schrodinger.tasks.jobtasks module

Job incorporation

If a CmdJobTask’s job registers an incorporation file with job control, the file can be accessed after the task is done via output.incorporation_file.

ComboJobTasks support the option to specify an incorporation file in the backend of the task using JobOutput. Example:

class MyJobTask(jobtasks.ComboJobTask):
    output: jobtasks.JobOutput

    def mainFunction(self):
        self.output.incorporation_file = 'foo.maegz'  # In backend

Specifying an incorporation file in the frontend of the task will have no effect and thus should never be done.

schrodinger.tasks.jobtasks.is_jobtask(task)[source]

Utility function to check if an object is a jobtask.

class schrodinger.tasks.jobtasks.AllowedHostTypes(value)[source]

Bases: schrodinger.models.jsonable.JsonableEnum

An enumeration.

CPU_ONLY = 1
GPU_ONLY = 2
CPU_AND_GPU = 3
class schrodinger.tasks.jobtasks.HostParam(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.Param

DataClass

alias of schrodinger.tasks.hosts.Host

__init__(default_value='localhost', allowed_types=AllowedHostTypes.CPU_ONLY, *args, **kwargs)[source]
Parameters
  • default_value (object) – The value to use in constructing the default value for the param. A new param will have the value returned by DataClass(default_value).

  • DataClass (type) – The type to use for values of this param.

  • deepcopyable (bool) – Whether values of this param are deepcopyable. If this param is not deepcopyable and its owner param is deepcopied, the copy’s subparam value will be identical.

  • _param_type – For internal use only.

blockSignals(self, bool) bool
childEvent(self, QChildEvent)
children(self) List[QObject]
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
getTypeHint()
inherits(self, str) bool
initAbstract()
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isSignalConnected(self, QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, int)
metaObject(self) QMetaObject
moveToThread(self, QThread)
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)
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) bool
signalsBlocked(self) bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = - 1) str
schrodinger.tasks.jobtasks.get_hosts()[source]
schrodinger.tasks.jobtasks.get_default_host(allowed_host_types=AllowedHostTypes.CPU_AND_GPU)[source]

Gets the default host for a job to run on, which will be the jobhost if this function is called from within a jobcontrol backend, or the localhost otherwise. If the specified host type is GPU_ONLY, and the localhost and jobhost don’t have GPUs, then the returned host will be the first gpu-enabled host returned from get_hosts().

class schrodinger.tasks.jobtasks.HostSettings(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

Variables

HOST_PLACEHOLDER_ARGS – Placeholders to pass into the -HOST argument when no host is available based on the currently allowed host types.

host
num_subjobs: 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
allowed_host_types: schrodinger.tasks.jobtasks.AllowedHostTypes
CPU_PLACEHOLDER_ARG = '<CPU-host-placeholder>'
GPU_PLACEHOLDER_ARG = '<GPU-host-placeholder>'
CPU_AND_GPU_PLACEHOLDER_ARG = '<host-placeholder>'
HOST_PLACEHOLDER_ARGS = {<AllowedHostTypes.CPU_ONLY: 1>: '<CPU-host-placeholder>', <AllowedHostTypes.GPU_ONLY: 2>: '<GPU-host-placeholder>', <AllowedHostTypes.CPU_AND_GPU: 3>: '<host-placeholder>'}
toCmdArg()[source]
initializeValue()[source]

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.

classmethod adapter55040(json_dict)[source]
toJsonImplementation()[source]

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns

A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

classmethod fromJsonImplementation(json_dict)[source]

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

Warning

This should never be called directly.

getHostPlaceholderArg() str[source]

Return the host placeholder argument for the currently allowed host types.

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)
allowed_host_typesChanged
allowed_host_typesReplaced
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)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
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

getAbstractParam(*args, **kwargs)
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(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
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.

hostChanged
hostReplaced
inherits(self, str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, int)
metaObject(self) QMetaObject
moveToThread(self, QThread)
num_subjobsChanged
num_subjobsReplaced
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(*args, **kwargs)
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
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(*args, **kwargs)
signalsBlocked(self) bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
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

tr(self, str, disambiguation: str = None, n: int = - 1) str
valueChanged
class schrodinger.tasks.jobtasks.IncorporationMode(value)[source]

Bases: schrodinger.models.jsonable.JsonableEnum

An enumeration.

