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.ResidueSimilarity(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

Identical = 1
Similar = 2
Dissimilar = 3
NA = 4
exception schrodinger.protein.alignment.AnchoredResidueError(message=None, blocking_anchors=<object object>)

Bases: RuntimeError

Exception to indicate that an action would break anchors.

When possible, the specific anchors that block the action are stored on the exception instance.

Variables

blocking_anchors (list[residue.Residue] or object) – Anchors that block the action or ALL_ANCHORS if all anchors block the action.

ALL_ANCHORS = <object object>
__init__(message=None, blocking_anchors=<object object>)
Parameters

  • message (str) – Exception message

  • blocking_anchors (list[residue.Residue]) – Anchored residues that block the action

exception schrodinger.protein.alignment.StructuredResidueError

Bases: RuntimeError

class schrodinger.protein.alignment.AlignmentSignals

Bases: PyQt6.QtCore.QObject

A collection of signals that can be emitted by an alignment

Variables

  • domainsChanged (QtCore.pyqtSignal) – TODO

  • 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.

  • 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.

  • alnSetsChanged (QtCore.pyqtSignal) – A signal emitted when the alignment set for one or more sequences changes.

Type

sequencesAboutToBeReordered: QtCore.pyqtSignals

Type

sequencesReordered: QtCore.pyqtSignals

domainsChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

invalidatedDomains

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

descriptorsCleared

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequencesAboutToBeInserted

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequencesInserted

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequencesAboutToBeRemoved

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequencesRemoved

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequenceResiduesChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequencesAboutToBeReordered

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequencesReordered

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequenceNameChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

annotationTitleChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

alignmentNumColumnsAboutToChange

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

alignmentNumColumnsChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

residuesAboutToBeRemoved

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

residuesRemoved

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

residuesAdded

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequenceVisibilityChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sequenceStructureChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

alignmentAboutToBeCleared

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

alignmentCleared

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

anchoredResiduesChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

alnSetChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

secondaryStructureChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

predictionsChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

pfamChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

kinaseFeaturesChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

kinaseConservationChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

property aln

Return the alignment that this signals object is reporting for. :rtype: BaseAlignment

emitSeqResChanged()
emitSeqNameChanged()
emitAnnTitleChanged()
allSignals()

Iterate over all signals in this object in alphabetical order. :rtype: Iter(QtCore.pyqtBoundSignal)

allSignalsAndNames()

Iterate over all signals in this object and their names in alphabetical order. :rtype: Iter(tuple(QtCore.pyqtBoundSignal, str))

class schrodinger.protein.alignment.BaseAlignment(sequences=None)

Bases: PyQt6.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 overridden in subclasses.

  • _SEQ_ANNOTATION_CLASS (type) – The class for sequence annotations. This value should be overridden in subclasses.

__init__(sequences=None)
Parameters

sequences (list) – An optional iterable of sequences

__len__()

Returns the number of sequences in the alignment

__contains__(seq)

Returns whether the sequence is present in the alignment

property annotations
property global_annotations

Returns the alignment-level annotations available for the alignment

property seq_annotations

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

property 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

sortByProperty(seq_prop, reverse=False)

Sort the sequences by a sequence property. Sequences that do not have the sequence property defined will be grouped at the end of the alignment (regardless of reverse)

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

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, sort=True)

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.

  • sort (bool) – Whether the returned list should be sorted.

Return type

A 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
getResiduesWithStructure()

Returns a list of all residues with structure

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.

Return type

frozenset(residue.Residue)

getAnchoredResiduesWithRef()
Returns

A frozenset of residues that are currently anchored with the corresponding reference sequence residues

Return type

frozenset(residue.Residue)

clearAnchors()
removeAnchors(residues)

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

Parameters

residues (iterable(residue.Residue)) – The residues to unanchor.

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)

Returns

An alignment corresponding to the start and end points specified

Return type

BaseAligment

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)

property 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(gap_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

gap_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()

For each sequence, return a list of the indices in that sequence for which the entire alignment contains gaps. (Indices will be omitted for a sequence if the sequence is shorter than the index.)

