schrodinger.application.livedesign.export_tasks module

exception schrodinger.application.livedesign.export_tasks.LDError

Bases: Exception

__init__(*args, **kwargs)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.livedesign.export_tasks.TaskType(value)

Bases: enum.Enum

An enumeration.

two_d = '2D'

three_d = '3D'

class schrodinger.application.livedesign.export_tasks.ExportType(value)

Bases: enum.Enum

An enumeration.

sdf = 'SDF'

maestro = 'MAESTRO'

maestro_sdf = 'MAESTRO_SDF'

class schrodinger.application.livedesign.export_tasks.LDExportTaskMixin

Bases: object

handleLDExceptions()

A context manager for handling that occur when interacting with LD.

Catches various exceptions and re-raises them as LDError with additional explanatory text.

Raises

LDError – if any exceptions occur in the context

class schrodinger.application.livedesign.export_tasks.MasterExportTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.livedesign.export_tasks.LDExportTaskMixin, schrodinger.tasks.tasks.BlockingFunctionTask

Primary LD export task. Responsible for

1. Preparing data for export

2. Launching subtasks that perform export processes

3. Communicating with the LD Export panel

Variables

exportFailed (QtCore.pyqtSignal) – a signal containing an error message describing export failures

input: schrodinger.application.livedesign.export_models.TaskInput

Input model for export tasks.

exportFailed

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

lr_url: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

result_urls: Set[str]

A Param to represent sets. Values of this param will have a mutated signal that will be emitted whenever any elment is added or removed from the set.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the set if specified.

num_success: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_failure: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

unexported_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

corp_ids: List[str]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

__init__(default_value=<object object>, _param_type=<object object>, **kwargs)

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

corp_idsChanged

corp_idsReplaced

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

lr_urlChanged

lr_urlReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

num_failureChanged

num_failureReplaced

num_successChanged

num_successReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

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.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

result_urlsChanged

result_urlsReplaced

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

unexported_itemsChanged

unexported_itemsReplaced

valueChanged

__init__(*args, **kwargs)

num_subtasks

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

mainFunction()

Create and launch export subtasks.

AUTO_TASKDIR = 1

CMDLINE = 1

DEFAULT_TASKDIR_SETTING = None

DONE = 3

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

FAILED = 2

GUI = 2

INTERRUPT_ENABLED = False

RUNNING = 1

TEMP_TASKDIR = 2

WAITING = 0

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters

• func – the function to add

• group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

• order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters

• func (typing.Callable) – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters

• func – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

calling_context: CallingContext

calling_contextChanged

calling_contextReplaced

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

failure_info

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)

getDebugString()

getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

handleLDExceptions()

A context manager for handling that occur when interacting with LD.

Catches various exceptions and re-raises them as LDError with additional explanatory text.

Raises

LDError – if any exceptions occur in the context

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

inputChanged

inputReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()

isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()

isRunning()

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

killTimer(self, int)

max_progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_progressChanged

max_progressReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

name: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

output: parameters.CompoundParam

outputChanged

outputReplaced

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

postprocessors()

Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()

Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

printDebug(*args)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters

• chain (FuncChainDecorator) – which chain to process

• result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progressChanged

progressReplaced

progress_string: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progress_stringChanged

progress_stringReplaced

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.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

Create a new task with the same input and settings (but no output)

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

run()

classmethod runFromCmdLine()

runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

• callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

• calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

status: Status

statusChanged

statusReplaced

taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone

taskFailed

taskStarted

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

valueChanged

wait(timeout=None)

Block until the task is finished executing or timeout seconds have passed.

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

Parameters

timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

class schrodinger.application.livedesign.export_tasks.BaseStructureExportTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.livedesign.export_tasks.LDExportTaskMixin, schrodinger.tasks.tasks.ThreadFunctionTask

Abstract task for exporting structure data to LiveDesign.

file_batches: List[schrodinger.application.livedesign.export_models.FileBatch]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

input: schrodinger.application.livedesign.export_models.TaskInput

Input model for export tasks.

