schrodinger.protein.alignment module

Classes for working with sequences containing alignment information (gaps) and collections thereof.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.alignment.ResidueSelection(residues, indices)

Bases: tuple

__add__

Return self+value.

__class__

alias of builtins.type

__contains__

Return key in self.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__

Return self[key].

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__

Implement iter(self).

__le__

Return self<=value.

__len__

Return len(self).

__lt__

Return self<value.

__module__ = 'schrodinger.protein.alignment'
__mul__

Return self*value.n

__ne__

Return self!=value.

static __new__(_cls, residues, indices)

Create new instance of ResidueSelection(residues, indices)

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()

Return a nicely formatted representation string

__rmul__

Return self*value.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

count(value) → integer -- return number of occurrences of value
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

indices

Alias for field number 1

residues

Alias for field number 0

class schrodinger.protein.alignment.ResidueSimilarity

Bases: enum.Enum

An enumeration.

Dissimilar = 3
Identical = 1
NA = 4
Similar = 2
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('Identical', <ResidueSimilarity.Identical: 1>), ('Similar', <ResidueSimilarity.Similar: 2>), ('Dissimilar', <ResidueSimilarity.Dissimilar: 3>), ('NA', <ResidueSimilarity.NA: 4>)]))
__module__ = 'schrodinger.protein.alignment'
exception schrodinger.protein.alignment.AnchoredResidueError

Bases: RuntimeError

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.alignment', '__weakref__': <attribute '__weakref__' of 'AnchoredResidueError' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.alignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setstate__()
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__
__traceback__
__weakref__

list of weak references to the object (if defined)

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.protein.alignment.StructuredResidueError

Bases: RuntimeError

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.alignment', '__weakref__': <attribute '__weakref__' of 'StructuredResidueError' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.alignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setstate__()
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__
__traceback__
__weakref__

list of weak references to the object (if defined)

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.protein.alignment.AlignmentSignals

Bases: PyQt5.QtCore.QObject

A collection of signals that can be emitted by an alignment

Variables:
  • sequencesAboutToBeInserted (QtCore.pyqtSignal) – A signal emitted before sequences are inserted into the alignment. Emitted with: (The index of the first sequence to be inserted, The index of the last sequence to be inserted)
  • sequencesInserted (QtCore.pyqtSignal) – A signal emitted after sequences are inserted into the alignment. Emitted with: (The index of the first sequence inserted, The index of the last sequence inserted)
  • sequencesAboutToBeRemoved (QtCore.pyqtSignal) – A signal emitted before sequences are removed from the alignment. Emitted with: (The index of the first sequence to be removed, The index of the last sequence to be removed)
  • sequencesRemoved (QtCore.pyqtSignal) – A signal emitted after sequences are removed from the alignment. Emitted with: (The index of the first sequence removed, The index of the last sequence removed)
  • sequenceResiduesChanged (QtCore.pyqtSignal) – A signal emitted after the contents of a sequence have changed. Note that this signal may also be emitted in response to a sequence changing length, as positions in the alignment may switch from blank to occupied or vice versa. Emitted with: (The modified sequence, The position of the first modified residue, The position of the last modified residue)
  • sequencesAboutToBeReordered – Signal emitted before reordering sequences
  • sequencesReordered – Signal emitted after sequences have been reordered
  • sequenceNameChanged (QtCore.pyqtSignal) – A signal emitted after a sequence has changed names. Emitted with: (The modified sequence)
  • annotationTitleChanged (QtCore.pyqtSignal) – A signal emitted after a sequence’s annotation has changed titles. Emitted with: (The sequence whose annotation title has been modified)
  • alignmentNumColumnsAboutToChange (QtCore.pyqtSignal) – A signal emitted before the alignment changes length. Emitted with: (The current length of the alignment, The new length of the alignment)
  • alignmentNumColumnsChanged (QtCore.pyqtSignal) – A signal emitted after the alignment changes length. Emitted with: (The old length of the alignment, The current length of the alignment)
  • residuesAboutToBeRemoved (QtCore.pyqtSignal) – A signal emitted before residues are to be removed. Emitted with a list of the residues to be removed.
  • residuesRemoved (QtCore.pyqtSignal) – A signal emitted after residues are removed. This signal is not emitted with any parameters, but the residues that were removed were listed with the corresponding residuesAboutToBeRemoved signal.
  • residuesAdded (QtCore.pyqtSignal) – A signal emitted with added residues. Note that this signal will be only be emitted once even if residues are added to multiple sequences. In addition, each individual sequence will emit a lengthChanged signal.
  • sequenceVisibilityChanged (QtCore.pyqtSignal) – A signal emitted when visibility of a sequence changes. Emitted with: (the sequence whose visibility is changing, the index of the sequence)
  • sequenceStructureChanged (QtCore.pyqtSignal) – A signal emitted when structure of a sequence changes. Emitted with: (the sequence whose visibility is changing, the index of the sequence)
  • alignmentAboutToBeCleared (QtCore.pyqtSignal) – A signal emitted just before all sequences are removed from the alignment.
  • alignmentCleared (QtCore.pyqtSignal) – A signal emitted just after all sequences have been removed from the alignment.
  • anchoredResiduesChanged – A signal emitted when one or more residues are anchored or unanchored.
Type:

sequencesAboutToBeReordered: QtCore.pyqtSignals

Type:

