schrodinger.trajectory.trajectory_gui_dir.traj_plot_models module

Tasks for performing trajectory analyses.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.AnalysisMode(value)

Bases: schrodinger.models.jsonable.JsonableEnum

Enum defining the analysis classes used.

Distance = 1
Angle = 2
Torsion = 3
RingAtomDistance = 4
RingRingDistance = 5
PlanarAngle = 6
RingAngle = 7
HydrogenBondFinder = 8
HalogenBondFinder = 9
SaltBridgeFinder = 10
ProtLigPiInter = 11
ProtProtPiInter = 12
RMSD = 13
AtomRMSF = 14
ResRMSF = 15
Gyradius = 16
PolarSurfaceArea = 17
SolventAccessibleSurfaceArea = 18
MolecularSurfaceArea = 19
PiPiFinder = 20
CatPiFinder = 21
Ramachandran = 22
Energy = 23
ConfWheelSmallMolecule = 24
ConfWheelResidue = 25
ConfWheelNucleotide = 26
schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.AnalysisModeInfo

alias of schrodinger.trajectory.trajectory_gui_dir.traj_plot_models._AnalysisModeInfo

class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.ResidueInfo(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

Model for protein residues in RMSF Residue

residue_names

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.

secondary_structures

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

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

DataClass

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

Example usage:

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

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

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

inherits(self, classname: 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, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

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

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: 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, name: 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, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

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

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

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

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

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
residue_namesChanged
residue_namesReplaced
secondary_structuresChanged
secondary_structuresReplaced
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

analysis_mode
cms_fname
msys_model

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
cms_model

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
trajectory

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
centroid_asl_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.

additional_args

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.

additional_kwargs

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

The constructor optionally takes a value_class keyword argument to specify what type of class the values will be. This information will be used for jsonifying the dictionary if specified. (Note that non-string keys are not currently supported for jsonification. This may change in the future. See PANEL-13029).

atom_labels

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.

fit_asl
for_multiseries_plot
atom_numbers

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.

residue_atoms

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

The constructor optionally takes a value_class keyword argument to specify what type of class the values will be. This information will be used for jsonifying the dictionary if specified. (Note that non-string keys are not currently supported for jsonification. This may change in the future. See PANEL-13029).

b_factors

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

The constructor optionally takes a value_class keyword argument to specify what type of class the values will be. This information will be used for jsonifying the dictionary if specified. (Note that non-string keys are not currently supported for jsonification. This may change in the future. See PANEL-13029).

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)
additional_argsChanged
additional_argsReplaced
additional_kwargsChanged
additional_kwargsReplaced
analysis_modeChanged
analysis_modeReplaced
atom_labelsChanged
atom_labelsReplaced
atom_numbersChanged
atom_numbersReplaced
b_factorsChanged
b_factorsReplaced
blockSignals(self, b: bool) bool
block_signal_propagation()
centroid_asl_listChanged
centroid_asl_listReplaced
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
cms_fnameChanged
cms_fnameReplaced
cms_modelChanged
cms_modelReplaced
classmethod configureParam()

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

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
fit_aslChanged
fit_aslReplaced
for_multiseries_plotChanged
for_multiseries_plotReplaced
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

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

inherits(self, classname: 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, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

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

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
msys_modelChanged
msys_modelReplaced
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: 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, name: 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, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

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

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

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

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

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
residue_atomsChanged
residue_atomsReplaced
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
trajectoryChanged
trajectoryReplaced
valueChanged
class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisOutput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

result

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.

system_title
legend_name
residue_info

Model for protein residues in RMSF Residue

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, b: bool) bool
block_signal_propagation()
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

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

inherits(self, classname: 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, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

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

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
legend_nameChanged
legend_nameReplaced
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: 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, name: 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, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

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

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

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

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

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
residue_infoChanged
residue_infoReplaced
resultChanged
resultReplaced
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
system_titleChanged
system_titleReplaced
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryEnergyInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

analysis_mode: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.AnalysisMode
cms_fname: 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
trj_dir: 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
cfg_fname: 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
set_names: 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.

set_asls: 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.

fit_asl: 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
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)
analysis_modeChanged
analysis_modeReplaced
blockSignals(self, b: bool) bool
block_signal_propagation()
cfg_fnameChanged
cfg_fnameReplaced
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
cms_fnameChanged
cms_fnameReplaced
classmethod configureParam()

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

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
fit_aslChanged
fit_aslReplaced
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

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

inherits(self, classname: 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, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

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

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: 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, name: 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, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

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

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

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

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

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

set_aslsChanged
set_aslsReplaced
set_namesChanged
set_namesReplaced
signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
trj_dirChanged
trj_dirReplaced
valueChanged
class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryEnergyOutput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.jobtasks._CmdJobTaskOutput

results_file: 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
system_title: 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
legend_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
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, b: bool) bool
block_signal_propagation()
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

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

incorporation_file: 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
incorporation_fileChanged
incorporation_fileReplaced
inherits(self, classname: 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, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