Returns

List of list of indices

Return type

list[list[int]]

minimizeAlignment()

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

getAlignmentMinimizedWithSpaces()

This method returns a new alignment and removes gap only columns however it leaves one gap column between blocks

Returns

the new, minimized alignment

Return type

BaseAlignment

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, *, match_type=False)

A generator over all columns.

Parameters

  • omit_gaps (bool) – Whether to omit gaps

  • match_type (bool) – Whether to match reference sequence type

seqMatchesRefType(seq)
getSeqsMatchingRefType()
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, additional_breaks=None, last_col=None)

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)

  • additional_breaks (list[int] or None) – If given, contiguous columns will be broken at the specified indices. I.e., no contiguous set of columns will contain both column i and column i-1.

  • last_col (int or None) – If given, the last column to consider when constructing contiguous columns. It not given, all columns will be considered.

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))

clearAllCaching()
addSeqsToAlnSet(seqs, set_name)

Add all given sequences to the specified alignment set (i.e. a named group of sequences that are always kept together in the alignment). Sequences already in the set will be ignored. All other sequences will be moved to the end of the set. (Except for the reference sequence: The specified set will be moved to the top of the alignment if the reference sequence is added.)

Parameters

  • seqs (Iterable[sequence.Sequence]) – The sequences to add to the set.

  • set_name (str) – The name of the set to add the sequences to. If no set of this name exists, one will be created.

removeSeqsFromAlnSet(seqs)

Remove all given sequences from any alignment sets they’re part of. Sequences not in a set will be ignored. All other sequences will be moved to the end of the set that they were in.

Parameters

seqs (Iterable[sequence.Sequence]) – The sequences to remove from alignment sets.

renameAlnSet(old_name, new_name)

Rename the specified alignment set.

Parameters

  • old_name (str) – The old name of the alignment set.

  • new_name (str) – The new name of the alignment set.

alnSetForSeq(seq)

Return the alignment set that contains the given sequence.

Parameters

seq (sequence.Sequence) – The sequence to retrieve the alignment set for.

Returns

The requested set. The calling scope must not modify the returned value. Will return None if seq is not part of any set.

Return type

AlignmentSet or None

hasAlnSets()

Does this alignment contain any alignment sets? :rtype: bool

alnSetNames()

Return all alignment set names. :rtype: set(str)

alnSets()

Iterate through all alignment sets.

Returns

An iterator through all alignment sets. The calling scope must not modify any of the sets.

Return type

dict_keys

getAlnSet(set_name)

Return the requested set.

Parameters

set_name (str) – The name of the set to retrieve.

Returns

The requested set. The calling scope must not modify the returned value.

Return type

AlignmentSet

Raises

ValueError – If no set with the given name was found.

gatherAlnSets()
getFrequencies(normalize=True)

Returns the frequencies of each residue in each column. Residues are sorted by decreasing frequency. Gapped positions are not counted when calculating frequencies.

Parameters

normalize (bool) – Whether to normalize the values; i.e. divide by the number of non-gaps in the column

Returns

frequencies of each residue in each alignment column

Return type

tuple(tuple(residue.Residue, float or int)))

getResidueSeqProps(value_types=None)

Get a list of all sequence properties that any residue has. If ‘value_types’ is defined, get only the specific property types listed.

Parameters

value_types (List) – list of specific properties types- str, int or float etc as structure.PROP_STRING,structure.PROP_INTEGER etc

Returns

All the sequence properties

Return type

list[properties.SequenceProperty]

getSeqsDescriptors()

Return a list of all the calculated descriptors of the sequences in the alignment.

Returns

All the sequence descriptors

Return type

list[properties.SequenceProperty]

property all_structures

Return an iterator over all sequence structures in the alignment. This does not repeat structures that belong to multiple sequences.

class schrodinger.protein.alignment.AlignmentSet(name, set_id)

Bases: set

A named group of sequences that are always kept together in the alignment.

__init__(name, set_id)
Parameters

  • name (str) – The name of the alignment set.

  • set_id (int) – A unique integer ID for the alignment set. Used to determine the color of the icon and text.

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.

