schrodinger.application.prepwizard2.tasks module¶

schrodinger.application.prepwizard2.tasks.hide_non_polar_hydrogens(st)¶: Hide all non-polar hydrogens in the given structure; except those that overlap with other atoms.

class schrodinger.application.prepwizard2.tasks.LoggerMixin(*args, **kwargs)¶

Bases: object

A Mixin for a task that provides a thin wrapper for a logger

__init__(*args, **kwargs)¶

logger¶

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

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

class schrodinger.application.prepwizard2.tasks.StructureInput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

struct: schrodinger.structure._structure.Structure¶

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)¶

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>¶

structChanged¶

structReplaced¶

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.application.prepwizard2.tasks.GenerateStatesSettings(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

use_epikx: 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

epik_pH: float¶

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

epik_pHt: float¶

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_states: 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

process_detected_ligands: 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

process_metals_and_ions: 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

process_non_water_solvents: 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

process_other_hets: 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

getHetTypesToProcess()¶: Return a list of HetType for het types that should be processed.

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]¶

epik_pHChanged¶

epik_pHReplaced¶

epik_pHtChanged¶

epik_pHtReplaced¶

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)¶

max_statesChanged¶

max_statesReplaced¶

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¶

process_detected_ligandsChanged¶

process_detected_ligandsReplaced¶

process_metals_and_ionsChanged¶

process_metals_and_ionsReplaced¶

process_non_water_solventsChanged¶

process_non_water_solventsReplaced¶

process_other_hetsChanged¶

process_other_hetsReplaced¶

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¶

use_epikxChanged¶

use_epikxReplaced¶

valueChanged¶

class schrodinger.application.prepwizard2.tasks.GenerateStatesInput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.GenerateStatesSettings, schrodinger.application.prepwizard2.tasks.StructureInput

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]¶

epik_pH: float¶

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

epik_pHChanged¶

epik_pHReplaced¶

epik_pHt: float¶

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

epik_pHtChanged¶

epik_pHtReplaced¶

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.

getHetTypesToProcess()¶: Return a list of HetType for het types that should be processed.

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)¶

max_states: 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_statesChanged¶

max_statesReplaced¶

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¶

process_detected_ligands: 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

process_detected_ligandsChanged¶

process_detected_ligandsReplaced¶

process_metals_and_ions: 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

process_metals_and_ionsChanged¶

process_metals_and_ionsReplaced¶

process_non_water_solvents: 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

process_non_water_solventsChanged¶

process_non_water_solventsReplaced¶

process_other_hets: 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

process_other_hetsChanged¶

process_other_hetsReplaced¶

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>¶

struct: schrodinger.structure._structure.Structure¶

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

structChanged¶

structReplaced¶

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¶

use_epikx: 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

use_epikxChanged¶

use_epikxReplaced¶

valueChanged¶

class schrodinger.application.prepwizard2.tasks.PreprocessInput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.StructureInput

Used as input model for the PreprocessTask and the “preprocess” section of the PPWorkflowTask and PPBatchWorkflowTask tasks. Also see prepare.PrepWizardSettings which has many similarities

reference_struct: schrodinger.structure._structure.Structure¶

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

preprocess_delete_far_waters: 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

preprocess_watdist: float¶

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

treat_metals: 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

assign_bond_orders: 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

use_ccd: 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

skip_assigned_residues: 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

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

Bases: schrodinger.models.parameters.CompoundParam

use_ccd: 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

skip_assigned_residues: 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)¶

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

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_assigned_residuesChanged¶

skip_assigned_residuesReplaced¶

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¶

use_ccdChanged¶

use_ccdReplaced¶

valueChanged¶

abo_options: schrodinger.application.prepwizard2.tasks.PreprocessInput.ABOOptions¶

add_hydrogens: 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

readd_hydrogens: 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

add_terminal_oxygens: 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

treat_disulfides: 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

treat_glycosylation: 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

treat_palmitoylation: 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

antibody_cdr_scheme: schrodinger.infra.util.AntibodyCDRScheme¶

renumber_ab_residues: 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

selenomethionines: 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

fillsidechains: 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

fillloops: 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

custom_fasta_file: schrodinger.tasks.tasks.TaskFile¶

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

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

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

coord = Coord()
coord.x = 4

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

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

cap_termini: 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

cap_termini_min_atoms: 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

run_epik: 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

idealize_hydrogen_tf: 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

generate_states_settings: schrodinger.application.prepwizard2.tasks.GenerateStatesSettings¶

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

isDefault()¶: Whether the current value of this instance matches the default value.

reset()¶: Reset all settings except pH, which is part of the global settings.

getNumSelected()¶: Return the number of pre-processing steps that are enabled.

