schrodinger.application.steps.transformers module¶

class schrodinger.application.steps.transformers.Standardizer(*args, **kwargs)¶

Bases: schrodinger.application.steps.basesteps.MolMapStep

Desalts and neutralizes the input molecules using RDKit logic.

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

mapFunction(mol)¶

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)¶

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.transformers.StereoChemistryRemover(*args, **kwargs)¶