schrodinger.protein.tasks.muscle module

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.

class schrodinger.protein.tasks.muscle.MuscleJob(aln, second_aln=None, quiet=True, maintain_order=True, seqtype='auto')

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, seqtype='auto')
Parameters

  • aln (ProteinAlignment) – Input sequences

  • second_aln (ProteinAlignment) – Second alignment for aligning multiple MSAs

  • maintain_order (bool) – Whether to maintain input order of sequences

  • seqtype – Sequence type. One of ‘auto’, ‘protein’, ‘rna’ or ‘dna’. In ‘auto’ mode, if >95 of the first 100 letters correspond to nucleotides, the file is treated as the relevant nucleotide type. Otherwise, it is treated as protein.

Dev note: - Unimplemented features: – Speedup options

run()

Run the MUSCLE alignment.

Returns

Aligned sequences

Return type

ProteinAlignment

blockSignals(self, b: bool) → bool
cancel()
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
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]
inherits(self, classname: str) → bool
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]

parent(self) → QObject
progressMade
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
removeEventFilter(self, a0: QObject)
sender(self) → QObject
senderSignalIndex(self) → int
setGapPenalties(gapopen, gapext)
setObjectName(self, name: str)
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) → bool
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)
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str