schrodinger.application.msv.gui.undoable_alignment module

class schrodinger.application.msv.gui.undoable_alignment.AlignmentSelectionModel(aln)

Bases: PyQt5.QtCore.QObject

A class that manages selection of residues in an undoable alignment. Because of limitations with Qt’s selection models, we store selection status in our own domain objects instead.

This class has an undo stack because selection is undoable in the MSV.

Variables:
  • _selection (weakref.WeakSet(schrodinger.protein.residue.Residue)) – The current selection state
  • _old_selection (weakref.WeakSet(schrodinger.protein.residue.Residue)) – The selection state from last time selectionChanged was emitted
  • selectionChanged (QtCore.pyqtSignal emitting set(schrodinger.protein.residue.Residue) and set(schrodinger.protein.residue.Residue)) – A signal emitted to notify listeners that selection has changed, with the set of residues that have been selected and the set of residues that have been deselected. Note that this is called on a single shot timer so that if selection is modified multiple times successively (ie by a “clear then select”), only one signal is emitted.
clearSelection()

Unselect all residues.

getSelection()
Returns:A set of currently selected residues
Return type:set(schrodinger.protein.residue.Residue)
isSelected(res)
Parameters:res (schrodinger.protein.residue.Residue) – The residue to determine the selection state of
Returns:whether res is selected
Return type:bool
onResiduesRemoved(residue_selection)

When residues are about to be removed, deselect those residues.

onSequencesAboutToBeRemoved(start, end)

When sequences are about to be removed, deselect all the residues in those sequences.

selectionChanged
setSelectionState(residues, selected)

Set the selection state of the provided residues.

Parameters:
  • residues (iterable of schrodinger.protein.residue) – The residues to select/unselect
  • selected (bool) – Whether to select or deselect the residues
setUndoStack(undo_stack)
Parameters:undo_stack (QtWidgets.QUndoStack) – The undo stack to push commands onto
class schrodinger.application.msv.gui.undoable_alignment.ProteinAlignment(sequences=None, is_workspace=False)

Bases: object

A ProteinAlignment class that presents the same interface as a regular ProteinAlignment but optionally accomplishes mutating operations via a command stack.

If no command stack is set on the object, commands are executed but cannot be undone.

Undoable protein alignments have an AlignmentSelectionModel because they are intended for use in GUIs, whereas normal non-undoable alignments don’t have a selection model because their use cases (aligning sequences) don’t require a concept of selection.

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
addGaps(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 – A list of lists of gap indices, one for each sequence in the alignment.
addOrReplaceSeqs(seqs, identifier_func)

Given seqs and an identifier_func, replaces seqs in the alignment matching the identifier_func and appends any additional seqs to the alignment

Parameters:
  • seqs (iterable of schrodinger.protein.sequence. Sequence) – The sequences to add to the alignment
  • identifier_func (callable) – A key function to uniquely identify sequences
addResidues(selection)

Adds the specified residues to the alignment

Parameters:selection (ResidueSelection) – A selection of residues
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(seqs, index=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, seq is appended
addSeqsByIndices(seq_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.
alignmentLocked(*args, **kwargs)

Whether every column in the alignment is locked

Return type:bool
Returns:Whether the alignment is locked
all_annotations
annotations
appendSubalignment(aln)

Append an alignment to this one

Parameters:aln (BaseAlignment or list of Sequence) – The alignment to append
calculateMatrix(*args, **kwargs)

Calculates a substitution matrix based on the current alignment.

clear(*args, **kwargs)

Remove all sequences and locked columns from the alignment.

columnHasAllSameResidues(*args, **kwargs)

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(*args, **kwargs)

Returns a range of alignment columns or all columns if indices are not specified.

Parameters:omit_gaps (bool) – Whether to omit gaps
connectSignals()

Connect the signals in self.signals to the signals emitted by self._aln

disulfide_bonds
findPattern(*args, **kwargs)

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
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.
static 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.
Return type:ProteinAlignment
Returns:Read alignment. The alignment can be empty if no sequence was present in the input file.
static 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
Return type:ProteinAlignment
Returns:The alignment
static 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)
getAlignedBlocks(*args, **kwargs)

Returns the indices of aligned blocks (regions without gaps).

getAlignmentQualityByColumn(*args, **kwargs)

Retrieve the alignment quality at a given column and update the cache if necessary.