APPEND = 'append'
APPENDINPLACE = 'appendinplace'
REPLACE = 'replace'
IGNORE = 'ignore'
APPENDNEW = 'appendnew'
class schrodinger.tasks.jobtasks.IncorporationParam(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.EnumParam

DEFAULT_ALLOWED_MODES = (<IncorporationMode.APPEND: 'append'>, <IncorporationMode.APPENDINPLACE: 'appendinplace'>, <IncorporationMode.IGNORE: 'ignore'>, <IncorporationMode.APPENDNEW: 'appendnew'>)
__init__(*args, allowed_modes=(<IncorporationMode.APPEND: 'append'>, <IncorporationMode.APPENDINPLACE: 'appendinplace'>, <IncorporationMode.IGNORE: 'ignore'>, <IncorporationMode.APPENDNEW: 'appendnew'>), **kwargs)[source]

EnumParam must be initialized with the Enum class that this param is to be based on as well as the default value.

Parameters
  • enum_class (enum.Enum) – the enum class to base this pram on

  • default_value (a member of the enum_class) – The default enum value. If not provided, the param will default to the first value of the enum.

DataClass

alias of object

blockSignals(self, bool) bool
childEvent(self, QChildEvent)
children(self) List[QObject]
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
getTypeHint()
inherits(self, str) bool
initAbstract()
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isSignalConnected(self, QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, int)
metaObject(self) QMetaObject
moveToThread(self, QThread)
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)
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) bool
signalsBlocked(self) bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = - 1) str
class schrodinger.tasks.jobtasks.JobConfig(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

Subclass JobConfig to customize what job settings are available for a given jobtask. To disable an option, set an ordinary (non-param) class variable with value None for that option.

Subclasses may add any arbitrary options as desired; it is the responsibility of the task to handle those options.

viewname: 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
jobname: 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
host_settings: schrodinger.tasks.jobtasks.HostSettings
Variables

HOST_PLACEHOLDER_ARGS – Placeholders to pass into the -HOST argument when no host is available based on the currently allowed host types.

incorporation = None
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)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
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(*args, **kwargs)
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(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
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.

host_settingsChanged
host_settingsReplaced
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(*args, **kwargs)
isSignalConnected(self, QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
jobnameChanged
jobnameReplaced
killTimer(self, int)
metaObject(self) QMetaObject
moveToThread(self, QThread)
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(*args, **kwargs)
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
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(*args, **kwargs)
signalsBlocked(self) bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
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(*args, **kwargs)

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns

A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

tr(self, str, disambiguation: str = None, n: int = - 1) str
valueChanged
viewnameChanged
viewnameReplaced
schrodinger.tasks.jobtasks.job_config_factory(allowed_host_types=AllowedHostTypes.CPU_ONLY, default_incorp_mode=None, supports_subjobs=False, viewname=None)[source]

Generate JobConfig objects with typical options.

Parameters
  • allowed_host_types (AllowedHostTypes or None) – Whether this job accepts cpu hosts, gpu hosts, or both. Pass None to disable remote hosts (always run on localhost)

  • default_incorp_mode (IncorporationMode or None) – The default disposition. Pass None for jobs that do not incorporate at all.

  • supports_subjobs (bool) – whether this job can be split into subjobs

  • viewname (str or None) – what viewname should be used for this type of job

class schrodinger.tasks.jobtasks.JobOutput(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.models.parameters.CompoundParam

Base class for jobtask output.

incorporation_file: schrodinger.tasks.tasks.TaskFile

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
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)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
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(*args, **kwargs)
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(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
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.

incorporation_fileChanged
incorporation_fileReplaced
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(*args, **kwargs)
isSignalConnected(self, QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, int)
metaObject(self) QMetaObject
moveToThread(self, QThread)
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(*args, **kwargs)
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
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(*args, **kwargs)
signalsBlocked(self) bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
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(*args, **kwargs)

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns

A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

tr(self, str, disambiguation: str = None, n: int = - 1) str
valueChanged
exception schrodinger.tasks.jobtasks.SetJobRuntimeError[source]

Bases: RuntimeError

An error while trying to a set a job on a task.