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

lr_url: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

result_urls: Set[str]

A Param to represent sets. Values of this param will have a mutated signal that will be emitted whenever any elment is added or removed from the set.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the set if specified.

num_success: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_failure: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

three_d_export_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

unexported_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

corp_ids: List[str]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

__init__(default_value=<object object>, _param_type=<object object>, **kwargs)

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

corp_idsChanged

corp_idsReplaced

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

lr_urlChanged

lr_urlReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

num_failureChanged

num_failureReplaced

num_successChanged

num_successReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

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.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

result_urlsChanged

result_urlsReplaced

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

thread(self) → QThread

three_d_export_itemsChanged

three_d_export_itemsReplaced

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

unexported_itemsChanged

unexported_itemsReplaced

valueChanged

__init__(*args, **kwargs)

prop_dicts

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

mainFunction()

Perform the LiveDesign export operation for each batch of structures.

get3DExportItems()

Returns

a list of 3D export items associated with this task

Return type

list[export_models.ThreeDExportItem]

AUTO_TASKDIR = 1

CMDLINE = 1

DEFAULT_TASKDIR_SETTING = None

DONE = 3

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

FAILED = 2

GUI = 2

INTERRUPT_ENABLED = False

MAX_THREAD_TASKS = 500

RUNNING = 1

TEMP_TASKDIR = 2

WAITING = 0

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters

• func – the function to add

• group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

• order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters

• func (typing.Callable) – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters

• func – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

calling_context: CallingContext

calling_contextChanged

calling_contextReplaced

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

failure_info

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

file_batchesChanged

file_batchesReplaced

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)

getDebugString()

getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

handleLDExceptions()

A context manager for handling that occur when interacting with LD.

Catches various exceptions and re-raises them as LDError with additional explanatory text.

Raises

LDError – if any exceptions occur in the context

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

inputChanged

inputReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()

isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()

isRunning()

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

@overrides: AbstractTask

Killing threads is dangerous and can leading to deadlocking on Windows, so we intentionally leave it unimplemented rather than using QThread.terminate.

killTimer(self, int)

max_progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_progressChanged

max_progressReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

name: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

output: parameters.CompoundParam

outputChanged

outputReplaced

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

postprocessors()

Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()

Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

printDebug(*args)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters

• chain (FuncChainDecorator) – which chain to process

• result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progressChanged

progressReplaced

progress_string: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progress_stringChanged

progress_stringReplaced

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.

qthread

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

Create a new task with the same input and settings (but no output)

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

run()

classmethod runFromCmdLine()

runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

• callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

• calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

status: Status

statusChanged

statusReplaced

taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone

taskFailed

taskStarted

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

valueChanged

wait(timeout=None)

Block until the task is finished executing or timeout seconds have passed.

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

Parameters

timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

class schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.livedesign.export_tasks.BaseStructureExportTask

Abstract structure export task for older (v8.6-) versions of LiveDesign.

__init__(*args, **kwargs)

structure_index_map

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

compound_batches

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

AUTO_TASKDIR = 1

CMDLINE = 1

DEFAULT_TASKDIR_SETTING = None

DONE = 3

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

FAILED = 2

GUI = 2

INTERRUPT_ENABLED = False

MAX_THREAD_TASKS = 500

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

__init__(default_value=<object object>, _param_type=<object object>, **kwargs)

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

corp_ids: List[str]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

corp_idsChanged

corp_idsReplaced

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

lr_url: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

lr_urlChanged

lr_urlReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

num_failure: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_failureChanged

num_failureReplaced

num_success: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_successChanged

num_successReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

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.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

result_urls: Set[str]

A Param to represent sets. Values of this param will have a mutated signal that will be emitted whenever any elment is added or removed from the set.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the set if specified.

result_urlsChanged

result_urlsReplaced

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

thread(self) → QThread

three_d_export_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

three_d_export_itemsChanged

three_d_export_itemsReplaced

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

unexported_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

unexported_itemsChanged

unexported_itemsReplaced

valueChanged

RUNNING = 1

TEMP_TASKDIR = 2

WAITING = 0

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters

• func – the function to add

• group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

• order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters

• func (typing.Callable) – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters

• func – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

calling_context: CallingContext

calling_contextChanged

calling_contextReplaced

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

failure_info

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

file_batches: List[schrodinger.application.livedesign.export_models.FileBatch]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

file_batchesChanged

file_batchesReplaced

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

get3DExportItems()

Returns

a list of 3D export items associated with this task

Return type

list[export_models.ThreeDExportItem]

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)

getDebugString()

getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

handleLDExceptions()

A context manager for handling that occur when interacting with LD.