Return type

cls

classmethod adapter48002(json_dict)
addDisulfideBond(res1, res2, known=True)

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

Parameters

  • res1 (residue.Residue) – A residue to link with a disulfide bond

  • res2 (residue.Residue) – Another residue to link with a disulfide bond

  • known (bool) – Whether the bond is known or predicted

Raises

ValueError – if either sequence is not in the alignment

removeDisulfideBond(bond)

Disconnect a disulfide bond. The bond may be either known or predicted.

Parameters

bond (residue.DisulfideBond) – The bond to disconnect

Raises

ValueError – if either sequence is not in the alignment

classmethod fromStructure(ct, eid=None)
Parameters

  • ct (schrodinger.structure.Structure) – The structure to convert

  • eid (str) – The entry id to assign to the created sequences. If not given, the entry id from the structure, if any, will be used.

Return type

cls

Returns

An alignment containing the sequences in the structure

classmethod 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.

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 schrodinger.protein.alignment.NucleicAcidAlignment(sequences=None)

Bases: schrodinger.protein.alignment.BaseAlignment

class schrodinger.protein.alignment.CombinedChainProteinAlignment(sequences=None, *, chains_to_combine=None)

Bases: schrodinger.protein.alignment._ProteinAlignment

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

__init__(sequences=None, *, chains_to_combine=None)
Parameters

  • sequences (list[sequence.ProteinSequence] or list[sequence.CombinedChainProteinSequence]) – A list of split-chain or combined-chain sequences to add to the alignment. If not given, an empty alignment will be created.

  • chains_to_combine (list[list[int]]) – Information about which split-chain sequences in split_undoable_aln should be included in which combined-chain sequence. Should be a list of lists of indices. Each index refers to the split-chain sequence at that position of split_undoable_aln, and split-chain sequences that are listed together will be combined into the same combined-chain sequence. Each split-chain sequence from split_undoable_aln must be referenced exactly once.

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
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 (Iterable[sequence.Sequence] or Iterable[sequence.CombinedChainProteinSequence]) – Sequences to remove

combinedSeqForSplitSeq(split_seq)

Get the combined-chain sequence that contains the given split-chain sequence.

Parameters

split_seq (sequence.Sequence) – The split-chain sequence

Returns

The combined-chain sequence

Return type

sequence.CombinedChainProteinSequence

combinedResForSplitRes(split_res)

Get the combined-chain residue for the given split-chain residue.

Parameters

res (residue.AbstractSequenceElement) – The split-chain residue

Returns

The combined-chain residue

Return type

residue.CombinedChainResidueWrapper

getInterChainAnchors()

Return all residues that are anchored to a different chain of the reference sequence (e.g. a residue in the second chain anchored to a reference residue from the first chain).

Returns

The anchored residues.

Return type

set[residue.Residue]

alignChainStarts()

Align chain starting positions (e.g. make sure that the start of the N-th chain occurs in the same column for all sequences). This method will add gaps at the starts and/or ends of chains to preserve anchoring.

Returns

A tuple of:

  • A list of chain starting indices. This will not include the starting index of the first chain, which is always 0.

  • The starting index of the first chain for which there’s no corresponding reference chain (e.g. the starting index for the third chain if there are only two chains in the reference sequence). This will be None if there are no chains without a corresponding reference chain.

Return type

tuple(list[int], int or None)

adjustChainStarts(adjust_by)

Move each chain break position to the right by the specified number of gaps. Note that chain breaks can only be moved along gaps, not residues.

Parameters

num_gaps (list[list[int]]) – The number of gaps to move each chain break by, given as adjust_by[sequence_index][chain_break_index] = adjustment. Note that no adjustment is given for the start of the first chain or the end of the last chain.

Raises

AssertionError – If some of the sequence elements to be removed aren’t actually gaps.

schrodinger.protein.alignment.get_contiguous_groups(nums)

Group numbers in a given list by contiguity. Each group that is returned will be a list of numbers where every value is an int that only differs from its neighbors by one.

e.g. [1, 2, 4] -> [[1, 2], [4]]

[1, 2, 4, 5, 10] -> [[1, 2], [4, 5], [10]]

Parameters

nums (list(int)) – A list of numbers to group

Returns

A list of groups of numbers, where the numbers in each group are contiguous

Return type

list(list(int))