schrodinger.application.steps.transformers module¶

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

Bases: schrodinger.application.steps.basesteps.MolMapStep

Creates a coordinate-less molecule that is neutralized and desalted.

This involves a conversion to a schrodinger.structure.Structure.

getLicenseRequirements()[source]¶

mapFunction(mol)[source]¶

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

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

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

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

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]

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.transformers.StereoChemistryRemover(*args, **kwargs)[source]¶