schrodinger.application.steps.enumerators module¶

class schrodinger.application.steps.enumerators.Transformer(*args, **kwargs)[source]¶

Bases: schrodinger.application.steps.basesteps.LoggerMixin, schrodinger.application.steps.dataclasses.FileInMixin, schrodinger.application.steps.dataclasses.MolOutMixin, schrodinger.tasks.stepper.MapStep

Enumerates unique sanitized products formed using the transformation from the input json file applied to compounds in the compounds_file of SMILES only file.

class Settings(*args, _param_type=<object object>, **kwargs)[source]¶

Bases: schrodinger.models.parameters.CompoundParam

compounds_file: schrodinger.tasks.stepper.StepperFile¶

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

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

blockSignals(self, bool) → bool¶

block_signal_propagation()¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

compounds_fileChanged¶

compounds_fileReplaced¶

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

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

classmethod defaultValue(*args, **kwargs)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

classmethod fromJson(json_obj)¶

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

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

classmethod fromJsonImplementation(json_dict)¶: Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam(*args, **kwargs)¶

classmethod getJsonBlacklist()¶

Override to customize what params are serialized.

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

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

classmethod getParamSignal(*args, **kwargs)¶

classmethod getParamValue(*args, **kwargs)¶

classmethod getSubParam(name)¶

Get the value of a subparam using the string name:

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

Note

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

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

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

getTypeHint()¶

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

inherits(self, str) → bool¶

initAbstract()¶

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

initializeValue()¶: Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)¶

classmethod isAbstract()¶: Whether the param is an “abstract” param.

isDefault(*args, **kwargs)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

classmethod owner()¶

Get the owner of the param:

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

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

classmethod ownerChain()¶

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

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

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

classmethod paramName()¶

Get the name of the param:

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

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

parent(self) → QObject¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

reset(*args, **kwargs)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

classmethod setParamValue(*args, **kwargs)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

classmethod setReference(param1, param2)¶

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

param1 – The first abstract param to keep synced
param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)¶

signalsBlocked(self) → bool¶

skip_eq_check()¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toDict(*args, **kwargs)¶

toJson(_mark_version=True)¶

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

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)¶

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

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

valueChanged¶

validateSettings()[source]¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type: list[TaskError or TaskWarning]

mapFunction(file)[source]¶

The main computation for this step. This function should take in a single input item and return an iterable of outputs. This allows a single output to produce multiple ouputs (e.g. enumeration).

The output may be yielded as a generator, in order to reduce memory usage.

If only a single output is produced for each input, return it as a single-element list.

Parameters

input –

this will be a single input item from the input source. Implementer is encouraged to use a more descriptive, context- specific variable name. Example:

def mapFunction(self, starting_smiles):
…

Input¶: alias of schrodinger.tasks.stepper.StepperFile

InputSerializer¶: alias of schrodinger.tasks.stepper._DynamicSerializer

Output¶: alias of rdkit.Chem.rdchem.Mol

OutputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

cleanUp()¶: Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

cleanUpTables()¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

getLicenseRequirements()¶

getOutputSerializer()¶

getOutputs()¶: Gets all the outputs in a list by fully iterating the output generator.

getRunInfo()¶

getStepId()¶

inherits(self, str) → bool¶

inputs()¶

installEventFilter(self, QObject)¶

isBigQueryBatched()¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

static is_bq_step(step)¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

prettyPrintRunInfo()¶: Format and print info about the step’s run.

progressUpdated¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

reduceFunction(inputs)¶

removeEventFilter(self, QObject)¶

report(prefix='')¶: Report the settings and batch settings for this step.

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputBQTable(bq_table, bq_dataset=None)¶

setInputFile(fname)¶

setInputs(*args, **kwargs)¶

setObjectName(self, str)¶

setOutputBQTable(bq_table)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

setSettings(*args, **kwargs)¶

setUp()¶: Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

writeOutputsToFile(fname)¶: Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

writeOutputsToTable()¶

class schrodinger.application.steps.enumerators.Synthesizer(*args, **kwargs)[source]¶

Bases: schrodinger.application.steps.basesteps.MolMapStep

Enumerates unique sanitized molecules from a combinatorial synthesis using routes based on the input molecules using the default reaction dictionary and reagent library.