Catches various exceptions and re-raises them as LDError with additional explanatory text.

Raises

LDError – if any exceptions occur in the context

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input: schrodinger.application.livedesign.export_models.TaskInput

Input model for export tasks.

inputChanged

inputReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()

isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()

isRunning()

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

@overrides: AbstractTask

Killing threads is dangerous and can leading to deadlocking on Windows, so we intentionally leave it unimplemented rather than using QThread.terminate.

killTimer(self, int)

mainFunction()

Perform the LiveDesign export operation for each batch of structures.

max_progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_progressChanged

max_progressReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

name: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

output: parameters.CompoundParam

outputChanged

outputReplaced

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

postprocessors()

Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()

Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

printDebug(*args)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters

• chain (FuncChainDecorator) – which chain to process

• result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progressChanged

progressReplaced

progress_string: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progress_stringChanged

progress_stringReplaced

prop_dicts

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

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.

qthread

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

Create a new task with the same input and settings (but no output)

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

run()

classmethod runFromCmdLine()

runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

• callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

• calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

status: Status

statusChanged

statusReplaced

taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone

taskFailed

taskStarted

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

valueChanged

wait(timeout=None)

Block until the task is finished executing or timeout seconds have passed.

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

Parameters

timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

class schrodinger.application.livedesign.export_tasks.Export2DTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86

Structure export task for 2D data for older (v8.6-) versions of LiveDesign.

__init__(*args, **kwargs)

generateExportFiles()

Create files necessary for the LiveDesign export and add them to the file_batches parameter. This includes a 2D structure (.sdf) file and an empty (but necessary) map file.

AUTO_TASKDIR = 1

CMDLINE = 1

DEFAULT_TASKDIR_SETTING = None

DONE = 3

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

FAILED = 2

GUI = 2

INTERRUPT_ENABLED = False

MAX_THREAD_TASKS = 500

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

__init__(default_value=<object object>, _param_type=<object object>, **kwargs)

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

corp_ids: List[str]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

corp_idsChanged

corp_idsReplaced

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

lr_url: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

lr_urlChanged

lr_urlReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

num_failure: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_failureChanged

num_failureReplaced

num_success: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_successChanged

num_successReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

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.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

result_urls: Set[str]

A Param to represent sets. Values of this param will have a mutated signal that will be emitted whenever any elment is added or removed from the set.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the set if specified.

result_urlsChanged

result_urlsReplaced

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

thread(self) → QThread

three_d_export_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

three_d_export_itemsChanged

three_d_export_itemsReplaced

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

unexported_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

unexported_itemsChanged

unexported_itemsReplaced

valueChanged

RUNNING = 1

TEMP_TASKDIR = 2

WAITING = 0

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters

• func – the function to add

• group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

• order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters

• func (typing.Callable) – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters

• func – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

calling_context: CallingContext

calling_contextChanged

calling_contextReplaced

childEvent(self, QChildEvent)

children(self) → List[QObject]

compound_batches

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

failure_info

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

file_batches: List[schrodinger.application.livedesign.export_models.FileBatch]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

file_batchesChanged

file_batchesReplaced

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

get3DExportItems()

Returns

a list of 3D export items associated with this task

Return type

list[export_models.ThreeDExportItem]

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)

getDebugString()

getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

handleLDExceptions()

A context manager for handling that occur when interacting with LD.

Catches various exceptions and re-raises them as LDError with additional explanatory text.

Raises

LDError – if any exceptions occur in the context

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input: schrodinger.application.livedesign.export_models.TaskInput

Input model for export tasks.

inputChanged

inputReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()

isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()

isRunning()

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

@overrides: AbstractTask

Killing threads is dangerous and can leading to deadlocking on Windows, so we intentionally leave it unimplemented rather than using QThread.terminate.

killTimer(self, int)

mainFunction()

Perform the LiveDesign export operation for each batch of structures.

max_progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_progressChanged

max_progressReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

name: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

output: parameters.CompoundParam

outputChanged

outputReplaced

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

postprocessors()

Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()

Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

printDebug(*args)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters

• chain (FuncChainDecorator) – which chain to process

• result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progressChanged

progressReplaced

progress_string: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progress_stringChanged

progress_stringReplaced

prop_dicts

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

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.

qthread

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

Create a new task with the same input and settings (but no output)

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

run()

classmethod runFromCmdLine()

runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

• callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

• calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

status: Status

statusChanged

statusReplaced

structure_index_map

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone

taskFailed

taskStarted

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

valueChanged

wait(timeout=None)

Block until the task is finished executing or timeout seconds have passed.

