schrodinger.application.steps.transformers module¶
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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
.-
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
¶
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__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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blockSignals
(self, bool) → bool¶
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childEvent
(self, QChildEvent)¶
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children
(self) → List[QObject]¶
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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.
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cleanUpTables
()¶
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connectNotify
(self, QMetaMethod)¶
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customEvent
(self, QEvent)¶
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deleteLater
(self)¶
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destroyed
¶ destroyed(self, object: QObject = None) [signal]
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disconnect
(self)¶
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disconnectNotify
(self, QMetaMethod)¶
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dumpObjectInfo
(self)¶
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dumpObjectTree
(self)¶
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dynamicPropertyNames
(self) → List[QByteArray]¶
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event
(self, QEvent) → bool¶
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eventFilter
(self, QObject, QEvent) → bool¶
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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
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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]
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getOutputSerializer
()¶
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getOutputs
()¶ Gets all the outputs in a list by fully iterating the output generator.
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getRunInfo
()¶
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getStepId
()¶
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inherits
(self, str) → bool¶
-
inputs
()¶
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installEventFilter
(self, QObject)¶
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isBigQueryBatched
()¶
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isSignalConnected
(self, QMetaMethod) → bool¶
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isWidgetType
(self) → bool¶
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isWindowType
(self) → bool¶
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static
is_bq_step
(step)¶
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killTimer
(self, int)¶
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metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
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objectName
(self) → str¶
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objectNameChanged
¶ objectNameChanged(self, str) [signal]
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outputs
(*args, **kwargs)¶
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parent
(self) → QObject¶
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prettyPrintRunInfo
()¶ Format and print info about the step’s run.
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progressUpdated
¶
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property
(self, str) → Any¶
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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¶
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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
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removeEventFilter
(self, QObject)¶
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report
(prefix='')¶ Report the settings and batch settings for this step.
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sender
(self) → QObject¶
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senderSignalIndex
(self) → int¶
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setBatchSettings
(*args, **kwargs)¶
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setInputBQTable
(bq_table, bq_dataset=None)¶
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setInputFile
(fname)¶
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setInputs
(*args, **kwargs)¶
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setObjectName
(self, str)¶
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setOutputBQTable
(bq_table)¶
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setParent
(self, QObject)¶
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setProperty
(self, str, Any) → bool¶
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setSettings
(*args, **kwargs)¶
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setUp
()¶ Hook for adding any type of work that needs to happen before any outputs are created.
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signalsBlocked
(self) → bool¶
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startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
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staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
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thread
(self) → QThread¶
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timerEvent
(self, QTimerEvent)¶
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tr
(self, str, disambiguation: str = None, n: int = - 1) → str¶
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validateSettings
()¶ Check whether the step settings are valid and return a list of
SettingsError
andSettingsWarning
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 tostr
. Override this method if more complex behavior is needed.
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writeOutputsToTable
()¶
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-
class
schrodinger.application.steps.transformers.
StereoChemistryRemover
(*args, **kwargs)[source]¶ Bases:
schrodinger.application.steps.basesteps.MolMapStep
Removes the stereo chemistry from a molecule.
-
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
¶
-
__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]
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getLicenseRequirements
()¶
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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
andSettingsWarning
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 tostr
. Override this method if more complex behavior is needed.
-
writeOutputsToTable
()¶
-