sequencesReordered: QtCore.pyqtSignals

sequencesAboutToBeInserted
sequencesInserted
sequencesAboutToBeRemoved
sequencesRemoved
sequenceResiduesChanged
sequencesAboutToBeReordered
sequencesReordered
sequenceNameChanged
annotationTitleChanged
alignmentNumColumnsAboutToChange
alignmentNumColumnsChanged
residuesAboutToBeRemoved
residuesRemoved
residuesAdded
sequenceVisibilityChanged
sequenceStructureChanged
alignmentAboutToBeCleared
alignmentCleared
anchoredResiduesChanged
emitSeqResChanged(first_res, last_res)
emitSeqNameChanged()
emitAnnTitleChanged()
__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.alignment', '__doc__': "\n A collection of signals that can be emitted by an alignment\n\n :ivar sequencesAboutToBeInserted: A signal emitted before sequences are\n inserted into the alignment. Emitted with: (The index of the first\n sequence to be inserted, The index of the last sequence to be inserted)\n :vartype sequencesAboutToBeInserted: `QtCore.pyqtSignal`\n\n :ivar sequencesInserted: A signal emitted after sequences are\n inserted into the alignment. Emitted with: (The index of the first\n sequence inserted, The index of the last sequence inserted)\n :vartype sequencesInserted: `QtCore.pyqtSignal`\n\n :ivar sequencesAboutToBeRemoved: A signal emitted before sequences are\n removed from the alignment. Emitted with: (The index of the first\n sequence to be removed, The index of the last sequence to be removed)\n :vartype sequencesAboutToBeRemoved: `QtCore.pyqtSignal`\n\n :ivar sequencesRemoved: A signal emitted after sequences are\n removed from the alignment. Emitted with: (The index of the first\n sequence removed, The index of the last sequence removed)\n :vartype sequencesRemoved: `QtCore.pyqtSignal`\n\n :ivar sequenceResiduesChanged: A signal emitted after the contents of a\n sequence have changed. Note that this signal may also be emitted in\n response to a sequence changing length, as positions in the alignment\n may switch from blank to occupied or vice versa. Emitted with: (The\n modified sequence, The position of the first modified residue, The\n position of the last modified residue)\n :vartype sequenceResiduesChanged: `QtCore.pyqtSignal`\n\n :ivar sequencesAboutToBeReordered: Signal emitted before reordering\n sequences\n :type: sequencesAboutToBeReordered: `QtCore.pyqtSignals`\n\n :ivar sequencesReordered: Signal emitted after sequences have been reordered\n :type: sequencesReordered: `QtCore.pyqtSignals`\n\n :ivar sequenceNameChanged: A signal emitted after a sequence has changed\n names. Emitted with: (The modified sequence)\n :vartype sequenceNameChanged: `QtCore.pyqtSignal`\n\n :ivar annotationTitleChanged: A signal emitted after a sequence's annotation\n has changed titles. Emitted with: (The sequence whose annotation title\n has been modified)\n :vartype annotationTitleChanged: `QtCore.pyqtSignal`\n\n :ivar alignmentNumColumnsAboutToChange: A signal emitted before the\n alignment changes length. Emitted with: (The current length of the\n alignment, The new length of the alignment)\n :vartype alignmentNumColumnsAboutToChange: `QtCore.pyqtSignal`\n\n :ivar alignmentNumColumnsChanged: A signal emitted after the alignment\n changes length. Emitted with: (The old length of the alignment, The\n current length of the alignment)\n :vartype alignmentNumColumnsChanged: `QtCore.pyqtSignal`\n\n :ivar residuesAboutToBeRemoved: A signal emitted before residues are to be\n removed. Emitted with a list of the residues to be removed.\n :vartype residuesAboutToBeRemoved: `QtCore.pyqtSignal`\n\n :ivar residuesRemoved: A signal emitted after residues are removed. This\n signal is not emitted with any parameters, but the residues that were\n removed were listed with the corresponding residuesAboutToBeRemoved\n signal.\n :vartype residuesRemoved: `QtCore.pyqtSignal`\n\n :ivar residuesAdded: A signal emitted with added residues. Note that this\n signal will be only be emitted once even if residues are added to\n multiple sequences. In addition, each individual sequence will emit a\n lengthChanged signal.\n :vartype residuesAdded: `QtCore.pyqtSignal`\n\n :ivar sequenceVisibilityChanged: A signal emitted when visibility of a\n sequence changes. Emitted with: (the sequence whose visibility is\n changing, the index of the sequence)\n :vartype sequenceVisibilityChanged: `QtCore.pyqtSignal`\n\n :ivar sequenceStructureChanged: A signal emitted when structure of a\n sequence changes. Emitted with: (the sequence whose visibility is\n changing, the index of the sequence)\n :vartype sequenceStructureChanged: `QtCore.pyqtSignal`\n\n :ivar alignmentAboutToBeCleared: A signal emitted just before all sequences\n are removed from the alignment.\n :vartype alignmentAboutToBeCleared: `QtCore.pyqtSignal`\n\n :ivar alignmentCleared: A signal emitted just after all sequences have been\n removed from the alignment.\n :vartype alignmentCleared: `QtCore.pyqtSignal`\n\n :ivar anchoredResiduesChanged: A signal emitted when one or more residues\n are anchored or unanchored.\n :vartype alignmentCleared: `QtCore.pyqtSignal`\n ", 'sequencesAboutToBeInserted': <unbound PYQT_SIGNAL AlignmentSignals.sequencesAboutToBeInserted[int, int]>, 'sequencesInserted': <unbound PYQT_SIGNAL AlignmentSignals.sequencesInserted[int, int]>, 'sequencesAboutToBeRemoved': <unbound PYQT_SIGNAL AlignmentSignals.sequencesAboutToBeRemoved[int, int]>, 'sequencesRemoved': <unbound PYQT_SIGNAL AlignmentSignals.sequencesRemoved[int, int]>, 'sequenceResiduesChanged': <unbound PYQT_SIGNAL AlignmentSignals.sequenceResiduesChanged[Sequence, int, int]>, 'sequencesAboutToBeReordered': <unbound PYQT_SIGNAL AlignmentSignals.sequencesAboutToBeReordered[]>, 'sequencesReordered': <unbound PYQT_SIGNAL AlignmentSignals.sequencesReordered[list]>, 'sequenceNameChanged': <unbound PYQT_SIGNAL AlignmentSignals.sequenceNameChanged[Sequence]>, 'annotationTitleChanged': <unbound PYQT_SIGNAL AlignmentSignals.annotationTitleChanged[Sequence]>, 'alignmentNumColumnsAboutToChange': <unbound PYQT_SIGNAL AlignmentSignals.alignmentNumColumnsAboutToChange[int, int]>, 'alignmentNumColumnsChanged': <unbound PYQT_SIGNAL AlignmentSignals.alignmentNumColumnsChanged[int, int]>, 'residuesAboutToBeRemoved': <unbound PYQT_SIGNAL AlignmentSignals.residuesAboutToBeRemoved[list]>, 'residuesRemoved': <unbound PYQT_SIGNAL AlignmentSignals.residuesRemoved[]>, 'residuesAdded': <unbound PYQT_SIGNAL AlignmentSignals.residuesAdded[list]>, 'sequenceVisibilityChanged': <unbound PYQT_SIGNAL AlignmentSignals.sequenceVisibilityChanged[Sequence, int]>, 'sequenceStructureChanged': <unbound PYQT_SIGNAL AlignmentSignals.sequenceStructureChanged[Sequence, int]>, 'alignmentAboutToBeCleared': <unbound PYQT_SIGNAL AlignmentSignals.alignmentAboutToBeCleared[]>, 'alignmentCleared': <unbound PYQT_SIGNAL AlignmentSignals.alignmentCleared[]>, 'anchoredResiduesChanged': <unbound PYQT_SIGNAL AlignmentSignals.anchoredResiduesChanged[]>, 'emitSeqResChanged': <function AlignmentSignals.emitSeqResChanged>, 'emitSeqNameChanged': <function AlignmentSignals.emitSeqNameChanged>, 'emitAnnTitleChanged': <function AlignmentSignals.emitAnnTitleChanged>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.alignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
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
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
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
class schrodinger.protein.alignment.BaseAlignment(sequences=None)

Bases: PyQt5.QtCore.QObject

Abstract base class for classes which handle alignment of various sequences and corresponding annotations.

This is a pure domain object intended to make it easy to work with aligned collections of sequences.

Some methods are decorated with @msv_utils.const in order to make it easy to write a wrapper for this class that supports undo/redo operations.

Variables:
  • _ALN_ANNOTATION_CLASS (type) – The class for alignment annotations. This value should be overriden in subclasses.
  • _SEQ_ANNOTATION_CLASS (type) – The class for sequence annotations. This value should be overriden in subclasses.
__init__(sequences=None)
Parameters:sequences (list) – An optional iterable of sequences
__len__()

Returns the number of sequences in the alignment

__iter__()

Returns an iterable of the sequences held in the alignment

__contains__(seq)

Returns whether the sequence is present in the alignment

__getitem__(index)

Returns the sequence at the index in the alignment

__str__()

Returns a str representation of the alignment

This is fairly detailed since it is very useful for debugging

__repr__()
Return type:str
Returns:A str representation of the alignment
__deepcopy__(memo)

We should be able to copy an alignment, getting back an alignment with all the essential data in the original alignment and sharing no references with it

global_annotations

Returns the alignment-level annotations available for the alignment

seq_annotations

Returns the sequence-level annotations available for sequences held in the alignment

all_annotations

Return a list of all annotations types in this alignment

getGlobalAnnotationData(index, annotation)

Returns column-level annotation data at an index in the alignment

Parameters:
  • index (int) – The index in the alignment
  • annotation (enum.Enum) – An enum representing the requested annotation, if any
num_columns
getWorkspaceCounts()

Summarize the visibility status of the alignment’s sequences

Returns:Counts of each type of visibility
Return type:collections.Counter
index(seq)

Returns the index of the specified sequence.

Parameters:seq (sequence.Sequence) – The requested sequence
Return type:int
Returns:The index of the requested sequence
reorderSequences(seq_indices)

Reorder the sequences in the alignment using the specified list of indices.

In the undoable version of this class, the private function is needed to perform the operation in an undoable operation.

Parameters:seq_indices – A list with the new indices for sequences
Type:list of int
Raises:ValueError – In the event that the list of indices does not match the length of the alignment
sort(*, key, reverse=False)

Sort the alignment by the specified criteria.

NOTE: Query sequence is not included in the sort.

Parameters:
  • key (function) – A function that takes a sequence and returns a value to sort by for each sequence. (required keyword-only argument)
  • reverse (bool) – Whether to sort in reverse (descending) order.
addSeq(seq, index=None)
Parameters:
  • seq (sequence.Sequence) – The sequence to add
  • start (int) – The index at which to insert; if None, seq is appended
addSeqs(sequences, start=None)

Add multiple sequences to the alignment

Parameters:
  • sequences (list of sequence.Sequence) – Sequences to add
  • start (int) – The index at which to insert; if None, seqs are appended
addSeqsByIndices(seq_index_map)

Insert a sequences at the specified indices in the alignment. The sequences will be added from lowest to highest to allow for specification of indexes that may be out of range of the current alignment until lower-indexed sequences have been added. Note that indexes that remain out of range will result in their corresponding sequence simply being appended to the end of the alignment.

Parameters:seq_index_map – Map of insertion indices to sequences to be added.
removeSeq(seq)

Remove a sequence from the alignment

Parameters:seq (sequence.Sequence) – The sequence to remove
removeSeqs(seqs)

Remove multiple sequences from the alignment

clear()

Clears the entire alignment of sequences

setReferenceSeq(seq)

Set the specified sequence as the reference sequence.

Parameters:seq (sequence) – Sequence to set as reference sequence
getReferenceSeq()

Returns the sequence that has been set as reference sequence or None if there is no reference sequence.

Returns:The reference sequence or None
Return type:Sequence or None
isReferenceSeq(seq)

Return whether or not a sequence is the reference sequence.

Parameters:seq (Sequence) – Sequence to check
Returns:True if the sequence is the reference sequence, False otherwise.
Return type:bool
getResidueIndices(residues)

Returns the indices (in the alignment) of the specified residues

Parameters:residues (list[residue.AbstractSequenceElement]) – The list of residues and gaps to get indices for.
Return type:A sorted list of (sequence index, residue index) tuples
Returns:list[tuple(int, int)]
removeElements(elements)

Removes the specified elements from the alignment.

