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)

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

reduceFunction(inputs)

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

Bases: schrodinger.application.steps.dataclasses.MolMolMixin, schrodinger.tasks.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)

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)

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

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.

writeOutputsToTable()

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)

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)

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

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.

writeOutputsToTable()

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

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

Input

alias of schrodinger.structure._structure.Structure

InputSerializer

alias of schrodinger.tasks.stepper._DynamicSerializer

Output

alias of schrodinger.structure._structure.Structure

OutputSerializer

alias of schrodinger.tasks.stepper._DynamicSerializer

Settings

alias of schrodinger.models.parameters.CompoundParam

__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)

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

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.

writeOutputsToTable()

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.tasks.stepper._DynamicSerializer

Output

alias of schrodinger.structure._structure.Structure

OutputSerializer

alias of schrodinger.tasks.stepper._DynamicSerializer

Settings

alias of schrodinger.models.parameters.CompoundParam

__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)

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

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.

writeOutputsToTable()

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.tasks.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

InputSerializer

alias of schrodinger.tasks.stepper._DynamicSerializer

property Output

OutputSerializer

alias of schrodinger.tasks.stepper._DynamicSerializer

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)

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

__len__()

addStep(step)

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()

hasBQBatching()

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 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)

setInputBQTable(bq_table, bq_dataset=None)

setInputFile(input_file: str, starting_step_id: 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.

setInputs(inputs: Iterable[Any], starting_step_id: 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, 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

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.

writeOutputsToTable()

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)

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

__len__()

addStep(step)

blockSignals(self, 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, 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()

hasBQBatching()

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 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)

setInputBQTable(bq_table, bq_dataset=None)

setInputFile(input_file: str, starting_step_id: 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.

setInputs(inputs: Iterable[Any], starting_step_id: 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, 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

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.

writeOutputsToTable()

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

OutputSerializer

alias of schrodinger.tasks.stepper._DynamicSerializer

STEPS = ()

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)

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

__len__()

addStep(step)

blockSignals(self, 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, 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()

hasBQBatching()

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 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)

setInputBQTable(bq_table, bq_dataset=None)

setInputFile(input_file: str, starting_step_id: 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.

setInputs(inputs: Iterable[Any], starting_step_id: 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, 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

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.

writeOutputsToTable()

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

InputSerializer

alias of schrodinger.tasks.stepper._DynamicSerializer

Output

alias of schrodinger.structure._structure.Structure

OutputSerializer

alias of schrodinger.tasks.stepper._DynamicSerializer

STEPS = ()

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)

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

__len__()

addStep(step)

blockSignals(self, 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, 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()

hasBQBatching()

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 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)

setInputBQTable(bq_table, bq_dataset=None)

setInputFile(input_file: str, starting_step_id: 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.

setInputs(inputs: Iterable[Any], starting_step_id: 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, 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

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.

writeOutputsToTable()

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.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

STEPS = ()

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)

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

__len__()

addStep(step)

blockSignals(self, 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, 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()

hasBQBatching()

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 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)

setInputBQTable(bq_table, bq_dataset=None)

setInputFile(input_file: str, starting_step_id: 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.

setInputs(inputs: Iterable[Any], starting_step_id: 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, 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

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.

writeOutputsToTable()