If the maximum number of products is less than the total number of combinations the route synthesis will be done by random sampling, which may yield fewer products than requested. Otherwise a systematic set of unique products will be yielded.

The settings contain:

core_smarts: the SMARTS that the products should have and needs to be: part of the input molecule.

depth: the maximum depth of the retrosynthetic routes to use. reagent_lib: an optional directory to prepend to the standard reagent

library search path

max_products: the maximum number of products try to synthesize for each: input molecule per route. Use 0 to force an exhaustive synthesis.
seed: seed for random number generator. If None, the random number: generator will not be seeded.

yield_input: whether the input molecule should be returned first

class Settings(*args, _param_type=<object object>, **kwargs)[source]¶

Bases: schrodinger.models.parameters.CompoundParam

core_smarts: 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

depth: 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

reagent_lib: schrodinger.tasks.stepper.StepperFolder¶

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_products: 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

seed: 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

yield_input: 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)¶: Initialize self. See help(type(self)) for accurate signature.

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

blockSignals(self, bool) → bool¶

block_signal_propagation()¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

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

connectNotify(self, QMetaMethod)¶

core_smartsChanged¶

core_smartsReplaced¶

customEvent(self, QEvent)¶

classmethod defaultValue(*args, **kwargs)¶

deleteLater(self)¶

depthChanged¶

depthReplaced¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

classmethod fromJson(json_obj)¶

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

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

classmethod fromJsonImplementation(json_dict)¶: Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam(*args, **kwargs)¶

classmethod getJsonBlacklist()¶

Override to customize what params are serialized.

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

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

classmethod getParamSignal(*args, **kwargs)¶

classmethod getParamValue(*args, **kwargs)¶

classmethod getSubParam(name)¶

Get the value of a subparam using the string name:

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

Note

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

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

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

getTypeHint()¶

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

inherits(self, str) → bool¶

initAbstract()¶

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

initializeValue()¶: Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)¶

classmethod isAbstract()¶: Whether the param is an “abstract” param.

isDefault(*args, **kwargs)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

max_productsChanged¶

max_productsReplaced¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

classmethod owner()¶

Get the owner of the param:

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

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

classmethod ownerChain()¶

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

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

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

classmethod paramName()¶

Get the name of the param:

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

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

parent(self) → QObject¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

reagent_libChanged¶

reagent_libReplaced¶

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

reset(*args, **kwargs)¶

seedChanged¶

seedReplaced¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

classmethod setParamValue(*args, **kwargs)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

classmethod setReference(param1, param2)¶

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

param1 – The first abstract param to keep synced
param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)¶

signalsBlocked(self) → bool¶

skip_eq_check()¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toDict(*args, **kwargs)¶

toJson(_mark_version=True)¶

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

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)¶

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

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

valueChanged¶

yield_inputChanged¶

yield_inputReplaced¶

validateSettings()[source]¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type: list[TaskError or TaskWarning]

setUp()[source]¶: Hook for adding any type of work that needs to happen before any outputs are created.

mapFunction(mol)[source]¶

Input¶: alias of rdkit.Chem.rdchem.Mol

InputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Output¶: alias of rdkit.Chem.rdchem.Mol

OutputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

cleanUp()¶: Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

cleanUpTables()¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

getLicenseRequirements()¶

getOutputSerializer()¶

getOutputs()¶: Gets all the outputs in a list by fully iterating the output generator.

getRunInfo()¶

getStepId()¶

inherits(self, str) → bool¶

inputs()¶

installEventFilter(self, QObject)¶

isBigQueryBatched()¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

static is_bq_step(step)¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

prettyPrintRunInfo()¶: Format and print info about the step’s run.

progressUpdated¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

reduceFunction(inputs)¶

The main computation for this step. This function should take in a iterable of inputs and return an iterable of outputs.

Example:

def reduceFunction(self, words):
    # Find all unique words
    seen_words = set()
    for word in words:
        if word not in seen_words:
            seen_words.add(word)
            yield word

removeEventFilter(self, QObject)¶

report(prefix='')¶: Report the settings and batch settings for this step.