Parameters:

elements (iterable(residue.AbstractSequenceElement)) – An iterable of elements.

Raises:
mutateResidues(seq_i, start, end, elements)

Mutate a sequence.

Parameters:
  • seq_i (int) – Index of seq to mutate
  • start (int) – Start index of seq region to mutate
  • end (int) – End index of seq region to mutate
  • elements (iterable(str) or iterable(ElementClass)) – Elements to mutate to
Raises:
replaceResiduesWithGaps(residues)

Replaces the specified residues with gaps

Parameters:residues (list) – A list of residues to replace with gaps
addElements(seq, res_i, elements)

Adds the specified elements (residues and/or gaps) to the alignment.

Parameters:
modifyingStructure()
suspendAnchors()

While inside this context, all anchors will be ignored. Upon exit, the anchors will be restored and an exception will be raised if any of the anchors are not aligned to the same reference residues they were aligned to at the start.

anchorResidues(residues)

Anchor the specified residues. If passed reference residues, all residues aligned to the reference residues will be anchored.

Anchored residues are constrained to stay aligned to the reference residue with the same column index at the time of anchoring. If elements are removed from the alignment, gaps are added before anchors to maintain alignment. If any other modifications are made to the alignment that would break an anchor, an exception is raised. However, calling code can temporarily take responsibility for maintaining the anchors within the suspendAnchors context.

Parameters:residues (list(residue.Residue)) – Residues to anchor.
getAnchoredResidues()
Returns:A frozenset of residues that are currently anchored.

:rtype : frozenset(residue.Residue)

getAnchoredResiduesWithRef()
Returns:A frozenset of residues that are currently anchored with the corresponding reference sequence residues

:rtype : frozenset(residue.Residue)

clearAnchors()
removeAnchors(residues)

Unanchor residues. If passed reference residues, all residues anchored to those reference residues will be unanchored.

Parameters:residues (iterable(residue.Residue)) – The residues to unanchor.
Raises:ValueError – When a residue is passed in that isn’t currently anchored.
getSubalignment(start, end)

Return another alignment containing the elements within the specified start and end indices

Parameters:
  • start (int) – The index at which the subalignment should start
  • end (int) – The index at which the subalignment should end (exclusive)
Return type:

BaseAligment

Returns:

An alignment corresponding to the start and end point specified

getDiscontinuousSubalignment(indices)

Given a list of indices, return a new alignment of sequences made up of the residues at those specified indices within this alignment.

Parameters:indices (list of (int, int)) – List of (seq index, residue index) tuples
Returns:A new subalignment
Return type:BaseAlignment
removeSubalignment(start, end)

Remove a block of the subalignment from the start to end points.

Parameters:
  • start (int) – The start index of the columns to remove
  • end (int) – The end index of the columns to remove (exclusive)
is_rectangular
insertSubalignment(aln, start)

Insert an alignment into the current alignment at the specified index

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The index at which to insert the alignment
Raises:

ValueError – if either alignment is not rectangular

replaceSubalignment(aln, start, end)

Replace a subsection of the alignment indicated by start and end indices with the specified alignment

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The starting index of the subsection to replace.
  • end (int) – The ending index of the subsection to replace.
Raises:

ValueError – if either alignment is not rectangular

getGaps()

Returns a list of list of gaps.

Returns:list(list(residue.Gap))
Return type:list
getTerminalGaps()

Returns the terminal gaps in all the sequences

Return type:list
Returns:list(list(residue.Gap))
removeAllGaps()

Removes all the gaps of the sequences in the alignment.

removeTerminalGaps()

Removes the gaps from the ends of every sequence in the alignment

addGapsByIndices(gap_indices)

Adds gaps to the alignment

Note:

the length of the gap_indices list must match the number of sequences in the alignment.

Parameters:

gap_indices (list[list[int]]) – A list of lists of gap indices, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Raises:
  • ValueError – if gap_indices is the wrong length
  • AnchoredResidueError – if any gap index is before an anchored col
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions.

Note:the length of the gap_indices list must match the number of sequences in the alignment.
Parameters:indices – A list of lists of indices to insert gaps before, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.
padAlignment()

Insert gaps into an alignment so that it forms a rectangular block

getGapOnlyColumns()

Returns a list of lists of indices columns that contain only gaps

Return type:list
Returns:List of list of indices
minimizeAlignment()

Minimizes the alignment, i.e. removes all gaps from the gap-only columns.

getColumn(index, omit_gaps=False)

Returns single alignment column at index position. Optionally, filters out gaps if omit_gaps is True.

Parameters:
  • index (int) – The index in the alignment
  • omit_gaps (bool) – Whether to omit the gaps
Returns:

Single alignment column at index position. Returns None to represent terminal gaps.

Return type:

tuple(residue.Residue or residue.Gap or None)

columns(omit_gaps=False)

A generator over all columns.

Parameters:omit_gaps (bool) – Whether to omit gaps
columnHasAllSameResidues(index)

Return whether or not the column at a specified index has all the same residues (excluding gaps).

Note that if any unknown residues are present, the column will not be considered to be of all the same residue type.

Parameters:index (int) – Index to check for uniformity`
Returns:True if the column is of uniform identity, False otherwise.
Return type:bool
getResidueSimilarity(res)

Return the similarity score of a residue to the current reference residue at the residues position in the alignment.

Parameters:res (residue.Residue) – Residue to get the similarity score for
Returns:Similarity score for this residue
Return type:float or None
elementsToContiguousColumns(elements, invert=False)

Get elements marking contiguous columns containing any of the passed elements

Parameters:
  • elements (iterable(AbstractSequenceElement)) – Elements to convert to columns
  • invert (bool) – Whether to invert logic (i.e. return columns not containing the passed elements)
Returns:

[start, end] elements of contiguous columns. Will be from the ref sequence unless the ref sequence is shorter than num_columns

Return type:

iterable(tuple(AbstractSequenceElement, AbstractSequenceElement))

getIdentities(omit_gaps=True)

Returns an alignment-length list of bools indicating which columns have identical residues

Parameters:omit_gaps (bool) – Whether gaps should be excluded from a column.
getSimilarityScore(seq)

Returns a sequence length array of similarity scores against the reference sequence

Gaps in the sequences are coded as None values.

getEntropy(frequencies)

Returns an alignment length array of residue entropy scores

getRedundantSequences(value)

Returns the indices of sequences below a specified identity threshold value.

Returns:The indices of sequences in the alignment below specified identity threshold
Return type:list of int
calculateMatrix()

Calculates a substitution matrix based on the current alignment.

