schrodinger.application.steps.basesteps module¶

class schrodinger.application.steps.basesteps.LoggerMixin(*args, **kwargs)¶

Bases: object

A mixin for stepper._BaseStep to allow debugging information about every input and output that is processed

__init__(*args, **kwargs)¶

reduceFunction(inputs)¶

class schrodinger.application.steps.basesteps.MolReduceStep(*args, **kwargs)¶

Bases: schrodinger.application.steps.dataclasses.MolMolMixin, schrodinger.stepper.stepper.ReduceStep

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

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶

blockSignals(self, b: bool) → bool¶

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

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, a0: QObject)¶

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(fname)¶

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(*args, **kwargs)¶

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: 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, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateSettings()¶

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]

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.

class schrodinger.application.steps.basesteps.MolMapStep(*args, **kwargs)¶

Bases: schrodinger.application.steps.basesteps.LoggerMixin, schrodinger.application.steps.basesteps.MolReduceStep

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

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶

blockSignals(self, b: bool) → bool¶

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

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, a0: QObject)¶

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(fname)¶

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(*args, **kwargs)¶

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: 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, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateSettings()¶

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]

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.

class schrodinger.application.steps.basesteps.MaeReduceStep(*args, **kwargs)¶

Bases: schrodinger.application.steps.dataclasses.MaeMaeMixin, schrodinger.stepper.stepper.ReduceStep

Input¶: alias of schrodinger.structure._structure.Structure

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

Output¶: alias of schrodinger.structure._structure.Structure

OutputSerializer¶: alias of schrodinger.stepper.stepper._DynamicSerializer

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶

blockSignals(self, b: bool) → bool¶

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

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, a0: QObject)¶

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(fname)¶

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(*args, **kwargs)¶

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: 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, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateSettings()¶

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]

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.

class schrodinger.application.steps.basesteps.MaeMapStep(*args, **kwargs)¶

Bases: schrodinger.application.steps.basesteps.LoggerMixin, schrodinger.application.steps.basesteps.MaeReduceStep

Input¶: alias of schrodinger.structure._structure.Structure

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

Output¶: alias of schrodinger.structure._structure.Structure

OutputSerializer¶: alias of schrodinger.stepper.stepper._DynamicSerializer

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶

blockSignals(self, b: bool) → bool¶

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

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, a0: QObject)¶

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

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(fname)¶

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(*args, **kwargs)¶

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: 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, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateSettings()¶

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]

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.

class schrodinger.application.steps.basesteps.OptionalStepsMixin¶

Bases: object

A mixin that provides optional steps for a Workflow class.

Whether the step is optional is determined by the OPTIONAL_SETTINGS_MAP, a dictionary with step classes as the key and the bool settings attributes as the value.

E.g.:

class ExampleOptionalStepChain(OptionalStepMixin, MolMolWorkflow):
    STEPS = (filters.UniqueSmilesFilter, filters.SmartsFilter,
             filters.PropertyFilter)

    OPTIONAL_SETTINGS_MAP = {filters.SmartsFilter: 'smarts_filter'}

    class Settings(parameters.CompoundParam):
        smarts_filter: bool = False

OPTIONAL_SETTINGS_MAP = {}¶

buildChain()¶

class schrodinger.application.steps.basesteps.Workflow(*args, **kwargs)¶

Bases: schrodinger.stepper.stepper.Chain

A chain of steps.

To define which steps should be present, populate the STEPS variable.

STEPS = ()¶

buildChain()¶: This method must be implemented by subclasses to build the chain. The chain is built by modifying self.steps. The chain’s composition may be dependent on self.settings.

property Input¶

property InputSerializer¶: The default serializer that simply uses json.loads and json.dumps

property Output¶

property OutputSerializer¶: The default serializer that simply uses json.loads and json.dumps

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶: See class docstring for info on the different constructor arguments.