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputBQTable(bq_table, bq_dataset=None)¶

setInputFile(fname)¶

setInputs(*args, **kwargs)¶

setObjectName(self, str)¶

setOutputBQTable(bq_table)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

setSettings(*args, **kwargs)¶

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

writeOutputsToFile(fname)¶: Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

writeOutputsToTable()¶

class schrodinger.application.steps.enumerators.Decorator(*args, **kwargs)[source]¶

Bases: schrodinger.application.steps.basesteps.MolMapStep

Enumerates unique sanitized molecules formed by replacing a hydrogen on a C, N, or O atom in the ligand with an R-group that was attached to an Ar.

The rgroup_atom_smarts setting allows for filtering of which reagents in the rgroup_file are used for the decoration reaction. The default value of ‘#6,#7,#8,#9,#16,#17,#35,#53’ is used if the rgroup_atom_smarts is an empty string or None.

The settings is a filters.ProfileSettings instance whose property_ranges are used to determine with R-groups are allowed to react.

seealso:: filters.ProfileSettings

Example R-group reagents:: C[Ar] N[Ar]

Example of a Decorator definition in a yaml file:

Decorator:: rgroup_atom_smarts: ‘*’ # allow all unique rgroup reagents rgroup_file: rgroups_small.smi core_smarts: c1ccccc1 property_ranges:

MolWt: [250, 500] RingCount: [0, 5] NumAromaticRings: [0, 3] NumAliphaticRings: [0, 5] NumSpiroAtoms: [0, 0]

LEAVING_MOL_WT = 40.956¶

class Settings(*args, _param_type=<object object>, **kwargs)[source]¶

Bases: schrodinger.application.steps.filters.ProfileSettings

rgroup_file: schrodinger.tasks.stepper.StepperFile¶

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

core_smarts: 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

rgroup_atom_smarts: 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

validate(step)[source]¶

Validate the settings on behalf of a step.

Parameters: step – stepper._BaseStep
Return type: list[TaskError or TaskWarning]

getReagentSmarts()[source]¶

getReagentMol()[source]¶

getReactionSmarts()[source]¶

getRGroups()[source]¶

DataClass¶

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

Example usage:

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

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

__init__(default_value=<object object>, _param_type=<object object>, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

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

blockSignals(self, bool) → bool¶

block_signal_propagation()¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

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

connectNotify(self, QMetaMethod)¶

core_smartsChanged¶

core_smartsReplaced¶

customEvent(self, QEvent)¶

classmethod defaultValue(*args, **kwargs)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

classmethod fromJson(json_obj)¶

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

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

classmethod fromJsonImplementation(json_dict)¶: Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam(*args, **kwargs)¶

classmethod getJsonBlacklist()¶

Override to customize what params are serialized.

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

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

classmethod getParamSignal(*args, **kwargs)¶

classmethod getParamValue(*args, **kwargs)¶

classmethod getSubParam(name)¶

Get the value of a subparam using the string name:

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

Note

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

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

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

getTypeHint()¶

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

inherits(self, str) → bool¶

initAbstract()¶

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

initializeValue()¶: Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)¶

classmethod isAbstract()¶: Whether the param is an “abstract” param.

isDefault(*args, **kwargs)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

classmethod owner()¶

Get the owner of the param:

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

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

classmethod ownerChain()¶

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

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

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

classmethod paramName()¶

Get the name of the param:

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

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

parent(self) → QObject¶

property(self, str) → Any¶

property_ranges: Dict[str, List[float]]¶

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

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

property_rangesChanged¶

property_rangesReplaced¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

reset(*args, **kwargs)¶

rgroup_atom_smartsChanged¶

rgroup_atom_smartsReplaced¶

rgroup_fileChanged¶

rgroup_fileReplaced¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

classmethod setParamValue(*args, **kwargs)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

classmethod setReference(param1, param2)¶

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

param1 – The first abstract param to keep synced
param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)¶

signalsBlocked(self) → bool¶

skip_eq_check()¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toDict(*args, **kwargs)¶

toJson(_mark_version=True)¶

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

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)¶

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

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

valueChanged¶

validateSettings()[source]¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type: list[TaskError or TaskWarning]

setUp()[source]¶: Hook for adding any type of work that needs to happen before any outputs are created.

mapFunction(mol)[source]¶

Input¶: alias of rdkit.Chem.rdchem.Mol

InputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Output¶: alias of rdkit.Chem.rdchem.Mol

OutputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

cleanUp()¶: Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

cleanUpTables()¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

getLicenseRequirements()¶

getOutputSerializer()¶

getOutputs()¶: Gets all the outputs in a list by fully iterating the output generator.

getRunInfo()¶

getStepId()¶

inherits(self, str) → bool¶

inputs()¶

installEventFilter(self, QObject)¶

isBigQueryBatched()¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

static is_bq_step(step)¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

prettyPrintRunInfo()¶: Format and print info about the step’s run.

progressUpdated¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

reduceFunction(inputs)¶

The main computation for this step. This function should take in a iterable of inputs and return an iterable of outputs.