clearAllCaching()
__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.alignment', '__doc__': '\n Abstract base class for classes which handle alignment of various sequences\n and corresponding annotations.\n\n This is a pure domain object intended to make it easy to work with aligned\n collections of sequences.\n\n Some methods are decorated with @msv_utils.const in order to make it easy to\n write a wrapper for this class that supports undo/redo operations.\n\n :cvar _ALN_ANNOTATION_CLASS: The class for alignment annotations. This\n value should be overriden in subclasses.\n :vartype _ALN_ANNOTATION_CLASS: type\n\n :cvar _SEQ_ANNOTATION_CLASS: The class for sequence annotations. This\n value should be overriden in subclasses.\n :vartype _SEQ_ANNOTATION_CLASS: type\n ', '_ALN_ANNOTATION_CLASS': None, '_SEQ_ANNOTATION_CLASS': None, '__init__': <function BaseAlignment.__init__>, '__len__': <function BaseAlignment.__len__>, '__iter__': <function BaseAlignment.__iter__>, '__contains__': <function BaseAlignment.__contains__>, '__getitem__': <function BaseAlignment.__getitem__>, '_getTextFormattedAlignment': <function BaseAlignment._getTextFormattedAlignment>, '_getAlignmentDescription': <function BaseAlignment._getAlignmentDescription>, '__str__': <function BaseAlignment.__str__>, '__repr__': <function BaseAlignment.__repr__>, '__deepcopy__': <function BaseAlignment.__deepcopy__>, '_copyAnchoringTo': <function BaseAlignment._copyAnchoringTo>, '_mapResidues': <function BaseAlignment._mapResidues>, 'global_annotations': <property object>, 'seq_annotations': <property object>, 'all_annotations': <property object>, 'getGlobalAnnotationData': <function BaseAlignment.getGlobalAnnotationData>, 'num_columns': <property object>, 'getWorkspaceCounts': <function BaseAlignment.getWorkspaceCounts>, '_sequenceVisibilityChanged': <function BaseAlignment._sequenceVisibilityChanged>, '_sequenceStructureChanged': <function BaseAlignment._sequenceStructureChanged>, 'index': <function BaseAlignment.index>, 'reorderSequences': <function BaseAlignment.reorderSequences>, 'sort': <function BaseAlignment.sort>, '_getSortIndices': <function BaseAlignment._getSortIndices>, '_recalculateNumColumns': <function BaseAlignment._recalculateNumColumns>, '_monitorSequence': <function BaseAlignment._monitorSequence>, '_stopMonitoringSequence': <function BaseAlignment._stopMonitoringSequence>, '_getSeqSignalsAndSlots': <function BaseAlignment._getSeqSignalsAndSlots>, '_sequenceLengthAboutToChange': <function BaseAlignment._sequenceLengthAboutToChange>, '_sequenceLengthChanged': <function BaseAlignment._sequenceLengthChanged>, '_checkAlignmentNumColumns': <function BaseAlignment._checkAlignmentNumColumns>, 'addSeq': <function BaseAlignment.addSeq>, 'addSeqs': <function BaseAlignment.addSeqs>, 'addSeqsByIndices': <function BaseAlignment.addSeqsByIndices>, 'removeSeq': <function BaseAlignment.removeSeq>, 'removeSeqs': <function BaseAlignment.removeSeqs>, '_assertCanRemoveRef': <function BaseAlignment._assertCanRemoveRef>, '_removeSeqByIndex': <function BaseAlignment._removeSeqByIndex>, '_resetCaches': <function BaseAlignment._resetCaches>, 'clear': <function BaseAlignment.clear>, '_seq_positions': <property object>, '_updateSequencePositionCache': <function BaseAlignment._updateSequencePositionCache>, '_getReferenceSeqReordering': <function BaseAlignment._getReferenceSeqReordering>, 'setReferenceSeq': <function BaseAlignment.setReferenceSeq>, '_assertCanSetReferenceSeq': <function BaseAlignment._assertCanSetReferenceSeq>, 'getReferenceSeq': <function BaseAlignment.getReferenceSeq>, 'isReferenceSeq': <function BaseAlignment.isReferenceSeq>, 'getResidueIndices': <function BaseAlignment.getResidueIndices>, '_assertCanRemove': <function BaseAlignment._assertCanRemove>, 'removeElements': <function BaseAlignment.removeElements>, '_getAnchorConservingGapIdxs': <function BaseAlignment._getAnchorConservingGapIdxs>, '_assertCanMutateResidues': <function BaseAlignment._assertCanMutateResidues>, 'mutateResidues': <function BaseAlignment.mutateResidues>, 'replaceResiduesWithGaps': <function BaseAlignment.replaceResiduesWithGaps>, 'addElements': <function BaseAlignment.addElements>, 'modifyingStructure': <function BaseAlignment.modifyingStructure>, 'suspendAnchors': <function BaseAlignment.suspendAnchors>, '_suspendAnchors': <function BaseAlignment._suspendAnchors>, '_unsuspendAnchors': <function BaseAlignment._unsuspendAnchors>, '_assertCanAnchor': <function BaseAlignment._assertCanAnchor>, 'anchorResidues': <function BaseAlignment.anchorResidues>, 'getAnchoredResidues': <function BaseAlignment.getAnchoredResidues>, 'getAnchoredResiduesWithRef': <function BaseAlignment.getAnchoredResiduesWithRef>, 'clearAnchors': <function BaseAlignment.clearAnchors>, '_clearAnchorsFromSeqs': <function BaseAlignment._clearAnchorsFromSeqs>, 'removeAnchors': <function BaseAlignment.removeAnchors>, '_assertCanInsert': <function BaseAlignment._assertCanInsert>, 'getSubalignment': <function BaseAlignment.getSubalignment>, 'getDiscontinuousSubalignment': <function BaseAlignment.getDiscontinuousSubalignment>, '_assertCanRemoveSubalignment': <function BaseAlignment._assertCanRemoveSubalignment>, 'removeSubalignment': <function BaseAlignment.removeSubalignment>, 'is_rectangular': <property object>, '_assertRectangular': <function BaseAlignment._assertRectangular>, 'insertSubalignment': <function BaseAlignment.insertSubalignment>, '_insertSubalignment': <function BaseAlignment._insertSubalignment>, 'replaceSubalignment': <function BaseAlignment.replaceSubalignment>, 'getGaps': <function BaseAlignment.getGaps>, 'getTerminalGaps': <function BaseAlignment.getTerminalGaps>, 'removeAllGaps': <function BaseAlignment.removeAllGaps>, 'removeTerminalGaps': <function BaseAlignment.removeTerminalGaps>, '_validateGapIndices': <function BaseAlignment._validateGapIndices>, 'addGapsByIndices': <function BaseAlignment.addGapsByIndices>, 'addGapsBeforeIndices': <function BaseAlignment.addGapsBeforeIndices>, 'padAlignment': <function BaseAlignment.padAlignment>, 'getGapOnlyColumns': <function BaseAlignment.getGapOnlyColumns>, 'minimizeAlignment': <function BaseAlignment.minimizeAlignment>, 'getColumn': <function BaseAlignment.getColumn>, 'columns': <function BaseAlignment.columns>, '_updateColumnSameResCache': <function BaseAlignment._updateColumnSameResCache>, '_updateResidueSimilarityCache': <function BaseAlignment._updateResidueSimilarityCache>, 'columnHasAllSameResidues': <function BaseAlignment.columnHasAllSameResidues>, 'getResidueSimilarity': <function BaseAlignment.getResidueSimilarity>, 'elementsToContiguousColumns': <function BaseAlignment.elementsToContiguousColumns>, 'getIdentities': <function BaseAlignment.getIdentities>, 'getSimilarityScore': <function BaseAlignment.getSimilarityScore>, 'getEntropy': <function BaseAlignment.getEntropy>, 'getRedundantSequences': <function BaseAlignment.getRedundantSequences>, 'calculateMatrix': <function BaseAlignment.calculateMatrix>, 'clearAllCaching': <function BaseAlignment.clearAllCaching>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.alignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
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
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
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
class schrodinger.protein.alignment.ProteinAlignment(sequences=None)

Bases: schrodinger.models.json.JsonableClassMixin, schrodinger.protein.alignment._ProteinAlignment

toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

setHydrophobicityWindowPadding(window_padding)

Sets hydrophobicity window padding value for each sequence in the protein alignment.

Parameters:window_padding (int) – number of values to pad each average with
setIsoelectricPointWindowPadding(window_padding)

Sets isoelectric point window padding value for each sequence in the protein alignment.

Parameters:window_padding (int) – number of values to pad each average with
addDisulfideBond(res1, res2)

Add a disulfide bond if both residues’ sequences are in the alignment

Parameters:
Raises:

ValueError – if either sequence is not in the alignment

removeDisulfideBond(res1, res2)

Remove a disulfide bond if both residues’ sequences are in the alignment

Parameters:
Raises:

ValueError – if either sequence is not in the alignment

static fromClustalFile(file_name)

Returns alignment read from file in Clustal .aln format preserving order of sequences.

Parameters:file_name (str) – Source file name.
Raises:IOError – If output file cannot be read.
Return type:ProteinAlignment
Returns:An alignment
Note:The alignment can be empty if no sequence was present in the input file.
toClustalFile(file_name, use_unique_names=True)

Writes aln to a Clustal alignment file.

Raises:

IOError – If output file cannot be written.

Parameters:
  • file_name (str) – Destination file name.
  • use_unique_names (bool) – If True, write unique name for each sequence.
classmethod fromFastaFile(file_name)

Returns alignment read from file in Clustal .aln format preserving order of sequences.

Raises:IOError – If the input file cannot be read.
Parameters:file_name (str) – name of input FASTA file
Returns:Read alignment. The alignment can be empty if no sequence was present in the input file.
Return type:ProteinAlignment
classmethod fromFastaString(lines)

Read sequences from FASTA-formatted text, creates sequences and appends them to alignment. Splits sequence name from the FASTA header.

Parameters:lines (list of str) – list of strings representing FASTA file
Returns:The alignment
Return type:ProteinAlignment
classmethod fromFastaStringList(strings)

Return an alignment object created from an iterable of sequence strings

Parameters:strings (Iterable of strings) – Sequences as iterable of strings (1D codes)
Returns:The alignment
Return type:ProteinAlignment
toFastaString(use_unique_names=True, maxl=50)

Convert ProteinAlignment object to list of sequence strings

Parameters:aln (ProteinAlignment) – Alignment data
toFastaStringList()

Convert self to list of fasta sequence strings

Return type:list
Returns:list of str
toFastaFile(file_name, use_unique_names=True, maxl=50)

Write self to specified FASTA file

Raises:IOError – If output file cannot be written.
findPattern(pattern)

Finds a specified PROSITE pattern in all sequences.