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

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
legend_nameChanged
legend_nameReplaced
log_file: 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
log_fileChanged
log_fileReplaced
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

output_files: List[TaskFile]

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.

output_filesChanged
output_filesReplaced
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, name: 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, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

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

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

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

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

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
results_fileChanged
results_fileReplaced
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
system_titleChanged
system_titleReplaced
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisTaskMixin

Bases: object

Mixin for task classes to perform trajectory analyses.

mainFunction()
class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisTaskMixin, schrodinger.tasks.tasks.BlockingFunctionTask

A blocking task to run relatively quick analyses.

input: schrodinger.models.parameters.CompoundParam
output: schrodinger.models.parameters.CompoundParam
AUTO_TASKDIR = 1
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

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

Example usage:

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

coord = Coord()
coord.note = "hello" # No error
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = 2
WAITING = 0
__init__(*args, **kwargs)
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.

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)
blockSignals(self, b: bool) bool
block_signal_propagation()
calling_context: schrodinger.tasks.tasks.CallingContext
calling_contextChanged
calling_contextReplaced
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
failure_info: schrodinger.tasks.tasks.FailureInfo

Dataclass for task failure information.

Printing an instance of this class will provide the minimum necessary human-readable representation of a recorded failure.

failure_infoChanged
failure_infoReplaced
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)
getDebugString()
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

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

getTaskFilename(fname)

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

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

inputChanged
inputReplaced
installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDebugEnabled()
isDefault()

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

isInterruptionRequested()
isRunning()
isSignalConnected(self, signal: QMetaMethod) bool
isStartable()
isWidgetType(self) bool
isWindowType(self) bool
kill()

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

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

killTimer(self, id: int)
mainFunction()
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, thread: 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, objectName: str) [signal]

outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
postprocessors()
Returns

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

Return type

list[typing.Callable]

preprocessors()
Returns

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

printDebug(*args)
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

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

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

Parameters
  • chain (FuncChainDecorator) – which chain to process

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

Returns

a list of the results from the functions

progress: int

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

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

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
progressChanged
progressReplaced
progress_string: str

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

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

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
progress_stringChanged
progress_stringReplaced
property(self, name: 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, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
replicate()

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

requestInterruption()

Request the task to stop.

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

reset(*args, **kwargs)

Resets this compound param to its default value:

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

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

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

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

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
run()
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, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(skip_preprocessing=False)

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

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

Parameters

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

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
status: schrodinger.tasks.tasks.Status
statusChanged
statusReplaced
taskDirSetting()

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

taskDone
taskFailed
taskStarted
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
wait(timeout=None)

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

Warning

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

Parameters

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

class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisSubprocTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisTaskMixin, schrodinger.tasks.tasks.ComboSubprocessTask

This is a general task to perform trajectory analyses

input: parameters.CompoundParam
output: parameters.CompoundParam
AUTO_TASKDIR = 1
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

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

Example usage:

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

coord = Coord()
coord.note = "hello" # No error
ENTRYPOINT = 'combotask_entry_point.py'
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = 2
WAITING = 0
__init__(*args, **kwargs)
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.

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, b: bool) bool
block_signal_propagation()
calling_context: CallingContext
calling_contextChanged
calling_contextReplaced
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
cmd

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

Example usage:

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

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

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

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
exit_code

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
failure_info: FailureInfo

Dataclass for task failure information.

Printing an instance of this class will provide the minimum necessary human-readable representation of a recorded failure.

failure_infoChanged
failure_infoReplaced
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)
getDebugString()
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

getLogAsString() str
getLogFilename()
classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

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

getTaskFilename(fname)

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

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

inputChanged
inputReplaced
installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isBackendMode()
isDebugEnabled()
isDefault()

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

isInterruptionRequested()
isRunning()
isSignalConnected(self, signal: QMetaMethod) bool
isStartable()
isWidgetType(self) bool
isWindowType(self) bool
property json_filename
property json_out_filename
kill()

@overrides: AbstractTask

Kill the subprocess and set the status to FAILED.

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

@overrides: AbstractCmdTask

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, thread: 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, objectName: str) [signal]

outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
postprocessors()
Returns

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

Return type

list[typing.Callable]

preprocessors()
Returns

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

printDebug(*args)
printingOutputToTerminal()
Returns

whether the StdOut and StdErr output from this task is being printed to the terminal

Return type

bool

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, name: 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.

qprocess

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

Example usage:

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

coord = Coord()
coord.note = "hello" # No error
receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
replicate()

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

requestInterruption()

Request the task to stop.

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

reset(*args, **kwargs)

Resets this compound param to its default value:

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

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

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

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

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
run()
runBackend()
runCmd(cmd)
runInProcess()
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, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setPrintingOutputToTerminal(print_to_terminal)

Set this task to print StdOut and StdErr output to terminal, or not. This must be set before starting the task to enable terminal output.

