schrodinger.protein.tasks.muscle module¶
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schrodinger.protein.tasks.muscle.
get_muscle_path
()¶ Returns the path to the MUSCLE executable.
Return type: str Returns: path to MUSCLE executable file, or None if the executable could not be located.
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class
schrodinger.protein.tasks.muscle.
MuscleJob
(aln, second_aln=None, quiet=True, maintain_order=True)¶ Bases:
schrodinger.protein.tasks.clustal.AbstractAlignmentJob
Runs alignment via MUSCLE program
Note: Muscle by default rearranges the order to put similar sequences together -
__init__
(aln, second_aln=None, quiet=True, maintain_order=True)¶ Parameters: - aln (ProteinAlignment) – Input sequences
- second_aln (ProteinAlignment) – Second alignment for aligning multiple MSAs
- maintain_order (bool) – Whether to maintain input order of sequences
Dev note: - Unimplemented features: – Speedup options
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run
()¶ Run the MUSCLE alignment.
Returns: Aligned sequences Return type: ProteinAlignment
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blockSignals
(self, bool) → bool¶
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cancel
()¶
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childEvent
(self, QChildEvent)¶
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children
(self) → List[QObject]¶
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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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inherits
(self, str) → bool¶
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installEventFilter
(self, QObject)¶
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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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killTimer
(self, int)¶
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metaObject
(self) → QMetaObject¶
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moveToThread
(self, QThread)¶
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objectName
(self) → str¶
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objectNameChanged
¶ objectNameChanged(self, str) [signal]
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parent
(self) → QObject¶
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progressMade
¶
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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.
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receivers
(self, PYQT_SIGNAL) → int¶
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removeEventFilter
(self, QObject)¶
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sender
(self) → QObject¶
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senderSignalIndex
(self) → int¶
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setGapPenalties
(gapopen, gapext)¶
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setObjectName
(self, str)¶
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setParent
(self, QObject)¶
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setProperty
(self, str, Any) → bool¶
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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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