Parameters:pattern (str) – PROSITE pattern to search in sequences. See protein.sequence.find_generalized_pattern for documentation.
Returns:List of matching residues
Return type:list of protein.residue.Residue
__class__

alias of sip.wrappertype

__contains__(seq)

Returns whether the sequence is present in the alignment

__deepcopy__(memo)

We should be able to copy an alignment, getting back an alignment with all the essential data in the original alignment and sharing no references with it

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.alignment', 'toJsonImplementation': <function ProteinAlignment.toJsonImplementation>, 'fromJsonImplementation': <classmethod object>, 'setHydrophobicityWindowPadding': <function ProteinAlignment.setHydrophobicityWindowPadding>, 'setIsoelectricPointWindowPadding': <function ProteinAlignment.setIsoelectricPointWindowPadding>, 'addDisulfideBond': <function ProteinAlignment.addDisulfideBond>, 'removeDisulfideBond': <function ProteinAlignment.removeDisulfideBond>, 'fromClustalFile': <staticmethod object>, 'toClustalFile': <function ProteinAlignment.toClustalFile>, 'fromFastaFile': <classmethod object>, 'fromFastaString': <classmethod object>, 'fromFastaStringList': <classmethod object>, 'toFastaString': <function ProteinAlignment.toFastaString>, 'toFastaStringList': <function ProteinAlignment.toFastaStringList>, 'toFastaFile': <function ProteinAlignment.toFastaFile>, 'findPattern': <function ProteinAlignment.findPattern>, '__doc__': None, '_ProteinAlignment_jsonAdapters': []})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__getitem__(index)

Returns the sequence at the index in the alignment

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(sequences=None)
Parameters:sequences (list) – An optional iterable of sequences
classmethod __init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__()

Returns an iterable of the sequences held in the alignment

__le__

Return self<=value.

__len__()

Returns the number of sequences in the alignment

__lt__

Return self<value.

__module__ = 'schrodinger.protein.alignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()
Return type:str
Returns:A str representation of the alignment
__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__()

Returns a str representation of the alignment

This is fairly detailed since it is very useful for debugging

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

addElements(seq, res_i, elements)

Adds the specified elements (residues and/or gaps) to the alignment.

Parameters:
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions.

Note:the length of the gap_indices list must match the number of sequences in the alignment.
Parameters:indices – A list of lists of indices to insert gaps before, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.
addGapsByIndices(gap_indices)

Adds gaps to the alignment

Note:

the length of the gap_indices list must match the number of sequences in the alignment.

Parameters:

gap_indices (list[list[int]]) – A list of lists of gap indices, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Raises:
  • ValueError – if gap_indices is the wrong length
  • AnchoredResidueError – if any gap index is before an anchored col
addSeq(seq, index=None)
Parameters:
  • seq (sequence.Sequence) – The sequence to add
  • start (int) – The index at which to insert; if None, seq is appended
addSeqs(sequences, start=None)

Add multiple sequences to the alignment

Parameters:
  • sequences (list of sequence.Sequence) – Sequences to add
  • start (int) – The index at which to insert; if None, seqs are appended
addSeqsByIndices(seq_index_map)

Insert a sequences at the specified indices in the alignment. The sequences will be added from lowest to highest to allow for specification of indexes that may be out of range of the current alignment until lower-indexed sequences have been added. Note that indexes that remain out of range will result in their corresponding sequence simply being appended to the end of the alignment.

Parameters:seq_index_map – Map of insertion indices to sequences to be added.
all_annotations

Return a list of all annotations types in this alignment

anchorResidues(residues)

Anchor the specified residues. If passed reference residues, all residues aligned to the reference residues will be anchored.

Anchored residues are constrained to stay aligned to the reference residue with the same column index at the time of anchoring. If elements are removed from the alignment, gaps are added before anchors to maintain alignment. If any other modifications are made to the alignment that would break an anchor, an exception is raised. However, calling code can temporarily take responsibility for maintaining the anchors within the suspendAnchors context.

Parameters:residues (list(residue.Residue)) – Residues to anchor.
blockSignals(self, bool) → bool
calculateMatrix()

Calculates a substitution matrix based on the current alignment.

childEvent(self, QChildEvent)
children(self) → object
clear()

Clears the entire alignment of sequences

clearAllCaching()
clearAnchors()
columnHasAllSameResidues(index)

Return whether or not the column at a specified index has all the same residues (excluding gaps).

Note that if any unknown residues are present, the column will not be considered to be of all the same residue type.

Parameters:index (int) – Index to check for uniformity`
Returns:True if the column is of uniform identity, False otherwise.
Return type:bool
columns(omit_gaps=False)

A generator over all columns.

Parameters:omit_gaps (bool) – Whether to omit gaps
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfide_bonds
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
elementsToContiguousColumns(elements, invert=False)

Get elements marking contiguous columns containing any of the passed elements

Parameters:
  • elements (iterable(AbstractSequenceElement)) – Elements to convert to columns
  • invert (bool) – Whether to invert logic (i.e. return columns not containing the passed elements)
Returns:

[start, end] elements of contiguous columns. Will be from the ref sequence unless the ref sequence is shorter than num_columns

Return type:

iterable(tuple(AbstractSequenceElement, AbstractSequenceElement))

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]

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from.
Returns:An instance of this class.

:rtype : cls

getAnchoredResidues()
Returns:A frozenset of residues that are currently anchored.

:rtype : frozenset(residue.Residue)

getAnchoredResiduesWithRef()
Returns:A frozenset of residues that are currently anchored with the corresponding reference sequence residues

:rtype : frozenset(residue.Residue)

getColumn(index, omit_gaps=False)

Returns single alignment column at index position. Optionally, filters out gaps if omit_gaps is True.

Parameters:
  • index (int) – The index in the alignment
  • omit_gaps (bool) – Whether to omit the gaps
Returns:

Single alignment column at index position. Returns None to represent terminal gaps.

Return type:

tuple(residue.Residue or residue.Gap or None)

getDiscontinuousSubalignment(indices)

Given a list of indices, return a new alignment of sequences made up of the residues at those specified indices within this alignment.

Parameters:indices (list of (int, int)) – List of (seq index, residue index) tuples
Returns:A new subalignment
Return type:BaseAlignment
getEntropy(frequencies)

Returns an alignment length array of residue entropy scores

getGapOnlyColumns()

Returns a list of lists of indices columns that contain only gaps

Return type:list
Returns:List of list of indices
getGaps()

Returns a list of list of gaps.

Returns:list(list(residue.Gap))
Return type:list
getGlobalAnnotationData(index, annotation)

Returns column-level annotation data at an index in the alignment

Parameters:
  • index (int) – The index in the alignment
  • annotation (enum.Enum) – An enum representing the requested annotation, if any
getIdentities(omit_gaps=True)

Returns an alignment-length list of bools indicating which columns have identical residues

Parameters:omit_gaps (bool) – Whether gaps should be excluded from a column.
getRedundantSequences(value)

Returns the indices of sequences below a specified identity threshold value.

Returns:The indices of sequences in the alignment below specified identity threshold
Return type:list of int
getReferenceSeq()

Returns the sequence that has been set as reference sequence or None if there is no reference sequence.

Returns:The reference sequence or None
Return type:Sequence or None
getResidueIndices(residues)

Returns the indices (in the alignment) of the specified residues

Parameters:residues (list[residue.AbstractSequenceElement]) – The list of residues and gaps to get indices for.
Return type:A sorted list of (sequence index, residue index) tuples
Returns:list[tuple(int, int)]
getResidueSimilarity(res)

Return the similarity score of a residue to the current reference residue at the residues position in the alignment.

Parameters:res (residue.Residue) – Residue to get the similarity score for
Returns:Similarity score for this residue
Return type:float or None
getSimilarityScore(seq)

Returns a sequence length array of similarity scores against the reference sequence

Gaps in the sequences are coded as None values.

getSubalignment(start, end)

Return another alignment containing the elements within the specified start and end indices

Parameters:
  • start (int) – The index at which the subalignment should start
  • end (int) – The index at which the subalignment should end (exclusive)
Return type:

BaseAligment

Returns:

An alignment corresponding to the start and end point specified

getTerminalGaps()

Returns the terminal gaps in all the sequences

Return type:list
Returns:list(list(residue.Gap))
getWorkspaceCounts()

Summarize the visibility status of the alignment’s sequences

Returns:Counts of each type of visibility
Return type:collections.Counter
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

global_annotations

Returns the alignment-level annotations available for the alignment

index(seq)

Returns the index of the specified sequence.

Parameters:seq (sequence.Sequence) – The requested sequence
Return type:int
Returns:The index of the requested sequence
inherits(self, str) → bool
insertSubalignment(aln, start)

Insert an alignment into the current alignment at the specified index

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The index at which to insert the alignment
Raises:

ValueError – if either alignment is not rectangular

installEventFilter(self, QObject)
isReferenceSeq(seq)

Return whether or not a sequence is the reference sequence.

