progress text description.
launcherToCmdList(slauncher)
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 for 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=0)

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

Parameters:
  • job (jobcontrol.Job) – job to register
  • show_progress_bar (int) – Whether or not to show a progress bar tracking the job’s status. If NO_PROGRESS_BAR, no progress bar will be shown. If PROGRESS_BAR_NO_TEXT, a progress bar will be shown. If PROGRESS_BAR_WITH_TEXT, a progress bar will be shown and will also display the job progress text description.
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.

Parameters:results (ValidationResults) – Set of results generated by validate()
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.

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)
setBaseSize(self, int, int)

setBaseSize(self, QSize)

setConfigDialogSettings(new_values)
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)
setMaximumSize(self, int, int)

setMaximumSize(self, QSize)

setMaximumWidth(self, int)
setMinimumHeight(self, int)
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)
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)
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)
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)
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 (schrodinger.utils.preferences.Preferences object) – The Preferences class to use to store the show/don’t show preference for this dialog. Note that the Preferences object must currently be set to the preference group containing key.
  • key (str) – The key to store the preference under
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.

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 and close the panel.

x(self) → int
y(self) → int
class schrodinger.ui.qt.appframework2.af2_template.SettingsInJobNamesTemplate(**kwargs)

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

This class includes panel settings in its job name

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.

setup()

In setup, make sure that self.jobnameDataChanged is called every time the jobname needs to be updated

jobnameData()

Reimplement jobnameData to return the data to be interpolated into the job name

DrawChildren = 2
DrawWindowBackground = 1
IGNORE_DELAYED_CALLBACKS = False
IgnoreMask = 4
NO_PROGRESS_BAR = 0
PROGRESS_BAR_NO_TEXT = 2
PROGRESS_BAR_WITH_TEXT = 1
class PaintDeviceMetric

Bases: int

__init__

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

bit_length() → int

Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6

conjugate()

Returns self, the complex conjugate of any int.

denominator

the denominator of a rational number in lowest terms

from_bytes(bytes, byteorder, *, signed=False) → int

Return the integer represented by the given array of bytes.

The bytes argument must be a bytes-like object (e.g. bytes or bytearray).

The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.

The signed keyword-only argument indicates whether two’s complement is used to represent the integer.

imag

the imaginary part of a complex number

numerator

the numerator of a rational number in lowest terms

real

the real part of a complex number

to_bytes(length, byteorder, *, signed=False) → bytes

Return an array of bytes representing an integer.

The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.

The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.

The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.

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

__init__

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

bit_length() → int

Number of bits necessary to represent self in binary. >>> bin(37) ‘0b100101’ >>> (37).bit_length() 6

conjugate()

Returns self, the complex conjugate of any int.

denominator

the denominator of a rational number in lowest terms

from_bytes(bytes, byteorder, *, signed=False) → int

Return the integer represented by the given array of bytes.

The bytes argument must be a bytes-like object (e.g. bytes or bytearray).

The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.

The signed keyword-only argument indicates whether two’s complement is used to represent the integer.

imag

the imaginary part of a complex number

numerator

the numerator of a rational number in lowest terms

real

the real part of a complex number

to_bytes(length, byteorder, *, signed=False) → bytes

Return an array of bytes representing an integer.

The integer is represented using length bytes. An OverflowError is raised if the integer is not representable with the given number of bytes.

The byteorder argument determines the byte order used to represent the integer. If byteorder is ‘big’, the most significant byte is at the beginning of the byte array. If byteorder is ‘little’, the most significant byte is at the end of the byte array. To request the native byte order of the host system, use `sys.byteorder’ as the byte order value.

The signed keyword-only argument determines whether two’s complement is used to represent the integer. If signed is False and a negative integer is given, an OverflowError is raised.

class RenderFlags

Bases: sip.simplewrapper

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

__init__

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, object)
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) → object
childrenRect(self) → QRect
childrenRegion(self) → QRegion
cleanup()
cleanupWriteCmd(cmdlist)

Removes options from the command that only work within Maestro. :param cmdlist: the job invocation command :type cmdlist: list

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.

cmdListToCmd(cmdlist)

Converts a command list to a command string.