Parameters:col_index (int) – Column of the residue
getColumn(*args, **kwargs)

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
Return type:

list
Returns:

Single alignment column at index position.
getDiscontinuousSubalignment(*args, **kwargs)

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(*args, **kwargs)

Returns an alignment length array of residue entropy scores

getFrequencies(*args, **kwargs)

Returns a dict mapping residues types to the frequency in the alignment

Parameters:
  • exclude (list) – A list of sequences to exclude
  • consider_gaps (bool) – Whether to consider gaps in calculating frequences
getGapIndicesByKeyFunc(*args, **kwargs)

Converts a gap_info list and key func into a list of gap indices

Gap information consists of (key for residue, number of gaps preceding it)

Parameters:
  • gap_info (list) – list of list of tuples
  • key_func (function) – callable that takes a residue and returns a key
Return type:

list of lists of int
Returns:

A list of gaps for each sequence in the alignment
getGapOnlyColumns(*args, **kwargs)

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

Return type:list
Returns:List of list of indices
getGaps(*args, **kwargs)

Returns a list of gap indices lists

Return type:list
Returns:A list of lists of ints
getGapsByKeyFunc(*args, **kwargs)

Given a key function to uniquely identify residues, build a list of lists with gap information for each sequence in the alignment

Gap information consists of (key for residue, number of gaps preceding it)

Parameters:key_func (function) – callable that takes a residue and returns a key
Return type:list
Returns:A list of lists with gaps information for each sequence in the alignment
getGlobalAnnotationData(*args, **kwargs)

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
getHiddenSeqCount(*args, **kwargs)

Return the number of sequences in the alignment that have an associated PT entry ID but are not currently visible in the Workspace.

Returns:number of hidden sequences
Return type:int
getIdentities(*args, **kwargs)

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(*args, **kwargs)

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(*args, **kwargs)

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
getResidueData(*args, **kwargs)

Returns residue-level data for the specified sequence at the specified index in the alignment, or None if no data is available.

If annotation is specified, the residue-level information for the residue is returned. If not, the residue object itself is returned.

Parameters:
  • seqnum (int) – The index of the sequence in the alignment
  • index (int) – The index of the residue in the sequence
  • annotation (enum.Enum) – An enum representing the requested annotation, if any
getResidueIndices(*args, **kwargs)

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

Parameters:residues –
Return type:list of (sequence index, residue index) tuples
Returns:A list of (int, int)
static getReversedSequenceOrdering(seq_indices)

Given a new ordering for sequences in an alignment, return an ordering that will restore the original order of sequences.

Given a an alignment [a, b, c, d, e] an ordering of [3, 1, 4, 2, 0] will rearrange the sequences into [d, b, e, c, a]. We need an ordering of [4, 1, 3, 0, 2] to restore the original arrangement of [a, b, c, d, e]. This method is used in undo operations.

Parameters:seq_indices – A list with the new indices for sequences
Type:list of int
Return type:list of int
Returns:An ordering list that will restore the original arrangement of sequences in the alignment
getSeqIndex(*args, **kwargs)
Parameters:seq (sequence.Sequence) – The requested sequence
Return type:int
Returns:The index of the requested sequence
getSimilarityScore(*args, **kwargs)

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

Gaps in the sequences are coded as None values.

getSubalignment(*args, **kwargs)

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
Return type:

BaseAligment
Returns:

An alignment corresponding to the start and end point specified
getTerminalGaps(*args, **kwargs)

Returns the indices of terminal gaps in all the sequences

Return type:list
Returns:A list of lists of ints
getVisibleSeqCount(*args, **kwargs)

Return the number of visible sequences in the alignment.

Returns:number of visible sequences
Return type:int
global_annotations
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
isReferenceSeq(*args, **kwargs)

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
isWorkspace()
Returns:Whether this alignment is controlled by the structure model and

only includes sequences that are currently included in the workspace. :rtype: bool

iterResidues(*args, **kwargs)

Yields a sequence of schrodinger.protein.residue.Residue objects in the alignment, omitting gaps.

lockedColumns(*args, **kwargs)

Returns a set with indices of locked columns.