Parameters:seq (Sequence) – Sequence to check
Returns:True if the sequence is the reference sequence, False otherwise.
Return type:bool
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_rectangular
killTimer(self, int)
metaObject(self) → QMetaObject
minimizeAlignment()

Minimizes the alignment, i.e. removes all gaps from the gap-only columns.

modifyingStructure()
moveToThread(self, QThread)
mutateResidues(seq_i, start, end, elements)

Mutate a sequence.

Parameters:
  • seq_i (int) – Index of seq to mutate
  • start (int) – Start index of seq region to mutate
  • end (int) – End index of seq region to mutate
  • elements (iterable(str) or iterable(ElementClass)) – Elements to mutate to
Raises:
num_columns
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

padAlignment()

Insert gaps into an alignment so that it forms a rectangular block

parent(self) → QObject
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
removeAllGaps()

Removes all the gaps of the sequences in the alignment.

removeAnchors(residues)

Unanchor residues. If passed reference residues, all residues anchored to those reference residues will be unanchored.

Parameters:residues (iterable(residue.Residue)) – The residues to unanchor.
Raises:ValueError – When a residue is passed in that isn’t currently anchored.
removeElements(elements)

Removes the specified elements from the alignment.

Parameters:

elements (iterable(residue.AbstractSequenceElement)) – An iterable of elements.

Raises:
removeEventFilter(self, QObject)
removeSeq(seq)

Remove a sequence from the alignment

Parameters:seq (sequence.Sequence) – The sequence to remove
removeSeqs(seqs)

Remove multiple sequences from the alignment

removeSubalignment(start, end)

Remove a block of the subalignment from the start to end points.

Parameters:
  • start (int) – The start index of the columns to remove
  • end (int) – The end index of the columns to remove (exclusive)
removeTerminalGaps()

Removes the gaps from the ends of every sequence in the alignment

reorderSequences(seq_indices)

Reorder the sequences in the alignment using the specified list of indices.

In the undoable version of this class, the private function is needed to perform the operation in an undoable operation.

Parameters:seq_indices – A list with the new indices for sequences
Type:list of int
Raises:ValueError – In the event that the list of indices does not match the length of the alignment
replaceResiduesWithGaps(residues)

Replaces the specified residues with gaps

Parameters:residues (list) – A list of residues to replace with gaps
replaceSubalignment(aln, start, end)

Replace a subsection of the alignment indicated by start and end indices with the specified alignment

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The starting index of the subsection to replace.
  • end (int) – The ending index of the subsection to replace.
Raises:

ValueError – if either alignment is not rectangular

sender(self) → QObject
senderSignalIndex(self) → int
seq_annotations

Returns the sequence-level annotations available for sequences held in the alignment

setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setReferenceSeq(seq)

Set the specified sequence as the reference sequence.

Parameters:seq (sequence) – Sequence to set as reference sequence
signalsBlocked(self) → bool
sort(*, key, reverse=False)

Sort the alignment by the specified criteria.

NOTE: Query sequence is not included in the sort.

Parameters:
  • key (function) – A function that takes a sequence and returns a value to sort by for each sequence. (required keyword-only argument)
  • reverse (bool) – Whether to sort in reverse (descending) order.
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspendAnchors()

While inside this context, all anchors will be ignored. Upon exit, the anchors will be restored and an exception will be raised if any of the anchors are not aligned to the same reference residues they were aligned to at the start.

thread(self) → QThread
timerEvent(self, QTimerEvent)
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
tr(self, str, disambiguation: str = None, n: int = -1) → str
class schrodinger.protein.alignment.NucleicAcidAlignment(sequences=None)

Bases: schrodinger.protein.alignment.BaseAlignment

__class__

alias of sip.wrappertype

__contains__(seq)

Returns whether the sequence is present in the alignment

__deepcopy__(memo)

We should be able to copy an alignment, getting back an alignment with all the essential data in the original alignment and sharing no references with it

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.alignment', '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__getitem__(index)

Returns the sequence at the index in the alignment

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(sequences=None)
Parameters:sequences (list) – An optional iterable of sequences
__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__()

Returns an iterable of the sequences held in the alignment

__le__

Return self<=value.

__len__()

Returns the number of sequences in the alignment

__lt__

Return self<value.

__module__ = 'schrodinger.protein.alignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()
Return type:str
Returns:A str representation of the alignment
__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__()

Returns a str representation of the alignment

This is fairly detailed since it is very useful for debugging

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

addElements(seq, res_i, elements)

Adds the specified elements (residues and/or gaps) to the alignment.

Parameters:
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions.

Note:the length of the gap_indices list must match the number of sequences in the alignment.
Parameters:indices – A list of lists of indices to insert gaps before, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.
addGapsByIndices(gap_indices)

Adds gaps to the alignment

Note:

the length of the gap_indices list must match the number of sequences in the alignment.

Parameters:

gap_indices (list[list[int]]) – A list of lists of gap indices, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Raises:
  • ValueError – if gap_indices is the wrong length
  • AnchoredResidueError – if any gap index is before an anchored col
addSeq(seq, index=None)
Parameters:
  • seq (sequence.Sequence) – The sequence to add
  • start (int) – The index at which to insert; if None, seq is appended
addSeqs(sequences, start=None)

Add multiple sequences to the alignment

Parameters:
  • sequences (list of sequence.Sequence) – Sequences to add
  • start (int) – The index at which to insert; if None, seqs are appended
addSeqsByIndices(seq_index_map)

Insert a sequences at the specified indices in the alignment. The sequences will be added from lowest to highest to allow for specification of indexes that may be out of range of the current alignment until lower-indexed sequences have been added. Note that indexes that remain out of range will result in their corresponding sequence simply being appended to the end of the alignment.

Parameters:seq_index_map – Map of insertion indices to sequences to be added.
all_annotations

Return a list of all annotations types in this alignment

anchorResidues(residues)

Anchor the specified residues. If passed reference residues, all residues aligned to the reference residues will be anchored.

Anchored residues are constrained to stay aligned to the reference residue with the same column index at the time of anchoring. If elements are removed from the alignment, gaps are added before anchors to maintain alignment. If any other modifications are made to the alignment that would break an anchor, an exception is raised. However, calling code can temporarily take responsibility for maintaining the anchors within the suspendAnchors context.

Parameters:residues (list(residue.Residue)) – Residues to anchor.
blockSignals(self, bool) → bool
calculateMatrix()

Calculates a substitution matrix based on the current alignment.

childEvent(self, QChildEvent)
children(self) → object
clear()

Clears the entire alignment of sequences

clearAllCaching()
clearAnchors()
columnHasAllSameResidues(index)

Return whether or not the column at a specified index has all the same residues (excluding gaps).

Note that if any unknown residues are present, the column will not be considered to be of all the same residue type.

Parameters:index (int) – Index to check for uniformity`
Returns:True if the column is of uniform identity, False otherwise.
Return type:bool
columns(omit_gaps=False)

A generator over all columns.

Parameters:omit_gaps (bool) – Whether to omit gaps
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
elementsToContiguousColumns(elements, invert=False)

Get elements marking contiguous columns containing any of the passed elements

Parameters:
  • elements (iterable(AbstractSequenceElement)) – Elements to convert to columns
  • invert (bool) – Whether to invert logic (i.e. return columns not containing the passed elements)
Returns:

[start, end] elements of contiguous columns. Will be from the ref sequence unless the ref sequence is shorter than num_columns

Return type:

iterable(tuple(AbstractSequenceElement, AbstractSequenceElement))

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]

getAnchoredResidues()
Returns:A frozenset of residues that are currently anchored.

:rtype : frozenset(residue.Residue)

getAnchoredResiduesWithRef()
Returns:A frozenset of residues that are currently anchored with the corresponding reference sequence residues

:rtype : frozenset(residue.Residue)

getColumn(index, omit_gaps=False)

Returns single alignment column at index position. Optionally, filters out gaps if omit_gaps is True.

Parameters:
  • index (int) – The index in the alignment
  • omit_gaps (bool) – Whether to omit the gaps
Returns:

Single alignment column at index position. Returns None to represent terminal gaps.

Return type:

tuple(residue.Residue or residue.Gap or None)

getDiscontinuousSubalignment(indices)

Given a list of indices, return a new alignment of sequences made up of the residues at those specified indices within this alignment.

Parameters:indices (list of (int, int)) – List of (seq index, residue index) tuples
Returns:A new subalignment
Return type:BaseAlignment
getEntropy(frequencies)

Returns an alignment length array of residue entropy scores

getGapOnlyColumns()

Returns a list of lists of indices columns that contain only gaps

Return type:list
Returns:List of list of indices
getGaps()

Returns a list of list of gaps.

Returns:list(list(residue.Gap))
Return type:list
getGlobalAnnotationData(index, annotation)

Returns column-level annotation data at an index in the alignment

Parameters:
  • index (int) – The index in the alignment
  • annotation (enum.Enum) – An enum representing the requested annotation, if any
getIdentities(omit_gaps=True)

Returns an alignment-length list of bools indicating which columns have identical residues

Parameters:omit_gaps (bool) – Whether gaps should be excluded from a column.
getRedundantSequences(value)

Returns the indices of sequences below a specified identity threshold value.

