schrodinger.trajectory.trajectory_gui_dir.traj_plot_models module¶

Tasks for performing trajectory analyses.

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).

b_factorsChanged¶

b_factorsReplaced¶

blockSignals(self, b: bool) → bool¶

block_signal_propagation()¶

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.

centroid_asl_listChanged¶

centroid_asl_listReplaced¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

cms_fname¶

cms_fnameChanged¶

cms_fnameReplaced¶

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

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_asl¶

fit_aslChanged¶

fit_aslReplaced¶

for_multiseries_plot¶

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_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

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_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).

residue_atomsChanged¶

residue_atomsReplaced¶

residue_typeChanged¶

residue_typeReplaced¶

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¶

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

trajectoryChanged¶

trajectoryReplaced¶

valueChanged¶

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

Bases: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.TrajectoryAnalysisSubprocTask

input: schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.RamachandranInput¶

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]

output: parameters.CompoundParam¶

outputChanged¶

outputReplaced¶

classmethod owner()¶

Get the owner of the param:

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

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

classmethod ownerChain()¶

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

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

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

classmethod paramName()¶

Get the name of the param:

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

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

parent(self) → QObject¶

postprocessors()¶

Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]

preprocessors()¶

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

printDebug(*args)¶

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.TrajectoryEnergyJobTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.tasks.jobtasks.CmdJobTask

Task for running Energy analysis jobs.

input: schrodinger.models.parameters.CompoundParam¶

output: parameters.CompoundParam¶

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

Bases: schrodinger.tasks.jobtasks.JobConfig

host_settings: schrodinger.tasks.jobtasks.HostSettings¶

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

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.

host_settingsChanged¶

host_settingsReplaced¶

incorporation = None¶

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¶

jobname: str¶

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

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

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

coord = Coord()
coord.x = 4

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

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

jobnameChanged¶

jobnameReplaced¶

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.

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¶

viewname: str¶

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

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

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

coord = Coord()
coord.x = 4

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

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

viewnameChanged¶

viewnameReplaced¶

makeCmd()¶

@overrides: tasks.AbstractCmdTask

Child classes must override.

writeSt2File(st2_file)¶: Write an *st2 file containing set ASLs for this task.

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¶

Output¶: alias of schrodinger.tasks.jobtasks._CmdJobTaskOutput

property PROGRAM_NAME¶

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: CallingContext¶

calling_contextChanged¶

calling_contextReplaced¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

classmethod configToJobConfigAdapter(json_dict)¶

classmethod configureParam()¶: @overrides: parameters.CompoundParam

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: 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

getJob() → Optional[schrodinger.job.jobcontrol.Job]¶

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

getShFilename()¶

classmethod getSubParam(name)¶

Get the value of a subparam using the string name:

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

Note

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

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

classmethod getSubParams()¶: Return a dictionary mapping subparam names to their values.

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

getTaskFilename(fname)¶: Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()¶

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

guard()¶: Context manager that saves any Exception raised inside

inWriteMode()¶

inherits(self, classname: str) → bool¶

initAbstract()¶

initConcrete()¶: Override to customize initialization of concrete params.

initializeValue()¶: @overrides: paramters.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¶

job_config: schrodinger.tasks.jobtasks.JobConfig¶

job_configChanged¶

job_configReplaced¶

job_id¶

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

Example usage:

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

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

kill()¶: @overrides: tasks.AbstractTask

killTimer(self, id: int)¶

max_progress: int¶

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

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

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

coord = Coord()
coord.x = 4

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

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

max_progressChanged¶

max_progressReplaced¶

metaObject(self) → QMetaObject¶

moveToThread(self, 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()¶: @overrides: tasks.AbstractTask

requestInterruption()¶

Request the task to stop.

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

reset(*args, **kwargs)¶

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()¶

runCmd(cmd)¶: @overrides: tasks.AbstractCmdTask

runPreprocessing(callback=None, calling_context=None)¶

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

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

Parameters

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

runToCmd(skip_preprocessing=False)¶

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

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

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

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

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

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

Parameters: job – jobcontrol.Job with results to incorporate into the task.

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: Status¶

statusChanged¶

statusReplaced¶

stop()¶

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.

write(skip_preprocessing=False)¶

writeStuZipFile()¶

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

Bases: schrodinger.models.parameters.CompoundParam

Model for an RMSF plot panel

secondary_structure_colors: bool¶

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

b_factor_plot: bool¶

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

color_workspace: bool¶

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)¶

b_factor_plotChanged¶

b_factor_plotReplaced¶

blockSignals(self, b: bool) → bool¶

block_signal_propagation()¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

color_workspaceChanged¶

color_workspaceReplaced¶

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

secondary_structure_colorsChanged¶

secondary_structure_colorsReplaced¶

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.SetRow(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

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.

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)¶

nameChanged¶

nameReplaced¶

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.

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.EnergyPlotModel(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

Model for an Energy plot panel

sets: List[schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.SetRow]¶: A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

selected_sets: List[schrodinger.trajectory.trajectory_gui_dir.traj_plot_models.SetRow]¶: A list param that contains CompoundParam instances. Signals will be emitted any time an item in the list changes or the contents of the list itself change. See _SignalContainer and _PLPSignalContainer for information on specific signals.

exclude_self_terms: bool¶

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

coulomb: bool¶

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

van_der_waals: bool¶

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

bond: bool¶

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)¶

angle: bool¶

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

angleChanged¶

angleReplaced¶

blockSignals(self, b: bool) → bool¶

block_signal_propagation()¶

bondChanged¶

bondReplaced¶

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)¶

coulombChanged¶

coulombReplaced¶

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]

dihedralChanged¶

dihedralReplaced¶

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¶

exclude_self_termsChanged¶

exclude_self_termsReplaced¶

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

selected_setsChanged¶

selected_setsReplaced¶

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.

setsChanged¶

setsReplaced¶

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¶

van_der_waalsChanged¶

van_der_waalsReplaced¶

dihedral: bool¶

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