__init__(*args, **kwargs)
args
with_traceback()

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

class schrodinger.tasks.jobtasks.JobBackendCmdMixin(*args, cmd_list=None, **kwargs)[source]

Bases: schrodinger.tasks.jobtasks._AbstractJobMixin

Base class for running backends that already support job control. Combine with an AbstractCmdTask. To use, override makeCmd.

__init__(*args, cmd_list=None, **kwargs)[source]
makeCmd()[source]

@overrides: tasks.AbstractCmdTask

Child classes must override.

property PROGRAM_NAME
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

inWriteMode()
initializeValue()

@overrides: paramters.CompoundParam

job_id

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
kill()

@overrides: tasks.AbstractTask

replicate()

@overrides: tasks.AbstractTask

runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

runToCmd(skip_preprocessing=False)

Does the same thing as start except it doesn’t actually launch the job. Instead it just returns the final job cmd.

Intended to be used for running jobtasks on JobDJ, which requires a job cmd rather than a task.

setJob(job: schrodinger.job.jobcontrol.Job)

” Use given jobcontrol.Job to incorporate job results into the task and run postprocessors. Example:

task = FooTask()
cmd = task.runToCommand()
job = jobcontrol.launch_job(cmd)
job.wait()
task.setJob(job)

If the job has not been downloaded, the task will be set to FAILED with a SetJobRuntimeError.

Parameters

jobjobcontrol.Job with results to incorporate into the task.

stop()
write(skip_preprocessing=False)
writeStuZipFile()
job_config: schrodinger.tasks.jobtasks.JobConfig
input: schrodinger.models.parameters.CompoundParam
class schrodinger.tasks.jobtasks.ComboJobMixin(*args, **kwargs)[source]

Bases: schrodinger.tasks.jobtasks._LaunchAPIMixin

Base class for running python code using the “combo” task pattern. Combine with AbstractComboTask. To use, define:

mainFunction (or, equivalently backendMain): the python function that will be executed in the backend process under job control.

write(skip_preprocessing=False)[source]
makeCmd()[source]

@overrides: tasks.AbstractCmdTask

Child classes must not override this method.

isBackendMode()[source]
getTaskDir()[source]
getTaskFilename(fname)[source]
runBackend()[source]

@overrides: AbstractComboTask

property PROGRAM_NAME
__init__(*args, **kwargs)
classmethod adapter55013(json_dict)
addInputDirectory(directory)

Add an input directory to be copied over with the job.

addLicenseReservation(license, num_tokens=1)

Add a license reservation for this job. This information is used by job control to ensure the job is only started once the required licenses become available.

In a preprocessor, (i.e. before launching the backend), a reservation should be added for each license that will be checked out directly by that backend. Example:

class GlideTask(ComboJobTask):

    @preprocessor
    def _reserveGlideLicense(self):
        # Reserve a Glide license.
        self.addLicenseReservation(license.GLIDE_MAIN)

    def mainFunction(self):
        # Check out the Glide license
        lic = license.License(license.GLIDE_MAIN)

        # ... Do computations requiring Glide ...

        lic.checkin()

Licenses that will be checked out by subjobs of this job do not need reservations added here; subjobs are responsible for their own license reservations.

Parameters
  • license (module-constant from schrodinger.utils.license (e.g. license.AUTODESIGNER)) – a license that will be used by the backend

  • num_tokens (int) – number of tokens for this license reservations

classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

getLogAsString() str
inWriteMode()
initConcrete()
initializeValue()

@overrides: paramters.CompoundParam

job_id

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
kill()

@overrides: tasks.AbstractTask

makeJobSpecFromCmd(cmd)
makeLaunchParams()
replicate()

@overrides: tasks.AbstractTask

runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

runToCmd(skip_preprocessing=False)

Does the same thing as start except it doesn’t actually launch the job. Instead it just returns the final job cmd.