__len__()¶

addStep(step)¶

blockSignals(self, b: bool) → bool¶

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings for the chain as well as for every step in the chain that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

reduceFunction(inputs)¶

removeEventFilter(self, a0: QObject)¶

report(prefix='')¶

Report the workflow steps and their settings (recursively).

Parameters: prefix (str) – the text to start each line with

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(input_file: str, starting_step_id: Optional[str] = None)¶: Set the input file for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(inputs: Iterable[Any], starting_step_id: Optional[str] = None)¶: Set the inputs for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: Any) → bool¶

setSettings(*args, **kwargs)¶

setStartingStep(starting_step: str)¶

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

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateChain()¶: Checks that the declaration of the chain is internally consistent - i.e. that each step is valid and each step’s Input class matches the preceding step’s Output class.

validateSettings()¶

Check whether the chain settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation simply returns problems from all child steps.

Return type: list[TaskError or TaskWarning]

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.

class schrodinger.application.steps.basesteps.MolMolWorkflow(*args, **kwargs)¶

Bases: schrodinger.application.steps.dataclasses.MolMolMixin, schrodinger.application.steps.basesteps.Workflow

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

STEPS = ()¶

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶

__len__()¶

addStep(step)¶

blockSignals(self, b: bool) → bool¶

buildChain()¶: This method must be implemented by subclasses to build the chain. The chain is built by modifying self.steps. The chain’s composition may be dependent on self.settings.

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings for the chain as well as for every step in the chain that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

reduceFunction(inputs)¶

removeEventFilter(self, a0: QObject)¶

report(prefix='')¶

Report the workflow steps and their settings (recursively).

Parameters: prefix (str) – the text to start each line with

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(input_file: str, starting_step_id: Optional[str] = None)¶: Set the input file for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(inputs: Iterable[Any], starting_step_id: Optional[str] = None)¶: Set the inputs for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: Any) → bool¶

setSettings(*args, **kwargs)¶

setStartingStep(starting_step: str)¶

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

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateChain()¶: Checks that the declaration of the chain is internally consistent - i.e. that each step is valid and each step’s Input class matches the preceding step’s Output class.

validateSettings()¶

Check whether the chain settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation simply returns problems from all child steps.

Return type: list[TaskError or TaskWarning]

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.

class schrodinger.application.steps.basesteps.MolMaeWorkflow(*args, **kwargs)¶

Bases: schrodinger.application.steps.dataclasses.MolInMixin, schrodinger.application.steps.dataclasses.MaeOutMixin, schrodinger.application.steps.basesteps.Workflow

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

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

Output¶: alias of schrodinger.structure._structure.Structure

property OutputSerializer¶: The default serializer that simply uses json.loads and json.dumps

STEPS = ()¶

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶

__len__()¶

addStep(step)¶

blockSignals(self, b: bool) → bool¶

buildChain()¶: This method must be implemented by subclasses to build the chain. The chain is built by modifying self.steps. The chain’s composition may be dependent on self.settings.

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings for the chain as well as for every step in the chain that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

reduceFunction(inputs)¶

removeEventFilter(self, a0: QObject)¶

report(prefix='')¶

Report the workflow steps and their settings (recursively).

Parameters: prefix (str) – the text to start each line with

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(input_file: str, starting_step_id: Optional[str] = None)¶: Set the input file for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(inputs: Iterable[Any], starting_step_id: Optional[str] = None)¶: Set the inputs for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: Any) → bool¶

setSettings(*args, **kwargs)¶

setStartingStep(starting_step: str)¶

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

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateChain()¶: Checks that the declaration of the chain is internally consistent - i.e. that each step is valid and each step’s Input class matches the preceding step’s Output class.

validateSettings()¶

Check whether the chain settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation simply returns problems from all child steps.