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)¶

abo_optionsChanged¶

abo_optionsReplaced¶

classmethod addSubParam(name, param, update_owner=True)¶

add_hydrogensChanged¶

add_hydrogensReplaced¶

add_terminal_oxygensChanged¶

add_terminal_oxygensReplaced¶

antibody_cdr_schemeChanged¶

antibody_cdr_schemeReplaced¶

assign_bond_ordersChanged¶

assign_bond_ordersReplaced¶

blockSignals(self, b: bool) → bool¶

block_signal_propagation()¶

cap_terminiChanged¶

cap_terminiReplaced¶

cap_termini_min_atomsChanged¶

cap_termini_min_atomsReplaced¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

custom_fasta_fileChanged¶

custom_fasta_fileReplaced¶

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¶

fillloopsChanged¶

fillloopsReplaced¶

fillsidechainsChanged¶

fillsidechainsReplaced¶

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.

generate_states_settingsChanged¶

generate_states_settingsReplaced¶

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.

idealize_hydrogen_tfChanged¶

idealize_hydrogen_tfReplaced¶

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.

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¶

preprocess_delete_far_watersChanged¶

preprocess_delete_far_watersReplaced¶

preprocess_watdistChanged¶

preprocess_watdistReplaced¶

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.

readd_hydrogensChanged¶

readd_hydrogensReplaced¶

receivers(self, signal: PYQT_SIGNAL) → int¶

reference_structChanged¶

reference_structReplaced¶

removeEventFilter(self, a0: QObject)¶

renumber_ab_residuesChanged¶

renumber_ab_residuesReplaced¶

run_epikChanged¶

run_epikReplaced¶

selenomethioninesChanged¶

selenomethioninesReplaced¶

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_assigned_residuesChanged¶

skip_assigned_residuesReplaced¶

skip_eq_check()¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

struct: schrodinger.structure._structure.Structure¶

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

structChanged¶

structReplaced¶

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¶

treat_disulfidesChanged¶

treat_disulfidesReplaced¶

treat_glycosylationChanged¶

treat_glycosylationReplaced¶

treat_metalsChanged¶

treat_metalsReplaced¶

treat_palmitoylationChanged¶

treat_palmitoylationReplaced¶

use_ccdChanged¶

use_ccdReplaced¶

valueChanged¶

class schrodinger.application.prepwizard2.tasks.PreprocessTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.ComboSubprocessTask

input: schrodinger.application.prepwizard2.tasks.PreprocessInput¶: Used as input model for the PreprocessTask and the “preprocess” section of the PPWorkflowTask and PPBatchWorkflowTask tasks. Also see prepare.PrepWizardSettings which has many similarities

output: List[schrodinger.structure._structure.Structure]¶

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.

validateInput()¶

mainFunction()¶

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.

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¶

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

Example usage:

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

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

findChild(self, type: 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¶

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

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

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)¶

logger¶

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

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)¶

classmethod runFromCmdLine()¶

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.

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

class schrodinger.application.prepwizard2.tasks.OptimizeHBondInput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.StructureInput

Model for the “Optimize H-bond Assignments” step of the workflow tab, i.e., OptimizeHBondTask.input

samplewater: 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

include_epik_states: 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

xtal: 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

simplified_pH: 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

use_propka: 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

propka_pH: float¶

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

label_pkas: 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

force_list: 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.

minimize_adj_h: 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

protassign_number_sequential_cycles: 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

protassign_max_cluster_size: 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

idealize_hydrogen_tf: 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)¶

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]

force_listChanged¶

force_listReplaced¶

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.

idealize_hydrogen_tfChanged¶

idealize_hydrogen_tfReplaced¶

include_epik_statesChanged¶

include_epik_statesReplaced¶

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)¶

label_pkasChanged¶

label_pkasReplaced¶

metaObject(self) → QMetaObject¶

minimize_adj_hChanged¶

minimize_adj_hReplaced¶

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¶

propka_pHChanged¶

propka_pHReplaced¶

protassign_max_cluster_sizeChanged¶

protassign_max_cluster_sizeReplaced¶

protassign_number_sequential_cyclesChanged¶

protassign_number_sequential_cyclesReplaced¶

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

samplewaterChanged¶

samplewaterReplaced¶

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¶

simplified_pHChanged¶

simplified_pHReplaced¶

skip_eq_check()¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

struct: schrodinger.structure._structure.Structure¶

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

structChanged¶

structReplaced¶

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¶

use_propkaChanged¶

use_propkaReplaced¶

valueChanged¶

xtalChanged¶

xtalReplaced¶

class schrodinger.application.prepwizard2.tasks.OptimizeHBondTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.SubprocessCmdTask

