schrodinger.protein.tasks.muscle module

schrodinger.protein.tasks.muscle.get_muscle_path()[source]

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)[source]

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)[source]
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

run()[source]

Run the MUSCLE alignment.

Returns

Aligned sequences

Return type

ProteinAlignment

blockSignals(self, bool) bool
cancel()
childEvent(self, QChildEvent)
children(self) List[QObject]
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, object: QObject = None) [signal]

disconnect(QMetaObject.Connection) bool
disconnect(self) None
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]
inherits(self, str) bool
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, int)
metaObject(self) QMetaObject
moveToThread(self, QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, str) [signal]

parent(self) QObject
progressMade
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
removeEventFilter(self, QObject)
sender(self) QObject
senderSignalIndex(self) int
setGapPenalties(gapopen, gapext)
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) bool
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