Parameters:cmdlist (list) – a list of commands
Returns:a command string with all arguments wrapped in double quotes
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, 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) → object
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 (schrodinger.utils.preferences.Preferences object) – The Preferences class to use to store the show/don’t show preference for this dialog. Note that the Preferences object must currently be set to the preference group containing key.
  • key (str) – The key to store the preference under
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(event)
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 (schrodinger.utils.preferences.Preferences object) – The Preferences class to use to store the show/don’t show preference for this dialog. Note that the Preferences object must currently be set to the preference group containing key.
  • key (str) – The key to store the preference under
Return type:

None

inherits(self, str) → bool
initPainter(self, QPainter)
inputMethodEvent(self, QInputMethodEvent)
inputMethodHints(self) → Qt.InputMethodHints
inputMethodQuery(self, Qt.InputMethodQuery) → Any
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
jobDir()
jobname()

Return the job name currently set for the current task.

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(oplsdir=None)

Call this function in start method if the calling script implements the launch api. This function requires implementation of getJobSpec to return the job specification.

Parameters:oplsdir (None, False or str) – If None (default), search widgets on the panel for a schrodinger.ui.qt.forcefield.ForceFieldSelector (or subclass thereof) and get any custom OPLS directory information from that widget. If False, do not use a custom OPLS directory. If a str, this is the path to use for the custom OPLS directory. Note that the OPLSDIR setting found by oplsdir=None is ambiguous if there is more than one ForceFieldSelector child widget, and that ForceFieldSelector widgets that are NOT child widgets of this panel - such as a widget on a dialog - will not be found. Setting this parameter to False for a panel that does not use a ForceFieldSelector widget avoids the widget search but will only shave a few thousandths of a second off job startup time even for very complex panels.
launchJobCmd(cmdlist, show_progress_bar=0, 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 (int) – Whether or not to show a progress bar tracking the job’s status. If NO_PROGRESS_BAR, no progress bar will be shown. If PROGRESS_BAR_NO_TEXT, a progress bar will be shown. If PROGRESS_BAR_WITH_TEXT, a progress bar will be shown and will also display the job progress text description.
  • 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=0)

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. If NO_PROGRESS_BAR, no progress bar will be shown. If PROGRESS_BAR_NO_TEXT, a progress bar will be shown. If PROGRESS_BAR_WITH_TEXT, a progress bar will be shown and will also display the job progress text description.
launchScript(script, script_args=None, input_files=[], structure_output_file=None, output_files=[], aux_modules=[], show_progress_bar=0, **kwargs)

DEPRECATED for 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 (int) – Whether or not to show a progress bar tracking the job’s status. If NO_PROGRESS_BAR, no progress bar will be shown. If PROGRESS_BAR_NO_TEXT, a progress bar will be shown. If PROGRESS_BAR_WITH_TEXT, a progress bar will be shown and will also display the job progress text description.
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 for 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=0)

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

Parameters:
  • job (jobcontrol.Job) – job to register
  • show_progress_bar (int) – Whether or not to show a progress bar tracking the job’s status. If NO_PROGRESS_BAR, no progress bar will be shown. If PROGRESS_BAR_NO_TEXT, a progress bar will be shown. If PROGRESS_BAR_WITH_TEXT, a progress bar will be shown and will also display the job progress text description.
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.

Parameters:results (ValidationResults) – Set of results generated by validate()
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.

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)
setBaseSize(self, int, int)

setBaseSize(self, QSize)

setConfigDialogSettings(new_values)
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)
setMaximumSize(self, int, int)

setMaximumSize(self, QSize)

setMaximumWidth(self, int)
setMinimumHeight(self, int)
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)
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)
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)
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)
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 (schrodinger.utils.preferences.Preferences object) – The Preferences class to use to store the show/don’t show preference for this dialog. Note that the Preferences object must currently be set to the preference group containing key.
  • key (str) – The key to store the preference under
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.

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 and close the panel.

x(self) → int
y(self) → int