Example:

def reduceFunction(self, words):
    # Find all unique words
    seen_words = set()
    for word in words:
        if word not in seen_words:
            seen_words.add(word)
            yield word

removeEventFilter(self, QObject)¶

report(prefix='')¶: Report the settings and batch settings for this step.

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputBQTable(bq_table, bq_dataset=None)¶

setInputFile(fname)¶

setInputs(*args, **kwargs)¶

setObjectName(self, str)¶

setOutputBQTable(bq_table)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

setSettings(*args, **kwargs)¶

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

writeOutputsToFile(fname)¶: Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

writeOutputsToTable()¶

class schrodinger.application.steps.enumerators.FragmenterMixin[source]¶

Bases: object

A mixin providing trimmer functionality for fragmenters.

BOND_SMARTS¶: alias of builtins.NotImplementedError

getBreakableBonds(mol)[source]¶

Return the bond indices in the molecule that are allowed to be broken.

Parameters: mol (Chem.Mol) – the molecule to fragment
Returns: a generator of bonds to break in the molecule
Return type: generator of int

fragmentToMolecule(fragment)[source]¶

Return the molecule version of the fragment.

Parameters: fragment (Chem.Mol) – the fragment
Returns: the molecule version of the fragment
Return type: Chem.Mol

isFragmentableMol(mol)[source]¶

Use this method to determine whether the molecule may be fragmented.

Parameters: mol (Chem.Mol) – the molecule to check
Returns: whether the molecule can/should be further fragmented
Return type: bool

isAcceptableFragment(mol)[source]¶

Use this method to determine which fragments are acceptable.

Parameters: mol (Chem.Mol) – the molecule to check
Returns: whether the fragment is acceptable
Return type: bool

trimmer(mol, max_fragments=500)[source]¶

Recursively trim the specified mol to generate maximally max_fragments fragment molecules.

Returns the input molecule first if it is an acceptable fragment.

Parameters

mol (Chem.Mol) – Mol to be fragmented.
max_fragments (int) – the total number of fragment molecules to generate

Returns

generator of trimmed molecules

Return type

generator of Chem.Mol

class schrodinger.application.steps.enumerators.Fragmenter(*args, **kwargs)[source]¶

Bases: schrodinger.application.steps.filters.MaxMolWtMixin, schrodinger.application.steps.enumerators.FragmenterMixin, schrodinger.application.steps.basesteps.MolMapStep

Recursively fragment molecules.

Unless it is filtered due to it’s molecular weight or core smarts, this step returns the original molecule first, followed by unique fragment molecules that contain the SMARTS substructure defined in settings and have a molecular weight less than or equal to the optional max_mol_wt setting. The number of molecules returned is limited by max_out in the settings. Fragmentation will only take place for bonds defined in BOND_SMARTS.

BOND_SMARTS = (<rdkit.Chem.rdchem.Mol object>, <rdkit.Chem.rdchem.Mol object>, <rdkit.Chem.rdchem.Mol object>, <rdkit.Chem.rdchem.Mol object>)¶

class Settings(*args, _param_type=<object object>, **kwargs)[source]¶

Bases: schrodinger.application.steps.filters.MaxMolWtSettings

core_smarts: 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

max_out: 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)¶: Initialize self. See help(type(self)) for accurate signature.

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

blockSignals(self, bool) → bool¶

block_signal_propagation()¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

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

connectNotify(self, QMetaMethod)¶

core_smartsChanged¶

core_smartsReplaced¶

customEvent(self, QEvent)¶

classmethod defaultValue(*args, **kwargs)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

classmethod fromJson(json_obj)¶

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

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

classmethod fromJsonImplementation(json_dict)¶: Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam(*args, **kwargs)¶

classmethod getJsonBlacklist()¶

Override to customize what params are serialized.