Intended to be used for running jobtasks on JobDJ, which requires a job cmd rather than a task.

setJob(job: schrodinger.job.jobcontrol.Job)

” Use given jobcontrol.Job to incorporate job results into the task and run postprocessors. Example:

task = FooTask()
cmd = task.runToCommand()
job = jobcontrol.launch_job(cmd)
job.wait()
task.setJob(job)

If the job has not been downloaded, the task will be set to FAILED with a SetJobRuntimeError.

Parameters

jobjobcontrol.Job with results to incorporate into the task.

stop()
wrapCmdInLaunchApi(cmd)
writeStuZipFile()
job_config: schrodinger.tasks.jobtasks.JobConfig
input: schrodinger.models.parameters.CompoundParam
class schrodinger.tasks.jobtasks.CmdJobTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.tasks.jobtasks.JobBackendCmdMixin, schrodinger.tasks.tasks.AbstractCmdTask

Class for running backends that already support jobcontrol.

CmdJobTask can either be subclassed to implement custom input/output params and other behavior, or can be instantiated and run directly by supplying the optional cmd_list constructor argument. For example:

task = jobtasks.CmdJobTask(cmd_list=[‘testapp’, ‘-t’, ‘1’]) task.start()

CmdJobTask has a standard output that auto-populates with output files from its respective job. Custom output classes must inherit CmdJobTask.Output.

Note that specifying cmd_list will bypass some custom functionality and should not be used with CmdJobTask subclasses.

Output

alias of schrodinger.tasks.jobtasks._CmdJobTaskOutput

__init__(*args, **kwargs)[source]
AUTO_TASKDIR = <object object>
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
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
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

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
childEvent(self, QChildEvent)
children(self) List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
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(*args, **kwargs)
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(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
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

inWriteMode()
inherits(self, str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: paramters.CompoundParam

input: schrodinger.models.parameters.CompoundParam

All CompoundParam instances are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()
isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) bool
isStartable()
isWidgetType(self) bool
isWindowType(self) bool
job_config: schrodinger.tasks.jobtasks.JobConfig

Subclass JobConfig to customize what job settings are available for a given jobtask. To disable an option, set an ordinary (non-param) class variable with value None for that option.

Subclasses may add any arbitrary options as desired; it is the responsibility of the task to handle those options.

job_configChanged
job_configReplaced
job_id

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
kill()

@overrides: tasks.AbstractTask

killTimer(self, int)
makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

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

Base class for CmdJobTask output. All params defined thus far are intended to be read-only, as CmdJobTask sets them during postprocessing.

Any new params defined by subclasses are safe to use as normal.

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()

@overrides: tasks.AbstractTask

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)
run()
runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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.

runToCmd(skip_preprocessing=False)

Does the same thing as start except it doesn’t actually launch the job. Instead it just returns the final job cmd.

Intended to be used for running jobtasks on JobDJ, which requires a job cmd rather than a task.

sender(self) QObject
senderSignalIndex(self) int
setJob(job: schrodinger.job.jobcontrol.Job)

” Use given jobcontrol.Job to incorporate job results into the task and run postprocessors. Example:

task = FooTask()
cmd = task.runToCommand()
job = jobcontrol.launch_job(cmd)
job.wait()
task.setJob(job)

If the job has not been downloaded, the task will be set to FAILED with a SetJobRuntimeError.

Parameters

jobjobcontrol.Job with results to incorporate into the task.

setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
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(*args, **kwargs)
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 = <PyQt5.QtCore.QMetaObject object>
status: Status
statusChanged
statusReplaced
stop()
taskDirSetting()

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

taskDone
taskFailed
taskStarted
thread(self) QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
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(*args, **kwargs)

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns

A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

tr(self, 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.

write(skip_preprocessing=False)
writeStuZipFile()
class schrodinger.tasks.jobtasks.ComboJobTask(*args, _param_type=<object object>, **kwargs)[source]

Bases: schrodinger.tasks.jobtasks.ComboJobMixin, schrodinger.tasks.tasks.AbstractComboTask

runBackend()[source]

@overrides: AbstractComboTask

getTaskDir()[source]

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).