A task optimized H-Bonds, i.e., to run the protein assignment (protassign)

input: schrodinger.application.prepwizard2.tasks.OptimizeHBondInput¶: Model for the “Optimize H-bond Assignments” step of the workflow tab, i.e., OptimizeHBondTask.input

output: schrodinger.structure._structure.Structure¶

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

message: 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

validateInput()¶

setInitialStatus()¶

prepareInput()¶

makeCmd()¶: Create the command to run ProtAssign without job control (-NOJOBID)

runCmd(cmd)¶

processOutput()¶

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.

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]¶

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¶

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

Example usage:

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

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

findChild(self, type: 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¶

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

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

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()¶

@overrides: AbstractTask

Kill the subprocess and set the status to FAILED.

killTimer(self, id: int)¶

logger¶

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

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¶

messageChanged¶

messageReplaced¶

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()¶

classmethod runFromCmdLine()¶

runPreprocessing(callback=None, calling_context=None)¶

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

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

Parameters

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, 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)¶

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¶

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.

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

class schrodinger.application.prepwizard2.tasks.CleanupInput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.StructureInput

Model for the “Clean Up” step of the workflow tab

run_impref: 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

force_field: 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

rmsd: float¶

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

fixheavy: 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

delete_far_waters: 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

watdist: float¶

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

delete_nonbridging_waters: 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

delwater_hbond_cutoff: 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

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)¶

delete_far_watersChanged¶

delete_far_watersReplaced¶

delete_nonbridging_watersChanged¶

delete_nonbridging_watersReplaced¶

delwater_hbond_cutoffChanged¶

delwater_hbond_cutoffReplaced¶

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]

fixheavyChanged¶

fixheavyReplaced¶

force_fieldChanged¶

force_fieldReplaced¶

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

rmsdChanged¶

rmsdReplaced¶

run_imprefChanged¶

run_imprefReplaced¶

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>¶

struct: schrodinger.structure._structure.Structure¶

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

structChanged¶

structReplaced¶

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¶

watdistChanged¶

watdistReplaced¶

class schrodinger.application.prepwizard2.tasks.DeleteWatersTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.BlockingFunctionTask

A task that may run water deletion and restrained minimization on a protein

input: schrodinger.application.prepwizard2.tasks.CleanupInput¶: Model for the “Clean Up” step of the workflow tab

output: schrodinger.structure._structure.Structure¶

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

validateInput()¶

mainFunction()¶

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.

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 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¶

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

Example usage:

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

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

findChild(self, type: 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

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

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)¶

logger¶

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

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()¶

classmethod runFromCmdLine()¶

runPreprocessing(callback=None, calling_context=None)¶

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

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

Parameters

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, 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¶

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.

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

class schrodinger.application.prepwizard2.tasks.CleanupTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.BlockingFunctionTask

A task that may run water deletion and restrained minimization on a protein

input: schrodinger.application.prepwizard2.tasks.CleanupInput¶: Model for the “Clean Up” step of the workflow tab

output: schrodinger.structure._structure.Structure¶

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

valence_error: 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

validateInput()¶

mainFunction()¶

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.

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 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¶

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

Example usage:

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

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

findChild(self, type: 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

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

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)¶

logger¶

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

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()¶

classmethod runFromCmdLine()¶

runPreprocessing(callback=None, calling_context=None)¶

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

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

Parameters

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, 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¶

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¶

valence_errorChanged¶

valence_errorReplaced¶

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.

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

class schrodinger.application.prepwizard2.tasks.PPWorkflowSettings(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

Settings for PPW workflow auto task.

preprocess: schrodinger.application.prepwizard2.tasks.PreprocessInput¶: Used as input model for the PreprocessTask and the “preprocess” section of the PPWorkflowTask and PPBatchWorkflowTask tasks. Also see prepare.PrepWizardSettings which has many similarities

hbond: schrodinger.application.prepwizard2.tasks.OptimizeHBondInput¶: Model for the “Optimize H-bond Assignments” step of the workflow tab, i.e., OptimizeHBondTask.input

cleanup: schrodinger.application.prepwizard2.tasks.CleanupInput¶: Model for the “Clean Up” step of the workflow tab

do_preprocess: 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

do_hbond: 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

do_cleanup: 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

use_pdb_ph_if_available: 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)¶

blockSignals(self, b: bool) → bool¶

block_signal_propagation()¶

childEvent(self, a0: QChildEvent)¶

children(self) → List[QObject]¶

cleanupChanged¶

cleanupReplaced¶

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)¶

do_cleanupChanged¶

do_cleanupReplaced¶

do_hbondChanged¶

do_hbondReplaced¶

do_preprocessChanged¶

do_preprocessReplaced¶

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.

