schrodinger.protein.sequence module

Implementation of ProteinSequence, Sequence, and StructureSequence class.

StructureSequence allows iteration over all sequences in a given protein CT, and iteration over residues of each (in sequence order).

schrodinger.protein.sequence.guess_seq_type(res_names)

Takes an iterable of residue names and returns the appropriate sequence class

Parameters:res_names (Iterable(str)) – An iterable of residue names. Note that all residue names must be uppercase.
Returns:The appropriate class for the input sequence
Return type:Type[AbstractSingleChainSequence]

Note that we use a pretty simple heuristic here.

schrodinger.protein.sequence.make_sequence(elements, *args, **kwargs)

Guesses the appropriates Sequence type from the names of residues and returns an instance with those residues.

Parameters:elements (list(str)) – A list of strings to examine
Return type:protein.Sequence
Returns:An instance of the appropriate type
class schrodinger.protein.sequence.Sequence

Bases: object

__init__

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

class schrodinger.protein.sequence.AbstractSequence(*args, **kwargs)

Bases: schrodinger.protein.sequence.Sequence, PyQt5.QtCore.QObject

A base class for single-chain and combined-chain biological sequences.

Variables:
  • ORIGIN (enum.Enum) – Possible sequence origins
  • AnnotationClass (annotation.SequenceAnnotations) – Class to use for annotations
  • ElementClass (Type[residue.Residue]) – Class to use for elements
  • ALPHABET (dict(str, residue.ElementType)) – A mapping of string representations of elements to element types
  • _gap_chars (tuple(str)) – A tuple of permissible gap characters in the element list; the first item will be used for serialization.
  • _unknown_res_type (residue.ElementType) – The type for an unknown residue
  • residuesChanged (QtCore.pyqtSignal) – A signal emitted when sequence residues are changed. Emitted with the indices of the first and last changed residues.
  • lengthAboutToChange (QtCore.pyqtSignal) – A signal emitted when the sequence length is about to change. Emitted with the old and new lengths.
  • lengthChanged (QtCore.pyqtSignal) – A signal emitted when the sequence length is changed. Emitted with the old and new lengths.
  • nameChanged (QtCore.pyqtSignal) – A signal emitted when the sequence name is changed.
  • visibilityChanged (QtCore.pyqtSignal) – A signal emitted when the visibility is changed.
  • structureChanged (QtCore.pyqtSignal) – A signal emitted when the structure changes.
  • annotationTitleChanged (QtCore.pyqtSignal) – A signal emitted when an annotation title is changed.
class ORIGIN

Bases: enum.Enum

An enumeration.

Maestro = 1
PyMOL = 2
AnnotationClass = None
ElementClass

alias of schrodinger.protein.residue.Residue

ALPHABET = {}
residuesRemoved
residuesAdded
residuesChanged
lengthAboutToChange
lengthChanged
nameChanged
visibilityChanged
structureChanged
annotationTitleChanged
pfamChanged
descriptorsCleared
__init__(*args, **kwargs)

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

residues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
getNextResidue(res)

Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getPreviousResidue(res)

Return the previous residue in the sequence (ignoring gaps) or None if this is the first residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
iterNeighbors()

Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.

None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.

Returns:Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue or None
Return type:iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
index(res)

Returns the index of the specified residue.

Parameters:res (residue.Residue) – The residue to find
Returns:The index of the residue
Return type:int
indices(residues)

Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)

Parameters:res (Iterable(residue.Residue)) – The residues to find indices of
Returns:The indices of the residues
Return type:list[int]
getRun(res)

For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.

Parameters:res (residue.AbstractSequenceElement) – Residue to get the run of
Reuturn:Set of residue indices in the run
Return type:set(int)
insertElements(index, elements)

Insert a list of elements or sequence element into this sequence.

If elements is a string or iterable of strings, residue numbers will be automatically assigned.

Parameters:
  • index (int) – The index at which to insert elements
  • elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
mutate(start, end, elements)

Mutate sequence elements starting at the given index to the provided elements.

Parameters:
  • start (int) – The index at which to start mutating
  • end (int) – The index of the last mutated element (exclusive)
  • elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
append(element)

Appends an element to the sequence

Parameters:element – The element to append to this sequence
Type:element: self.ElementClass or basestring
extend(elements)

Extends the sequence with elements from an iterable

Parameters:elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
getSubsequence(start, end)

Return a sequence containing a subset of the elements in this one

Parameters:
  • start (int) – The index at which the subsequence should start
  • end (int) – The index at which the subsequence should end (exclusive)
Returns:

The requested subsequence

Return type:

AbstractSequence

removeElements(eles)

Remove elements from the sequence.

Parameters:eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence.
Raises:ValueError – If any of the given elements are not in the sequence.
gap_char
getGaplessLength()
Returns:Length of this sequence ignoring gaps
Return type:int
getGaps()
Return type:list(residue.Gap)
Returns:The gaps in the sequence.
addGapsByIndices(gap_idxs)

Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Parameters:gap_idxs (list(int)) – A list of gap indices
validateGapIndices(gap_idxs)

Make sure that the specified gap indices are valid input for addGapsByIndices. If the indices are invalid, a ValueError will be raised. Indices are considered invalid if:

  • they refer to a position that’s more than one residue past the end of the sequence
  • they are negative
Parameters:gap_idxs (list[int]) – The gap indices to validate
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.