Parameters

print_to_terminal (bool) – whether to send process output to terminal

setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

@overrides: AbstractTask

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
status: Status
statusChanged
statusReplaced
taskDirSetting()

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

taskDone
taskFailed
taskStarted
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
wait(timeout=None)

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

Warning

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

Parameters

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

class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.ConformationWheelOutput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisOutput

result_labels: 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.

residue_label: 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
dihedral_asls: 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)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

dihedral_aslsChanged
dihedral_aslsReplaced
disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

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

inherits(self, classname: 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, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

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

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
legend_name
legend_nameChanged
legend_nameReplaced
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: 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, name: 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, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

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

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

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

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

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

Model for protein residues in RMSF Residue

residue_infoChanged
residue_infoReplaced
residue_labelChanged
residue_labelReplaced
result

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.

resultChanged
resultReplaced
result_labelsChanged
result_labelsReplaced
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
system_title
system_titleChanged
system_titleReplaced
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.ConformationWheelSubprocTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisSubprocTask

output: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.ConformationWheelOutput
AUTO_TASKDIR = 1
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

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

Example usage:

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

coord = Coord()
coord.note = "hello" # No error
ENTRYPOINT = 'combotask_entry_point.py'
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = 2
WAITING = 0
__init__(*args, **kwargs)
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.

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, b: bool) bool
block_signal_propagation()
calling_context: CallingContext
calling_contextChanged
calling_contextReplaced
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
cmd

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

Example usage:

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

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

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

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
exit_code

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
failure_info: FailureInfo

Dataclass for task failure information.

Printing an instance of this class will provide the minimum necessary human-readable representation of a recorded failure.

failure_infoChanged
failure_infoReplaced
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

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

Parameters

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

Returns

An instance of this class.

Return type

cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)
getDebugString()
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters

group (FuncGroupMarker) – the group marker

Returns

the functions in the specified group, in order

Return type

list

classmethod getJsonBlacklist()

Override to customize what params are serialized.

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

..NOTE

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

getLogAsString() str
getLogFilename()
classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

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

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

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

classmethod getSubParam(name)

Get the value of a subparam using the string name:

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

Note

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

Parameters

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

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

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

getTaskFilename(fname)

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

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input: parameters.CompoundParam
inputChanged
inputReplaced
installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isBackendMode()
isDebugEnabled()
isDefault()

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

isInterruptionRequested()
isRunning()
isSignalConnected(self, signal: QMetaMethod) bool
isStartable()
isWidgetType(self) bool
isWindowType(self) bool
property json_filename
property json_out_filename
kill()

@overrides: AbstractTask

Kill the subprocess and set the status to FAILED.

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

@overrides: AbstractCmdTask

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, thread: 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, objectName: str) [signal]

outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
postprocessors()
Returns

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

Return type

list[typing.Callable]

preprocessors()
Returns

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

printDebug(*args)
printingOutputToTerminal()
Returns

whether the StdOut and StdErr output from this task is being printed to the terminal

Return type

bool

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, name: 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.

qprocess

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

Example usage:

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

coord = Coord()
coord.note = "hello" # No error
receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
replicate()

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

requestInterruption()

Request the task to stop.

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

reset(*args, **kwargs)

Resets this compound param to its default value:

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

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

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

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

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
run()
runBackend()
runCmd(cmd)
runInProcess()
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, name: str)
classmethod setParamValue(obj, value)

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

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

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

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

setParent(self, a0: QObject)
setPrintingOutputToTerminal(print_to_terminal)

Set this task to print StdOut and StdErr output to terminal, or not. This must be set before starting the task to enable terminal output.

Parameters

print_to_terminal (bool) – whether to send process output to terminal

setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

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

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

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

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

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

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

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

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

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

Parameters

taskdir_spec – one of the four options listed above

start(*args, **kwargs)

@overrides: AbstractTask

startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
status: Status
statusChanged
statusReplaced
taskDirSetting()

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

taskDone
taskFailed
taskStarted
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

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

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

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
wait(timeout=None)

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

Warning

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

Parameters

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

class schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.RamachandranInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisInput

residue_type: schrodinger.ui.qt.rama.RamaResidueType
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)
additional_args

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.

additional_argsChanged
additional_argsReplaced
additional_kwargs

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

The constructor optionally takes a value_class keyword argument to specify what type of class the values will be. This information will be used for jsonifying the dictionary if specified. (Note that non-string keys are not currently supported for jsonification. This may change in the future. See PANEL-13029).

additional_kwargsChanged
additional_kwargsReplaced
analysis_mode
analysis_modeChanged
analysis_modeReplaced
atom_labels

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.

atom_labelsChanged
atom_labelsReplaced
atom_numbers

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.

atom_numbersChanged
atom_numbersReplaced
b_factors

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

The constructor optionally takes a value_class keyword argument to specify what type of class the values will be. This information will be used for jsonifying the dictionary if specified. (Note that non-string keys are not currently supported for jsonification. This may change in the future. See PANEL-13029).