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

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

classmethod getParamSignal(*args, **kwargs)¶

classmethod getParamValue(*args, **kwargs)¶

classmethod getSubParam(name)¶

Get the value of a subparam using the string name:

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

Note

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

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

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

getTypeHint()¶

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

inherits(self, str) → bool¶

initAbstract()¶

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

initializeValue()¶: Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)¶

classmethod isAbstract()¶: Whether the param is an “abstract” param.

isDefault(*args, **kwargs)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

max_mol_wt: 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_mol_wtChanged¶

max_mol_wtReplaced¶

max_outChanged¶

max_outReplaced¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

classmethod owner()¶

Get the owner of the param:

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

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

classmethod ownerChain()¶

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

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

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

classmethod paramName()¶

Get the name of the param:

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

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

parent(self) → QObject¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

reset(*args, **kwargs)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

classmethod setParamValue(*args, **kwargs)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

classmethod setReference(param1, param2)¶

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

param1 – The first abstract param to keep synced
param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)¶

signalsBlocked(self) → bool¶

skip_eq_check()¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toDict(*args, **kwargs)¶

toJson(_mark_version=True)¶

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

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)¶

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

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

valueChanged¶

validateSettings()[source]¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type: list[TaskError or TaskWarning]

setUp()[source]¶: Hook for adding any type of work that needs to happen before any outputs are created.

hasCoreSmarts(mol)[source]¶

isAcceptableFragment(mol)[source]¶

Use this method to determine which fragments are acceptable.

Parameters: mol (Chem.Mol) – the molecule to check
Returns: whether the fragment is acceptable
Return type: bool

isFragmentableMol(mol)[source]¶

Use this method to determine whether the molecule may be fragmented.

Parameters: mol (Chem.Mol) – the molecule to check
Returns: whether the molecule can/should be further fragmented
Return type: bool

getBreakableBonds(mol)[source]¶

Return the bond indices in the molecule that are allowed to be broken.

Parameters: mol (Chem.Mol) – the molecule to fragment
Returns: a generator of bonds to break in the molecule
Return type: generator of int

getBreakableCoreBonds(mol)[source]¶

Return the set of breakable core bond indices in the molecule.

Parameters: mol (Chem.Mol) – the molecule to fragment
Returns: a generator of breakable core bond indices in the molecule
Return type: generator of int

mapFunction(mol)[source]¶

Input¶: alias of rdkit.Chem.rdchem.Mol

InputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Output¶: alias of rdkit.Chem.rdchem.Mol

OutputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

cleanUp()¶: Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

cleanUpTables()¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

fragmentToMolecule(fragment)¶

Return the molecule version of the fragment.

Parameters: fragment (Chem.Mol) – the fragment
Returns: the molecule version of the fragment
Return type: Chem.Mol

getLicenseRequirements()¶

getOutputSerializer()¶

getOutputs()¶: Gets all the outputs in a list by fully iterating the output generator.

getRunInfo()¶

getStepId()¶

hasAcceptableMolWt(mol)¶

Check if the specified mol passes molecular weight checks.

Parameters: mol (Chem.Mol) – Mol to be checked.
Returns: True if the mol passes molecular weight check, False otherwise.
Return type: bool

inherits(self, str) → bool¶

inputs()¶

installEventFilter(self, QObject)¶

isBigQueryBatched()¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

static is_bq_step(step)¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

prettyPrintRunInfo()¶: Format and print info about the step’s run.

progressUpdated¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

reduceFunction(inputs)¶

The main computation for this step. This function should take in a iterable of inputs and return an iterable of outputs.

Example:

def reduceFunction(self, words):
    # Find all unique words
    seen_words = set()
    for word in words:
        if word not in seen_words:
            seen_words.add(word)
            yield word

removeEventFilter(self, QObject)¶

report(prefix='')¶: Report the settings and batch settings for this step.

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputBQTable(bq_table, bq_dataset=None)¶

setInputFile(fname)¶

setInputs(*args, **kwargs)¶

setObjectName(self, str)¶

setOutputBQTable(bq_table)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

setSettings(*args, **kwargs)¶

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

trimmer(mol, max_fragments=500)¶

Recursively trim the specified mol to generate maximally max_fragments fragment molecules.