hbondChanged¶

hbondReplaced¶

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¶

preprocessChanged¶

preprocessReplaced¶

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¶

use_pdb_ph_if_availableChanged¶

use_pdb_ph_if_availableReplaced¶

valueChanged¶

class schrodinger.application.prepwizard2.tasks.PPWorkflowInput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.StructureInput, schrodinger.application.prepwizard2.tasks.PPWorkflowSettings

Settings and structure input for PPW workflow tasks.

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]¶

cleanup: schrodinger.application.prepwizard2.tasks.CleanupInput¶: Model for the “Clean Up” step of the workflow tab

cleanupChanged¶

cleanupReplaced¶

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)¶

do_cleanup: 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

do_cleanupChanged¶

do_cleanupReplaced¶

do_hbond: 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

do_hbondChanged¶

do_hbondReplaced¶

do_preprocess: 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

do_preprocessChanged¶

do_preprocessReplaced¶

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.

hbond: schrodinger.application.prepwizard2.tasks.OptimizeHBondInput¶: Model for the “Optimize H-bond Assignments” step of the workflow tab, i.e., OptimizeHBondTask.input

hbondChanged¶

hbondReplaced¶

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¶

preprocess: schrodinger.application.prepwizard2.tasks.PreprocessInput¶: Used as input model for the PreprocessTask and the “preprocess” section of the PPWorkflowTask and PPBatchWorkflowTask tasks. Also see prepare.PrepWizardSettings which has many similarities

preprocessChanged¶

preprocessReplaced¶

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>¶

struct: schrodinger.structure._structure.Structure¶

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

structChanged¶

structReplaced¶

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¶

use_pdb_ph_if_available: 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

use_pdb_ph_if_availableChanged¶

use_pdb_ph_if_availableReplaced¶

valueChanged¶

class schrodinger.application.prepwizard2.tasks.PPWorkflowOutput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

structs: List[schrodinger.structure._structure.Structure]¶

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.

postprocess_valence_error: 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)¶

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¶

postprocess_valence_errorChanged¶

postprocess_valence_errorReplaced¶

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>¶

structsChanged¶

structsReplaced¶

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.application.prepwizard2.tasks.PPWorkflowTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.jobtasks.ComboJobTask

Runs the entire workflow. Intended to be created by PPBatchWorkflowTask.

input: schrodinger.application.prepwizard2.tasks.PPWorkflowInput¶: Settings and structure input for PPW workflow tasks.

output: schrodinger.application.prepwizard2.tasks.PPWorkflowOutput¶

backendMain()¶

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¶

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¶

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

Example usage:

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

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

findChild(self, type: 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.

getLogAsString() → str¶

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()¶

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

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.

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¶

job_config: JobConfig¶

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

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

job_configChanged¶

job_configReplaced¶

job_id¶

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

Example usage:

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

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

property json_filename¶

property json_out_filename¶

kill()¶: @overrides: tasks.AbstractTask

killTimer(self, id: int)¶

logger¶

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

Example usage:

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

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

mainFunction()¶

makeCmd()¶

@overrides: tasks.AbstractCmdTask

Child classes must override.

max_progress: int¶

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

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

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

coord = Coord()
coord.x = 4

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

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

max_progressChanged¶

max_progressReplaced¶

metaObject(self) → QMetaObject¶

moveToThread(self, 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()¶

runBackend()¶: @overrides: AbstractComboTask

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

classmethod runFromCmdLine()¶: @overrides: tasks.AbstractTask

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.

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(*args, **kwargs)¶: @overrides: AbstractTask

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.

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

write(skip_preprocessing=False)¶

writeStuZipFile()¶

class schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

struct_file: schrodinger.tasks.tasks.TaskFile¶

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

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

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

coord = Coord()
coord.x = 4

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

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

settings: schrodinger.application.prepwizard2.tasks.PPWorkflowSettings¶: Settings for PPW workflow auto task.