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

Parameters

timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

class schrodinger.application.livedesign.export_tasks.Export3DTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.livedesign.export_tasks.BaseStructureExportTask86

Structure export task for 3D data for older (v8.6-) versions of LiveDesign.

__init__(*args, **kwargs)

generateExportFiles()

Create files necessary for the LiveDesign export and add them to the file_batches parameter. This includes a 3D structure file and a corresponding map file.

AUTO_TASKDIR = 1

CMDLINE = 1

DEFAULT_TASKDIR_SETTING = None

DONE = 3

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

FAILED = 2

GUI = 2

INTERRUPT_ENABLED = False

MAX_THREAD_TASKS = 500

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

__init__(default_value=<object object>, _param_type=<object object>, **kwargs)

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

corp_ids: List[str]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

corp_idsChanged

corp_idsReplaced

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

lr_url: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

lr_urlChanged

lr_urlReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

num_failure: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_failureChanged

num_failureReplaced

num_success: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_successChanged

num_successReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

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.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

result_urls: Set[str]

A Param to represent sets. Values of this param will have a mutated signal that will be emitted whenever any elment is added or removed from the set.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the set if specified.

result_urlsChanged

result_urlsReplaced

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

thread(self) → QThread

three_d_export_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

three_d_export_itemsChanged

three_d_export_itemsReplaced

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

unexported_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

unexported_itemsChanged

unexported_itemsReplaced

valueChanged

RUNNING = 1

TEMP_TASKDIR = 2

WAITING = 0

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters

• func – the function to add

• group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

• order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters

• func (typing.Callable) – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters

• func – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

calling_context: CallingContext

calling_contextChanged

calling_contextReplaced

childEvent(self, QChildEvent)

children(self) → List[QObject]

compound_batches

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

failure_info

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

file_batches: List[schrodinger.application.livedesign.export_models.FileBatch]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

file_batchesChanged

file_batchesReplaced

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

get3DExportItems()

Returns

a list of 3D export items associated with this task

Return type

list[export_models.ThreeDExportItem]

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)

getDebugString()

getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

handleLDExceptions()

A context manager for handling that occur when interacting with LD.

Catches various exceptions and re-raises them as LDError with additional explanatory text.

Raises

LDError – if any exceptions occur in the context

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input: schrodinger.application.livedesign.export_models.TaskInput

Input model for export tasks.

inputChanged

inputReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()

isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()

isRunning()

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

@overrides: AbstractTask

Killing threads is dangerous and can leading to deadlocking on Windows, so we intentionally leave it unimplemented rather than using QThread.terminate.

killTimer(self, int)

mainFunction()

Perform the LiveDesign export operation for each batch of structures.

max_progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_progressChanged

max_progressReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

name: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

output: parameters.CompoundParam

outputChanged

outputReplaced

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

postprocessors()

Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()

Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

printDebug(*args)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters

• chain (FuncChainDecorator) – which chain to process

• result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progressChanged

progressReplaced

progress_string: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progress_stringChanged

progress_stringReplaced

prop_dicts

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

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.

qthread

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

Create a new task with the same input and settings (but no output)

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

run()

classmethod runFromCmdLine()

runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

• callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

• calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

status: Status

statusChanged

statusReplaced

structure_index_map

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone

taskFailed

taskStarted

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

valueChanged

wait(timeout=None)

Block until the task is finished executing or timeout seconds have passed.

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

Parameters

timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

class schrodinger.application.livedesign.export_tasks.ExportTask87(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.livedesign.export_tasks.BaseStructureExportTask

Export structure task for newer (v8.7+) versions of LiveDesign.