Returns the input molecule first if it is an acceptable fragment.

Parameters

mol (Chem.Mol) – Mol to be fragmented.
max_fragments (int) – the total number of fragment molecules to generate

Returns

generator of trimmed molecules

Return type

generator of Chem.Mol

validateMaxMolWtSettings()¶

Returns: A settings error if the max mol. weight setting is not properly set, None otherwise.
Return type: stepper.SettingsError or None

writeOutputsToFile(fname)¶: Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

writeOutputsToTable()¶

class schrodinger.application.steps.enumerators.Appender(*args, **kwargs)[source]¶

Bases: schrodinger.application.steps.basesteps.MolReduceStep

Appends the molecules from the optional settings’ smiles_file.

Note the smiles file should not have a header and only contain one SMILES per line.

class Settings(*args, _param_type=<object object>, **kwargs)[source]¶

Bases: schrodinger.models.parameters.CompoundParam

smiles_file: schrodinger.tasks.stepper.StepperFile¶

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

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

blockSignals(self, bool) → bool¶

block_signal_propagation()¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

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

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

classmethod defaultValue(*args, **kwargs)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

classmethod fromJson(json_obj)¶

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

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

classmethod fromJsonImplementation(json_dict)¶: Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam(*args, **kwargs)¶

classmethod getJsonBlacklist()¶

Override to customize what params are serialized.

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

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

classmethod getParamSignal(*args, **kwargs)¶

classmethod getParamValue(*args, **kwargs)¶

classmethod getSubParam(name)¶

Get the value of a subparam using the string name:

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

Note

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

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

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

getTypeHint()¶

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

inherits(self, str) → bool¶

initAbstract()¶

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

initializeValue()¶: Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, QObject)¶

classmethod isAbstract()¶: Whether the param is an “abstract” param.

isDefault(*args, **kwargs)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

classmethod owner()¶

Get the owner of the param:

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

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

classmethod ownerChain()¶

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

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

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

classmethod paramName()¶

Get the name of the param:

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

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

parent(self) → QObject¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

reset(*args, **kwargs)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

classmethod setParamValue(*args, **kwargs)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

classmethod setReference(param1, param2)¶

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

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

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

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6

Parameters

param1 – The first abstract param to keep synced
param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(*args, **kwargs)¶

signalsBlocked(self) → bool¶

skip_eq_check()¶

smiles_fileChanged¶

smiles_fileReplaced¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toDict(*args, **kwargs)¶

toJson(_mark_version=True)¶

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

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation(*args, **kwargs)¶

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

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

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

valueChanged¶

validateSettings()[source]¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type: list[TaskError or TaskWarning]

reduceFunction(inputs)[source]¶

The main computation for this step. This function should take in a iterable of inputs and return an iterable of outputs.

Example:

def reduceFunction(self, words):
    # Find all unique words
    seen_words = set()
    for word in words:
        if word not in seen_words:
            seen_words.add(word)
            yield word

Input¶: alias of rdkit.Chem.rdchem.Mol

InputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Output¶: alias of rdkit.Chem.rdchem.Mol

OutputSerializer¶: alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → List[QObject]¶

cleanUp()¶: Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

cleanUpTables()¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, object: QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → List[QByteArray]¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

getLicenseRequirements()¶

getOutputSerializer()¶

getOutputs()¶: Gets all the outputs in a list by fully iterating the output generator.

getRunInfo()¶

getStepId()¶

inherits(self, str) → bool¶

inputs()¶

installEventFilter(self, QObject)¶

isBigQueryBatched()¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

static is_bq_step(step)¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

prettyPrintRunInfo()¶: Format and print info about the step’s run.

progressUpdated¶

property(self, str) → Any¶

pyqtConfigure(...)¶: Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

report(prefix='')¶: Report the settings and batch settings for this step.

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputBQTable(bq_table, bq_dataset=None)¶

setInputFile(fname)¶

setInputs(*args, **kwargs)¶

setObjectName(self, str)¶

setOutputBQTable(bq_table)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

setSettings(*args, **kwargs)¶

setUp()¶: Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = - 1) → str¶

writeOutputsToFile(fname)¶: Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

writeOutputsToTable()¶

schrodinger.application.steps.enumerators module¶

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