schrodinger.protein.tasks.binding_site_align module

class schrodinger.protein.tasks.binding_site_align.Result(other_name, rmsd)

Bases: tuple

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

count()

Return number of occurrences of value.

index()

Return first index of value.

Raises ValueError if the value is not present.

other_name

Alias for field number 0

rmsd

Alias for field number 1

class schrodinger.protein.tasks.binding_site_align.BindingSiteAlignmentTask(*args, cmd_list=None, **kwargs)

Bases: schrodinger.tasks.jobtasks.CmdJobTask

Manages binding site alignment job for input structures.

class Input(default_value=<object object>, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

sts

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.

binding_site_cutoff

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
mapping_dist

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
previously_aligned

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
align_sel_res_only

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
res_list

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)

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

classmethod addSubParam(name, param, update_owner=True)
align_sel_res_onlyChanged
align_sel_res_onlyReplaced
binding_site_cutoffChanged
binding_site_cutoffReplaced
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(self)
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.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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 accss 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(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
mapping_distChanged
mapping_distReplaced
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
previously_alignedChanged
previously_alignedReplaced
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)
res_listChanged
res_listReplaced
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>
stsChanged
stsReplaced
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)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
class Output(default_value=<object object>, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

sts

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.

rmsd_rows

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)

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

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(self)
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.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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 accss 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(*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)
rmsd_rowsChanged
rmsd_rowsReplaced
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>
stsChanged
stsReplaced
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)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
DEFAULT_TASKDIR_SETTING = <object object>
writeInputFiles()
makeCmd()

Returns command list based on input params :return: Command for align_binding_sites backend :rtype: list(str)

readOutputFiles()
AUTO_TASKDIR = <object object>
CMDLINE = 1
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
PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, cmd_list=None, **kwargs)

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

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(self)
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.

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
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 accss 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
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
job_config

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)
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
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)
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
progressChanged
progressReplaced
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

runPostprocessing(callback=None)
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(*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
statusChanged
statusReplaced
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)
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.

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()