Variables

• EMPTY_PATH_TUPLE (tuple[NoneType, NoneType]) – a tuple of None to use as a default return value st_path_map if a key is not defined

• st_path_map (dict[structure.Structure, tuple[str, str] or tuple[None, None]]) – a dictionary mapping structures to a tuple of (absolute path, relative path) where they have been stored as .mae files

EMPTY_PATH_TUPLE = (None, None)

__init__(*args, **kwargs)

st_path_map

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

generateExportFiles()

Create files necessary for the LiveDesign export and add them to the file_batches parameter. This includes a SDF file (2D), a zipped directory of MAE files (3D), and a TSV file (mapping) that describes the relationship between the two.

AUTO_TASKDIR = 1

CMDLINE = 1

DEFAULT_TASKDIR_SETTING = None

DONE = 3

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

FAILED = 2

GUI = 2

INTERRUPT_ENABLED = False

MAX_THREAD_TASKS = 500

class Output(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

__init__(default_value=<object object>, _param_type=<object object>, **kwargs)

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

corp_ids: List[str]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

corp_idsChanged

corp_idsReplaced

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

lr_url: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

lr_urlChanged

lr_urlReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

num_failure: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_failureChanged

num_failureReplaced

num_success: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

num_successChanged

num_successReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

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.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

result_urls: Set[str]

A Param to represent sets. Values of this param will have a mutated signal that will be emitted whenever any elment is added or removed from the set.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the set if specified.

result_urlsChanged

result_urlsReplaced

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

thread(self) → QThread

three_d_export_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

three_d_export_itemsChanged

three_d_export_itemsReplaced

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

unexported_items: List[schrodinger.application.livedesign.export_models.ThreeDExportItem]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

unexported_itemsChanged

unexported_itemsReplaced

valueChanged

RUNNING = 1

TEMP_TASKDIR = 2

WAITING = 0

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters

• func – the function to add

• group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

• order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters

• func (typing.Callable) – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters

• func – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

calling_context: CallingContext

calling_contextChanged

calling_contextReplaced

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

failure_info

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

file_batches: List[schrodinger.application.livedesign.export_models.FileBatch]

A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

file_batchesChanged

file_batchesReplaced

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

get3DExportItems()

Returns

a list of 3D export items associated with this task

Return type

list[export_models.ThreeDExportItem]

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)

getDebugString()

getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

handleLDExceptions()

A context manager for handling that occur when interacting with LD.

Catches various exceptions and re-raises them as LDError with additional explanatory text.

Raises

LDError – if any exceptions occur in the context

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input: schrodinger.application.livedesign.export_models.TaskInput

Input model for export tasks.

inputChanged

inputReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()

isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()

isRunning()

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

@overrides: AbstractTask

Killing threads is dangerous and can leading to deadlocking on Windows, so we intentionally leave it unimplemented rather than using QThread.terminate.

killTimer(self, int)

mainFunction()

Perform the LiveDesign export operation for each batch of structures.

max_progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_progressChanged

max_progressReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

name: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

output: parameters.CompoundParam

outputChanged

outputReplaced

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

postprocessors()

Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()

Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

printDebug(*args)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters

• chain (FuncChainDecorator) – which chain to process

• result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progressChanged

progressReplaced

progress_string: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progress_stringChanged

progress_stringReplaced

prop_dicts

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

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.

qthread

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

Create a new task with the same input and settings (but no output)

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

run()

classmethod runFromCmdLine()

runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

• callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

• calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

status: Status

statusChanged

statusReplaced

taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone

taskFailed

taskStarted

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

valueChanged

wait(timeout=None)

Block until the task is finished executing or timeout seconds have passed.

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

Parameters

timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

class schrodinger.application.livedesign.export_tasks.AttachmentExportTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.application.livedesign.export_tasks.LDExportTaskMixin, schrodinger.tasks.tasks.ThreadFunctionTask

Export task for FFC attachment data.

Variables

attachment_data_map (dict[str, export_models.AttachmentData]) – a dictionary mapping the column name for an attachment to a data class storing other information about that attachment

input: schrodinger.application.livedesign.export_models.AttachmentTaskInput

Input model for FFC attachment export task.

output: schrodinger.application.livedesign.export_models.AttachmentTaskOutput

Output model for FFC attachment export task.

__init__(*args, **kwargs)

attachment_data_map

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

mainFunction()

Upload the attachment files and associate them with the appropriate LiveReport cells.