Return type:set
Returns:A set of indices

The set is a copy of our internal set, so modifying it has no effect on our private attribute

makeResidueSelection(*args, **kwargs)

Returns a residue selection object matching the specified residues

Parameters:residues (list) – A list of residues
Return type:ResidueSelection
Returns:An object containing selection information
max_length
mergePairwiseAlignments(*args, **kwargs)

Merges several pairwise alignments into one flat alignment while preserving relative residue positions. The original sequences are modified. After executing this function, all reference sequences (first pair members) will be identical.

Example. Let’s assume we have three pairwise query/template alignments:

Q1: ACDEFGHI T1: ~~DEF~~~

Q2: ~~~ACDEFGHI T2: TTT~~DE~~H~

Q3: ACDEF~~GHI~ T3: ACD~~PPGH~Y

Note the reference sequence is identical in all cases, but it has gaps in different positions. After running mergePairwiseAlignments, the result is:

Q1: ~~~ACDEF~~GHI T1: ~~~~~DEF~~~~~

Q2: ~~~ACDEF~~GHI T2: TTT~~DE~~~~H~

Q3: ~~~ACDEF~~GHI~ T3: ~~~ACD~~PPGH~Y

Now the queries have gaps in identical positions, and aligned residues are in positions equivalent to these in original alignments.

Parameters:sequence_pairs (list of list of sequences) – List of [query, template] pairs.
minimizeAlignment()

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

mutateResidues(mutations)

Mutate the residues at the specified locations in the alignment

Note that the individual sequences will emit a signal announcing the mutation

Parameters:mutations (list of tuples (seq_i, res_i, replacement)) –
static padAlignment(aln)

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

Parameters:aln (schrodinger.protein.Alignment) – An alignment to pad
removeAllGaps()

Removes all the gaps of the sequences in the alignment. This also unlocks all columns

removeAllSeqs()

Clears the entire alignment of sequences

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
removeGaps(gap_indices)
Parameters:gap_indices (list of list of ints) – Indices of gaps to remove
removeResidues(residues)

Removes the specified residues from the alignment and emits the signals.residuesRemoved signal with the selection

Parameters:residues (list) – The residues to remove
removeSeq(seq)

Remove a sequence from the alignment

Parameters:seq (sequence.Sequence) – The sequence to remove
removeSeqByIndex(index)

Remove a Sequence from the alignment

Parameters:index (int) – The index of 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, including column locks in that region

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

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
replaceSeq(seq, index)

Replace the sequence at the specified index with the elements in the specified sequence

Note that this leaves the original sequence itself intact so that it continues to be monitored

Parameters:
  • seq (iterable of schrodinger.protein.residue. Residue) – The sequence whose elements we use
  • index (int) – The index of the sequence to replace
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 index at which to insert the alignment
resMatchesReferenceRes(*args, **kwargs)

Return True if the residue of a sequence at a column in the alignment matches the reference residue.

Parameters:
  • row_index (int) – Index of the sequence containing the residue to check
  • col_index (int) – Column of the residue to check
Returns:

True if the residue at the specified index matches the reference, False otherwise.
Return type:

bool
seq_annotations
setAllLocks(lock=True)

Convenience method to set all the locks to the specified lock state at once

Parameters:lock (bool) – Whether to lock or unlock the specified columns
setGaps(gap_indices)

Sets gaps on the alignment

Parameters:gap_indices – A list of lists of gap indices, one for each sequence in the alignment.
setLockedColumns(columns, lock=True)

Sets the columns to the specified lock state

Parameters:
  • columns (iterable) – an iterable of columns to set, specified by index
  • lock (bool) – Whether to lock or unlock columns
  • reset (bool) – Whether to reset the locks or add to existing ones
setReferenceSeq(seq)

Set the specified sequence as the reference sequence.

Parameters:seq (sequence) – Sequence to set as reference sequence
setUndoStack(undo_stack)
Parameters:undo_stack (QtWidgets.QUndoStack Set the undo stack on the object) – The undo stack on which to push commands
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.
  • reverse – Whether to sort in reverse (descending) order.
staticMetaObject
toClustalFile(*args, **kwargs)

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.
toFastaFile(*args, **kwargs)

Write self to specified FASTA file

Raises:IOError – If output file cannot be written.
toFastaString(*args, **kwargs)

Convert ProteinAlignment object to list of sequence strings

Parameters:aln (ProteinAlignment) – Alignment data
toFastaStringList(*args, **kwargs)

Convert self to list of fasta sequence strings

Return type:list
Returns:list of str