Returns:The indices of sequences in the alignment below specified identity threshold
Return type:list of int
getReferenceSeq()

Returns the sequence that has been set as reference sequence or None if there is no reference sequence.

Returns:The reference sequence or None
Return type:Sequence or None
getResidueIndices(residues)

Returns the indices (in the alignment) of the specified residues

Parameters:residues (list[residue.AbstractSequenceElement]) – The list of residues and gaps to get indices for.
Return type:A sorted list of (sequence index, residue index) tuples
Returns:list[tuple(int, int)]
getResidueSimilarity(res)

Return the similarity score of a residue to the current reference residue at the residues position in the alignment.

Parameters:res (residue.Residue) – Residue to get the similarity score for
Returns:Similarity score for this residue
Return type:float or None
getSimilarityScore(seq)

Returns a sequence length array of similarity scores against the reference sequence

Gaps in the sequences are coded as None values.

getSubalignment(start, end)

Return another alignment containing the elements within the specified start and end indices

Parameters:
  • start (int) – The index at which the subalignment should start
  • end (int) – The index at which the subalignment should end (exclusive)
Return type:

BaseAligment

Returns:

An alignment corresponding to the start and end point specified

getTerminalGaps()

Returns the terminal gaps in all the sequences

Return type:list
Returns:list(list(residue.Gap))
getWorkspaceCounts()

Summarize the visibility status of the alignment’s sequences

Returns:Counts of each type of visibility
Return type:collections.Counter
global_annotations

Returns the alignment-level annotations available for the alignment

index(seq)

Returns the index of the specified sequence.

Parameters:seq (sequence.Sequence) – The requested sequence
Return type:int
Returns:The index of the requested sequence
inherits(self, str) → bool
insertSubalignment(aln, start)

Insert an alignment into the current alignment at the specified index

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The index at which to insert the alignment
Raises:

ValueError – if either alignment is not rectangular

installEventFilter(self, QObject)
isReferenceSeq(seq)

Return whether or not a sequence is the reference sequence.

Parameters:seq (Sequence) – Sequence to check
Returns:True if the sequence is the reference sequence, False otherwise.
Return type:bool
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_rectangular
killTimer(self, int)
metaObject(self) → QMetaObject
minimizeAlignment()

Minimizes the alignment, i.e. removes all gaps from the gap-only columns.

modifyingStructure()
moveToThread(self, QThread)
mutateResidues(seq_i, start, end, elements)

Mutate a sequence.

Parameters:
  • seq_i (int) – Index of seq to mutate
  • start (int) – Start index of seq region to mutate
  • end (int) – End index of seq region to mutate
  • elements (iterable(str) or iterable(ElementClass)) – Elements to mutate to
Raises:
num_columns
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

padAlignment()

Insert gaps into an alignment so that it forms a rectangular block

parent(self) → QObject
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
removeAllGaps()

Removes all the gaps of the sequences in the alignment.

removeAnchors(residues)

Unanchor residues. If passed reference residues, all residues anchored to those reference residues will be unanchored.

Parameters:residues (iterable(residue.Residue)) – The residues to unanchor.
Raises:ValueError – When a residue is passed in that isn’t currently anchored.
removeElements(elements)

Removes the specified elements from the alignment.

Parameters:

elements (iterable(residue.AbstractSequenceElement)) – An iterable of elements.

Raises:
removeEventFilter(self, QObject)
removeSeq(seq)

Remove a sequence from the alignment

Parameters:seq (sequence.Sequence) – The sequence to remove
removeSeqs(seqs)

Remove multiple sequences from the alignment

removeSubalignment(start, end)

Remove a block of the subalignment from the start to end points.

Parameters:
  • start (int) – The start index of the columns to remove
  • end (int) – The end index of the columns to remove (exclusive)
removeTerminalGaps()

Removes the gaps from the ends of every sequence in the alignment

reorderSequences(seq_indices)

Reorder the sequences in the alignment using the specified list of indices.

In the undoable version of this class, the private function is needed to perform the operation in an undoable operation.

Parameters:seq_indices – A list with the new indices for sequences
Type:list of int
Raises:ValueError – In the event that the list of indices does not match the length of the alignment
replaceResiduesWithGaps(residues)

Replaces the specified residues with gaps

Parameters:residues (list) – A list of residues to replace with gaps
replaceSubalignment(aln, start, end)

Replace a subsection of the alignment indicated by start and end indices with the specified alignment

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The starting index of the subsection to replace.
  • end (int) – The ending index of the subsection to replace.
Raises:

ValueError – if either alignment is not rectangular

sender(self) → QObject
senderSignalIndex(self) → int
seq_annotations

Returns the sequence-level annotations available for sequences held in the alignment

setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setReferenceSeq(seq)

Set the specified sequence as the reference sequence.

Parameters:seq (sequence) – Sequence to set as reference sequence
signalsBlocked(self) → bool
sort(*, key, reverse=False)

Sort the alignment by the specified criteria.

NOTE: Query sequence is not included in the sort.

Parameters:
  • key (function) – A function that takes a sequence and returns a value to sort by for each sequence. (required keyword-only argument)
  • reverse (bool) – Whether to sort in reverse (descending) order.
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspendAnchors()

While inside this context, all anchors will be ignored. Upon exit, the anchors will be restored and an exception will be raised if any of the anchors are not aligned to the same reference residues they were aligned to at the start.

thread(self) → QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = -1) → str
class schrodinger.protein.alignment.CombinedChainProteinAlignment(sequences=None)

Bases: schrodinger.protein.alignment._ProteinAlignment

An alignment containing combined-chain sequences (sequence.CombinedChainProteinSequence objects).

addSeqs(seqs, start=None)

Add multiple sequences to the alignment. Note that either single-chain sequences or combined-chain sequences may be added (but not both at the same time).

Parameters:
__class__

alias of sip.wrappertype

__contains__(seq)

Returns whether the sequence is present in the alignment

__deepcopy__(memo)

We should be able to copy an alignment, getting back an alignment with all the essential data in the original alignment and sharing no references with it

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.alignment', '__doc__': '\n An alignment containing combined-chain sequences\n (`sequence.CombinedChainProteinSequence` objects).\n ', '_mapResidues': <function CombinedChainProteinAlignment._mapResidues>, 'addSeqs': <function CombinedChainProteinAlignment.addSeqs>, '_isCombinedChainSeq': <function CombinedChainProteinAlignment._isCombinedChainSeq>, '_addSplitSeqs': <function CombinedChainProteinAlignment._addSplitSeqs>, '_addNewChainsToExistingSeqs': <function CombinedChainProteinAlignment._addNewChainsToExistingSeqs>, '_combineSequences': <function CombinedChainProteinAlignment._combineSequences>, 'removeSeqs': <function CombinedChainProteinAlignment.removeSeqs>, '_removeSplitSeqs': <function CombinedChainProteinAlignment._removeSplitSeqs>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__getitem__(index)

Returns the sequence at the index in the alignment

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(sequences=None)
Parameters:sequences (list) – An optional iterable of sequences
__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__()

Returns an iterable of the sequences held in the alignment

__le__

Return self<=value.

__len__()

Returns the number of sequences in the alignment

__lt__

Return self<value.

__module__ = 'schrodinger.protein.alignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()
Return type:str
Returns:A str representation of the alignment
__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__()

Returns a str representation of the alignment

This is fairly detailed since it is very useful for debugging

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

addElements(seq, res_i, elements)

Adds the specified elements (residues and/or gaps) to the alignment.

Parameters:
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions.

Note:the length of the gap_indices list must match the number of sequences in the alignment.
Parameters:indices – A list of lists of indices to insert gaps before, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.
addGapsByIndices(gap_indices)

Adds gaps to the alignment

Note:

the length of the gap_indices list must match the number of sequences in the alignment.

Parameters:

gap_indices (list[list[int]]) – A list of lists of gap indices, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Raises:
  • ValueError – if gap_indices is the wrong length
  • AnchoredResidueError – if any gap index is before an anchored col
addSeq(seq, index=None)
Parameters:
  • seq (sequence.Sequence) – The sequence to add
  • start (int) – The index at which to insert; if None, seq is appended
addSeqsByIndices(seq_index_map)

Insert a sequences at the specified indices in the alignment. The sequences will be added from lowest to highest to allow for specification of indexes that may be out of range of the current alignment until lower-indexed sequences have been added. Note that indexes that remain out of range will result in their corresponding sequence simply being appended to the end of the alignment.

Parameters:seq_index_map – Map of insertion indices to sequences to be added.
all_annotations

Return a list of all annotations types in this alignment

anchorResidues(residues)

Anchor the specified residues. If passed reference residues, all residues aligned to the reference residues will be anchored.