AUTO_TASKDIR = 1

CMDLINE = 1

DEFAULT_TASKDIR_SETTING = None

DONE = 3

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

FAILED = 2

GUI = 2

INTERRUPT_ENABLED = False

MAX_THREAD_TASKS = 500

RUNNING = 1

TEMP_TASKDIR = 2

WAITING = 0

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters

• func – the function to add

• group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.

• order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.

addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters

• func (typing.Callable) – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters

• func – the function to add

• order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

calling_context: CallingContext

calling_contextChanged

calling_contextReplaced

childEvent(self, QChildEvent)

children(self) → List[QObject]

classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0

deleteLater(self)

destroyed

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

disconnect(QMetaObject.Connection) → bool

disconnect(self) → None

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

failure_info

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

findChild(self, type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject

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

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

findChildren(self, type, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)

getDebugString()

getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')

classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3

Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

handleLDExceptions()

A context manager for handling that occur when interacting with LD.

Catches various exceptions and re-raises them as LDError with additional explanatory text.

Raises

LDError – if any exceptions occur in the context

inherits(self, str) → bool

initAbstract()

initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

inputChanged

inputReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()

isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()

isRunning()

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

@overrides: AbstractTask

Killing threads is dangerous and can leading to deadlocking on Windows, so we intentionally leave it unimplemented rather than using QThread.terminate.

killTimer(self, int)

max_progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

max_progressChanged

max_progressReplaced

metaObject(self) → QMetaObject

moveToThread(self, QThread)

name: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

outputChanged

outputReplaced

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'

parent(self) → QObject

postprocessors()

Returns

A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()

Return type

list[typing.Callable]

preprocessors()

Returns

A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)

printDebug(*args)

processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters

• chain (FuncChainDecorator) – which chain to process

• result_callback – the callback that will get called with the result of each function in the chain

Returns

a list of the results from the functions

progress: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progressChanged

progressReplaced

progress_string: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str

progress_stringChanged

progress_stringReplaced

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.

qthread

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

Create a new task with the same input and settings (but no output)

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5

run()

classmethod runFromCmdLine()

runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

• callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

• calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10

Parameters

• param – The owner param to set a subparam value of.

• value – The value to set the subparam value to.

setParent(self, QObject)

setProperty(self, str, Any) → bool

classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

• param1 – The first abstract param to keep synced

• param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

• value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

• kwargs – For internal use only.

signalsBlocked(self) → bool

skip_eq_check()

specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters

skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt6.QtCore.QMetaObject object>

status: Status

statusChanged

statusReplaced

taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone

taskFailed

taskStarted

thread(self) → QThread

timerEvent(self, QTimerEvent)

toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(str, disambiguation: str = None, n: int = - 1) → str

valueChanged

wait(timeout=None)

Block until the task is finished executing or timeout seconds have passed.

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

Parameters

timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

schrodinger.application.livedesign.export_tasks.export_to_ld(ld_client, project_name, lr_name, lr_id, prop_dicts, publish_data, compound_source, export_type, map_file_path, sdf_file_path=None, three_d_file_path=None)

Export the supplied data to LiveDesign.

Parameters

• ld_client (ldclient.LDClient) – LD client session

• project_name (str) – the name of the LiveDesign project

• lr_name (str) – the name of the LiveReport

• lr_id (int) – the ID of the LiveReport

• prop_dicts (dict(str, str)) – property arguments that specify which structure properties should be converted into LiveDesign columns

• publish_data (bool) – whether the exported data should be published globally for all LiveDesign users

• compound_source (str or None) – the compound source argument required for certain LD versions

• export_type (ExportType) – the type of export to perform.

• map_file_path (str) – the path of the mapping file

• sdf_file_path (str or NoneType) – optionally, the path of an SDF file

• three_d_file_path (str or NoneType) – optionally, the path of an 3D file

Returns

task id

Return type

int

schrodinger.application.livedesign.export_tasks.create_live_report(ld_client, ld_models, proj_name, title)

Create a new LiveReport.

Parameters

• ld_client (client.LDClient) – the LiveDesign client instance

• ld_models (module) – the livedesign models module

• proj_name (str) – the name of the project to which the LiveReport should be added

• title (str) – the desired LiveReport title

Returns

the new LiveReport

Return type

models.LiveReport