Return type: list[TaskError or TaskWarning]

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.

class schrodinger.application.steps.basesteps.MaeMaeWorkflow(*args, **kwargs)¶

Bases: schrodinger.application.steps.dataclasses.MaeMaeMixin, schrodinger.application.steps.basesteps.Workflow

Input¶: alias of schrodinger.structure._structure.Structure

property InputSerializer¶: The default serializer that simply uses json.loads and json.dumps

Output¶: alias of schrodinger.structure._structure.Structure

property OutputSerializer¶: The default serializer that simply uses json.loads and json.dumps

STEPS = ()¶

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶

__len__()¶

addStep(step)¶

blockSignals(self, b: bool) → bool¶

buildChain()¶: This method must be implemented by subclasses to build the chain. The chain is built by modifying self.steps. The chain’s composition may be dependent on self.settings.

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings for the chain as well as for every step in the chain that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

reduceFunction(inputs)¶

removeEventFilter(self, a0: QObject)¶

report(prefix='')¶

Report the workflow steps and their settings (recursively).

Parameters: prefix (str) – the text to start each line with

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(input_file: str, starting_step_id: Optional[str] = None)¶: Set the input file for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(inputs: Iterable[Any], starting_step_id: Optional[str] = None)¶: Set the inputs for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: Any) → bool¶

setSettings(*args, **kwargs)¶

setStartingStep(starting_step: str)¶

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

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateChain()¶: Checks that the declaration of the chain is internally consistent - i.e. that each step is valid and each step’s Input class matches the preceding step’s Output class.

validateSettings()¶

Check whether the chain settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation simply returns problems from all child steps.

Return type: list[TaskError or TaskWarning]

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.

class schrodinger.application.steps.basesteps.FileMolWorkflow(*args, **kwargs)¶

Bases: schrodinger.application.steps.dataclasses.FileInMixin, schrodinger.application.steps.dataclasses.MolOutMixin, schrodinger.application.steps.basesteps.Workflow

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

property InputSerializer¶: The default serializer that simply uses json.loads and json.dumps

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

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

STEPS = ()¶

Settings¶: alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)¶

__len__()¶

addStep(step)¶

blockSignals(self, b: bool) → bool¶

buildChain()¶: This method must be implemented by subclasses to build the chain. The chain is built by modifying self.steps. The chain’s composition may be dependent on self.settings.

childEvent(self, a0: 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.

connectNotify(self, signal: QMetaMethod)¶

customEvent(self, a0: QEvent)¶

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]

getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

getLicenseRequirements()¶

getMetricsLoggerDepth() → Optional[int]¶

getOutputSerializer()¶

getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]¶

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

getResources(param_type, resource_type)¶

Get the stepper resources in the settings for the chain as well as for every step in the chain that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

param_type (tasks._TaskResource) – the resource parameter type
resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()¶

getStepDepth() → int¶: Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()¶

inherits(self, classname: str) → bool¶

initializeTopics()¶

inputs()¶

installEventFilter(self, a0: QObject)¶

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]

outputs(*args, **kwargs)¶

parent(self) → QObject¶

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

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¶

reduceFunction(inputs)¶

removeEventFilter(self, a0: QObject)¶

report(prefix='')¶

Report the workflow steps and their settings (recursively).

Parameters: prefix (str) – the text to start each line with

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setBatchSettings(*args, **kwargs)¶

setInputFile(input_file: str, starting_step_id: Optional[str] = None)¶: Set the input file for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setInputs(inputs: Iterable[Any], starting_step_id: Optional[str] = None)¶: Set the inputs for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setObjectName(self, name: str)¶

setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])¶

setParent(self, a0: QObject)¶

setProperty(self, name: str, value: Any) → bool¶

setSettings(*args, **kwargs)¶

setStartingStep(starting_step: str)¶

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

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt6.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, a0: QTimerEvent)¶

property topic_prefix¶

property topic_suffix¶

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str¶

usingPubsub()¶

validateChain()¶: Checks that the declaration of the chain is internally consistent - i.e. that each step is valid and each step’s Input class matches the preceding step’s Output class.

validateSettings()¶

Check whether the chain settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation simply returns problems from all child steps.

Return type: list[TaskError or TaskWarning]

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.