AUTO_TASKDIR = <object object>
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
ENTRYPOINT = 'combotask_entry_point.py'
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)
classmethod adapter55013(json_dict)
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.

addInputDirectory(directory)

Add an input directory to be copied over with the job.

addLicenseReservation(license, num_tokens=1)

Add a license reservation for this job. This information is used by job control to ensure the job is only started once the required licenses become available.

In a preprocessor, (i.e. before launching the backend), a reservation should be added for each license that will be checked out directly by that backend. Example:

class GlideTask(ComboJobTask):

    @preprocessor
    def _reserveGlideLicense(self):
        # Reserve a Glide license.
        self.addLicenseReservation(license.GLIDE_MAIN)

    def mainFunction(self):
        # Check out the Glide license
        lic = license.License(license.GLIDE_MAIN)

        # ... Do computations requiring Glide ...

        lic.checkin()

Licenses that will be checked out by subjobs of this job do not need reservations added here; subjobs are responsible for their own license reservations.

Parameters
  • license (module-constant from schrodinger.utils.license (e.g. license.AUTODESIGNER)) – a license that will be used by the backend

  • num_tokens (int) – number of tokens for this license reservations

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)
backendMain()
blockSignals(self, bool) bool
block_signal_propagation()
calling_context

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
childEvent(self, QChildEvent)
children(self) List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChild(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) QObject
findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) List[QObject]
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(*args, **kwargs)
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.

getLogAsString() str
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
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.

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

inWriteMode()
inherits(self, str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: paramters.CompoundParam

input: parameters.CompoundParam

All CompoundParam instances are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isBackendMode()
isDebugEnabled()
isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) bool
isStartable()
isWidgetType(self) bool
isWindowType(self) bool
job_config: JobConfig

Subclass JobConfig to customize what job settings are available for a given jobtask. To disable an option, set an ordinary (non-param) class variable with value None for that option.

Subclasses may add any arbitrary options as desired; it is the responsibility of the task to handle those options.

job_configChanged
job_configReplaced
job_id

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 json_filename
property json_out_filename
kill()

@overrides: tasks.AbstractTask

killTimer(self, int)
mainFunction()
makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must not override this method.

makeJobSpecFromCmd(cmd)
makeLaunchParams()
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

All CompoundParam instances are automatically serializable if their subparams are serializable. To serialize and deserialize, use the schrodinger json module:

from schrodinger.models import json
class Coord(parameters.CompoundParam):
    x: int
    y: int

c1 = Coord(x=1, y=2)
c1_string = json.dumps(c1)
c2 = json.loads(c1_string, DataClass=Coord)
assert c1 == c2
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()

@overrides: tasks.AbstractTask

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)
run()
runCmd(cmd)

@overrides: tasks.AbstractCmdTask

classmethod runFromCmdLine()

@overrides: tasks.AbstractTask

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.

runToCmd(skip_preprocessing=False)

Does the same thing as start except it doesn’t actually launch the job. Instead it just returns the final job cmd.

Intended to be used for running jobtasks on JobDJ, which requires a job cmd rather than a task.

sender(self) QObject
senderSignalIndex(self) int
setJob(job: schrodinger.job.jobcontrol.Job)

” Use given jobcontrol.Job to incorporate job results into the task and run postprocessors. Example:

task = FooTask()
cmd = task.runToCommand()
job = jobcontrol.launch_job(cmd)
job.wait()
task.setJob(job)

If the job has not been downloaded, the task will be set to FAILED with a SetJobRuntimeError.

Parameters

jobjobcontrol.Job with results to incorporate into the task.

setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
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(*args, **kwargs)
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)

@overrides: AbstractTask

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status: Status
statusChanged
statusReplaced
stop()
taskDirSetting()

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

taskDone
taskFailed
taskStarted
thread(self) QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
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(*args, **kwargs)

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns

A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

tr(self, 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.

wrapCmdInLaunchApi(cmd)
write(skip_preprocessing=False)
writeStuZipFile()