Anchored residues are constrained to stay aligned to the reference residue with the same column index at the time of anchoring. If elements are removed from the alignment, gaps are added before anchors to maintain alignment. If any other modifications are made to the alignment that would break an anchor, an exception is raised. However, calling code can temporarily take responsibility for maintaining the anchors within the suspendAnchors context.

Parameters:residues (list(residue.Residue)) – Residues to anchor.
blockSignals(self, bool) → bool
calculateMatrix()

Calculates a substitution matrix based on the current alignment.

childEvent(self, QChildEvent)
children(self) → object
clear()

Clears the entire alignment of sequences

clearAllCaching()
clearAnchors()
columnHasAllSameResidues(index)

Return whether or not the column at a specified index has all the same residues (excluding gaps).

Note that if any unknown residues are present, the column will not be considered to be of all the same residue type.

Parameters:index (int) – Index to check for uniformity`
Returns:True if the column is of uniform identity, False otherwise.
Return type:bool
columns(omit_gaps=False)

A generator over all columns.

Parameters:omit_gaps (bool) – Whether to omit gaps
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfide_bonds
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
elementsToContiguousColumns(elements, invert=False)

Get elements marking contiguous columns containing any of the passed elements

Parameters:
  • elements (iterable(AbstractSequenceElement)) – Elements to convert to columns
  • invert (bool) – Whether to invert logic (i.e. return columns not containing the passed elements)
Returns:

[start, end] elements of contiguous columns. Will be from the ref sequence unless the ref sequence is shorter than num_columns

Return type:

iterable(tuple(AbstractSequenceElement, AbstractSequenceElement))

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]

getAnchoredResidues()
Returns:A frozenset of residues that are currently anchored.

:rtype : frozenset(residue.Residue)

getAnchoredResiduesWithRef()
Returns:A frozenset of residues that are currently anchored with the corresponding reference sequence residues

:rtype : frozenset(residue.Residue)

getColumn(index, omit_gaps=False)

Returns single alignment column at index position. Optionally, filters out gaps if omit_gaps is True.

Parameters:
  • index (int) – The index in the alignment
  • omit_gaps (bool) – Whether to omit the gaps
Returns:

Single alignment column at index position. Returns None to represent terminal gaps.

Return type:

tuple(residue.Residue or residue.Gap or None)

getDiscontinuousSubalignment(indices)

Given a list of indices, return a new alignment of sequences made up of the residues at those specified indices within this alignment.

Parameters:indices (list of (int, int)) – List of (seq index, residue index) tuples
Returns:A new subalignment
Return type:BaseAlignment
getEntropy(frequencies)

Returns an alignment length array of residue entropy scores

getGapOnlyColumns()

Returns a list of lists of indices columns that contain only gaps

Return type:list
Returns:List of list of indices
getGaps()

Returns a list of list of gaps.

Returns:list(list(residue.Gap))
Return type:list
getGlobalAnnotationData(index, annotation)

Returns column-level annotation data at an index in the alignment

Parameters:
  • index (int) – The index in the alignment
  • annotation (enum.Enum) – An enum representing the requested annotation, if any
getIdentities(omit_gaps=True)

Returns an alignment-length list of bools indicating which columns have identical residues

Parameters:omit_gaps (bool) – Whether gaps should be excluded from a column.
getRedundantSequences(value)

Returns the indices of sequences below a specified identity threshold value.

Returns:The indices of sequences in the alignment below specified identity threshold
Return type:list of int
getReferenceSeq()

Returns the sequence that has been set as reference sequence or None if there is no reference sequence.

Returns:The reference sequence or None
Return type:Sequence or None
getResidueIndices(residues)

Returns the indices (in the alignment) of the specified residues

Parameters:residues (list[residue.AbstractSequenceElement]) – The list of residues and gaps to get indices for.
Return type:A sorted list of (sequence index, residue index) tuples
Returns:list[tuple(int, int)]
getResidueSimilarity(res)

Return the similarity score of a residue to the current reference residue at the residues position in the alignment.

Parameters:res (residue.Residue) – Residue to get the similarity score for
Returns:Similarity score for this residue
Return type:float or None
getSimilarityScore(seq)

Returns a sequence length array of similarity scores against the reference sequence

Gaps in the sequences are coded as None values.

getSubalignment(start, end)

Return another alignment containing the elements within the specified start and end indices

Parameters:
  • start (int) – The index at which the subalignment should start
  • end (int) – The index at which the subalignment should end (exclusive)
Return type:

BaseAligment

Returns:

An alignment corresponding to the start and end point specified

getTerminalGaps()

Returns the terminal gaps in all the sequences

Return type:list
Returns:list(list(residue.Gap))
getWorkspaceCounts()

Summarize the visibility status of the alignment’s sequences

Returns:Counts of each type of visibility
Return type:collections.Counter
global_annotations

Returns the alignment-level annotations available for the alignment

index(seq)

Returns the index of the specified sequence.

Parameters:seq (sequence.Sequence) – The requested sequence
Return type:int
Returns:The index of the requested sequence
inherits(self, str) → bool
insertSubalignment(aln, start)

Insert an alignment into the current alignment at the specified index

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The index at which to insert the alignment
Raises:

ValueError – if either alignment is not rectangular

installEventFilter(self, QObject)
isReferenceSeq(seq)

Return whether or not a sequence is the reference sequence.

Parameters:seq (Sequence) – Sequence to check
Returns:True if the sequence is the reference sequence, False otherwise.
Return type:bool
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_rectangular
killTimer(self, int)
metaObject(self) → QMetaObject
minimizeAlignment()

Minimizes the alignment, i.e. removes all gaps from the gap-only columns.

modifyingStructure()
moveToThread(self, QThread)
mutateResidues(seq_i, start, end, elements)

Mutate a sequence.

Parameters:
  • seq_i (int) – Index of seq to mutate
  • start (int) – Start index of seq region to mutate
  • end (int) – End index of seq region to mutate
  • elements (iterable(str) or iterable(ElementClass)) – Elements to mutate to
Raises:
num_columns
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

padAlignment()

Insert gaps into an alignment so that it forms a rectangular block

parent(self) → QObject
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
removeAllGaps()

Removes all the gaps of the sequences in the alignment.

removeAnchors(residues)

Unanchor residues. If passed reference residues, all residues anchored to those reference residues will be unanchored.

Parameters:residues (iterable(residue.Residue)) – The residues to unanchor.
Raises:ValueError – When a residue is passed in that isn’t currently anchored.
removeElements(elements)

Removes the specified elements from the alignment.

Parameters:

elements (iterable(residue.AbstractSequenceElement)) – An iterable of elements.

Raises:
removeEventFilter(self, QObject)
removeSeq(seq)

Remove a sequence from the alignment

Parameters:seq (sequence.Sequence) – The sequence to remove
removeSubalignment(start, end)

Remove a block of the subalignment from the start to end points.

Parameters:
  • start (int) – The start index of the columns to remove
  • end (int) – The end index of the columns to remove (exclusive)
removeTerminalGaps()

Removes the gaps from the ends of every sequence in the alignment

reorderSequences(seq_indices)

Reorder the sequences in the alignment using the specified list of indices.

In the undoable version of this class, the private function is needed to perform the operation in an undoable operation.

Parameters:seq_indices – A list with the new indices for sequences
Type:list of int
Raises:ValueError – In the event that the list of indices does not match the length of the alignment
replaceResiduesWithGaps(residues)

Replaces the specified residues with gaps

Parameters:residues (list) – A list of residues to replace with gaps
replaceSubalignment(aln, start, end)

Replace a subsection of the alignment indicated by start and end indices with the specified alignment

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The starting index of the subsection to replace.
  • end (int) – The ending index of the subsection to replace.
Raises:

ValueError – if either alignment is not rectangular

sender(self) → QObject
senderSignalIndex(self) → int
seq_annotations

Returns the sequence-level annotations available for sequences held in the alignment

setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setReferenceSeq(seq)

Set the specified sequence as the reference sequence.

Parameters:seq (sequence) – Sequence to set as reference sequence
signalsBlocked(self) → bool
sort(*, key, reverse=False)

Sort the alignment by the specified criteria.

NOTE: Query sequence is not included in the sort.

Parameters:
  • key (function) – A function that takes a sequence and returns a value to sort by for each sequence. (required keyword-only argument)
  • reverse (bool) – Whether to sort in reverse (descending) order.
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspendAnchors()

While inside this context, all anchors will be ignored. Upon exit, the anchors will be restored and an exception will be raised if any of the anchors are not aligned to the same reference residues they were aligned to at the start.

thread(self) → QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = -1) → str
removeSeqs(seqs)

Remove multiple sequences from the alignment. Note that either single- chain sequences or combined-chain sequences may be added (but not both at the same time).

Parameters:sequences (list[sequence.Sequence] or list[sequence.CombinedChainProteinSequence]) – Sequences to remove