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

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.

settingsChanged¶

settingsReplaced¶

signalsBlocked(self) → bool¶

skip_eq_check()¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

struct_fileChanged¶

struct_fileReplaced¶

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.application.prepwizard2.tasks.PPBatchWorkflowTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.jobtasks.CmdJobTask

Task for the auto PPW2 workflow, both single structure and batch. This task runs the $SCHRODINGER/utilities/prepwizard driver.

input: schrodinger.application.prepwizard2.tasks.PPBatchWorkflowInput¶

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

Bases: schrodinger.tasks.jobtasks._CmdJobTaskOutput

output_filename: schrodinger.tasks.tasks.TaskFile¶

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

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

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

coord = Coord()
coord.x = 4

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

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

DataClass¶

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

Example usage:

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

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

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

classmethod addSubParam(name, param, update_owner=True)¶

blockSignals(self, 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)¶

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_filenameChanged¶

output_filenameReplaced¶

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

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

Bases: schrodinger.tasks.jobtasks.JobConfig

incorporation¶

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¶

incorporationChanged¶

incorporationReplaced¶

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.

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¶

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.

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¶

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

Example usage:

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

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

findChild(self, type: 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()¶

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

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: 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)¶

logger¶

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

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)¶

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

classmethod runFromCmdLine()¶: @overrides: tasks.AbstractTask

runPreprocessing(callback=None, calling_context=None)¶

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

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

Parameters

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

runToCmd(skip_preprocessing=False)¶

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

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

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

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

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

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

Parameters: 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.

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

write(skip_preprocessing=False)¶

writeStuZipFile()¶

class schrodinger.application.prepwizard2.tasks.GenerateStatesTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.ComboSubprocessTask

A task that will run epik to generate states

input: schrodinger.application.prepwizard2.tasks.GenerateStatesInput¶

output: List[schrodinger.structure._structure.Structure]¶

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.

validateInput()¶

validateLicenses()¶

mainFunction()¶

applyHetStates(applied_states, state_sts, no_hets_recep_st, all_recep_metals)¶: For each complex in <applied_states>, apply states for another het, based on the het states in <state_sts>. Return list of new complexes.

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.

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¶

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

Example usage:

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

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

findChild(self, type: 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¶

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

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

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)¶

logger¶

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

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)¶

classmethod runFromCmdLine()¶

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.

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

class schrodinger.application.prepwizard2.tasks.ProteinRefinementInput(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.StructureInput

force_field: 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

rmsd: float¶

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

fixheavy: 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)¶

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]

fixheavyChanged¶

fixheavyReplaced¶

force_fieldChanged¶

force_fieldReplaced¶

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

rmsdChanged¶

rmsdReplaced¶

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>¶

struct: schrodinger.structure._structure.Structure¶

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

structChanged¶

structReplaced¶

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.application.prepwizard2.tasks.ProteinRefinementTask(*args, _param_type=<object object>, **kwargs)¶

Bases: schrodinger.application.prepwizard2.tasks.LoggerMixin, schrodinger.tasks.tasks.SubprocessCmdTask

A task to run the protein refinement (restrained minimization, i.e., impref)

input: schrodinger.application.prepwizard2.tasks.ProteinRefinementInput¶

output: schrodinger.structure._structure.Structure¶

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

validateInput()¶

prepareInput()¶

makeCmd()¶: Create the command to run impref not under job control (-NOJOBID)

processOutput()¶

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.

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]¶

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¶

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

Example usage:

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

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

findChild(self, type: 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¶

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

info(text)¶

Log the text as informational.

Parameters: text (str) – the info text to log

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()¶

@overrides: AbstractTask

Kill the subprocess and set the status to FAILED.

killTimer(self, id: int)¶

logger¶

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

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()¶

runCmd(cmd)¶

classmethod runFromCmdLine()¶

runPreprocessing(callback=None, calling_context=None)¶

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

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

Parameters

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, 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)¶

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¶

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.

warning(text)¶

Log the text as a warning.

Parameters: text (str) – the warning text to log

schrodinger.application.prepwizard2.tasks.update_params(to_params, from_params)¶

Update the to_params with the values in from_params.

Parameters

to_params (parameters.CompoundParam) – the parameters to update
from_params (parameters.CompoundParam) – the parameters to get the values from

schrodinger.application.prepwizard2.tasks.generate_annotation(task)¶

Return the annotation text to use for a finished task.

Parameters: task (schrodinger.tasks.tasks.AbstractTask) – the task
Returns: the note to use
Return type: str

schrodinger.application.prepwizard2.tasks.annotate_entry_title(st, annotation)¶

Annotates the structure title by putting a note on the structure title, only if it is the ANNOTATIONS.

Will replace the existing note at the end of the title, if one is found. If no exact match is found at the end, the new note is appended.

Parameters

st (structure.Structure) – the new structure which needs annotated title
annotation (str) – one of the known annotation strings