Parameters:indices (list(int)) – A list of indices to insert gaps before.
removeTerminalGaps()

Remove gaps from the end of the sequence

getTerminalGaps()

Return terminal gaps.

Returns:A list of terminal gaps (in ascending index order)
Return type:list(residue.Gap)
getGapCount()
Returns:the number of gaps in the sequence
Return type:int
removeAllGaps()

Remove gaps from the sequence

annotations
getAnnotation(index, annotation)

Returns the annotation at the specified index or None for a gap.

Raises:ValueError – if the annotation is not available
getNumAnnValues(ann)
clearAllCaching()

This method should be implemented in subclasses that cache any data.

setPfam(new_pfam, pfam_name)
clearPfam()
hasPfam()
hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
getStructure()
Returns:The associated structure. Will return None if there is no associated structure.
Return type:schrodinger.structure.Structure or NoneType
setStructure(struc)

Set the associated structure. Can only be used on sequences with an associated structure.

Parameters:struc (schrodinger.structure.Structure) – The new structure for this sequence
Raises:RuntimeError – If there’s no structure associated with this sequence object.
getIdentity(other, consider_gaps=True, only_consider=None)

Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)

Return type:

float

getSimilarity(other, consider_gaps=True, only_consider=None)

Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getConservation(other, consider_gaps=True, only_consider=None)

Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.

The homology criterion is based on “side chain chemistry” descriptor matching.

Parameters:
Returns:

The sequence conservation score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(other, consider_gaps=True, only_consider=None)

Return the total score of similarity between the sequence and a other sequence, assuming that they’re already aligned.

Parameters:
  • consider_gaps (bool) – Ignored because the similarity with a gap is 0.0
  • only_consider (set or None) – A set of residues to restrict attention to
  • other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:

The total sequence similarity score

Return type:

float

getStructureResForRes(res)
Parameters:res (residue.Residue) – Residue to get structure residue for
Returns:Structure residue or None if no matching residue is found
Return type:schrodinger.structure._Residue or NoneType
structuredResidueCount()

Get the number of residues in this sequence with an associated structured residue. :rtype: int

hasStructuredResidues()

Return whether this sequence has any structured residues. This method is equivalent to bool(seq.structuredResidueCount()) but doesn’t (typically) require iterating through the entire sequence.

Return type:bool
getProperty(seq_prop)

Get the sequence’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the sequence property
Returns:The value of the sequence property
Return type:float or None
updateDescriptors(descriptors, property_source)

Updates the descriptor dicts with new descriptor values

Parameters:
  • descriptors (dict[str, float]) – A dict mapping descriptor names to their values
  • property_source (properties.PropertySource) – The source of the descriptors
clearDescriptors()
hasDescriptors()
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → List[QObject]
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

inherits(self, str) → bool
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

parent(self) → QObject
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.sequence.AbstractSingleChainSequence(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=None)

Bases: schrodinger.protein.sequence.AbstractSequence

Base class for single-chain biological sequences

Note: Protein-specific functionality should go in ProteinSequence.

Variables:sequenceCopied (QtCore.pyqtSignal) – A signal emitted when this sequence is copied. Emitted with the sequence being copied and the newly created copy. This signal is used by the structure model to make sure that the newly created copy is kept in sync with the structure.
sequenceCopied
__init__(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=None)

Make a sequence object from a list of strings and/or self.ElementClass

Strings are converted to self.ElementClass using a mapping of strings to element types.

Parameters:
  • elements (iterable(self.ElementClass or None) or iterable(str or None)) – An iterable of elements making up the sequence. `None`s are interpretted as gaps.
  • name (str) – The name of the sequence (possibly shortened), used for display purposes. For a FASTA sequence, this should be a short identifier such as the Uniprot ID.
  • origin (Sequence.ORIGIN or None) – A piece of metadata indicating where the sequence came from
  • entry_id – An entry associated with the sequence, if any
  • entry_name – An entry name associated with the sequence, if any
  • pdb_id – An id associated with the sequence, if any
  • chain (str) – The chain to which the sequence belongs
  • structure_chain (str) – The chain of the structure this sequence is associated with. This is usually the same as chain if the sequence has a structure but isn’t necessarily.
  • long_name (str) – The full name of the sequence. For a FASTA sequence, this should be the full FASTA header.
  • resnums (Iterable(int)) – Residue numbers to assign to elements. If not given, residues will be numbered starting from one. Regardless of what’s given here, no residue numbering will occur if elements is an iterable of ElementClass and any element already has a residue number set. If this iterable is shorter than elements, additional numbers will be generated by incrementing the last number present.
Type:

str

Type:

str

Type:

str

__len__()
__contains__(item)
classmethod makeSeqElement(element)
Parameters:element (str or cls.ElementClass) – A sequence element or string representation thereof
Returns:sequence element
Return type:cls.ElementClass
classmethod isValid(elements)
Parameters:elements (iterable(str) or str) – An iterable of string representations of elements making up the sequence
Returns:Tuple indicating whether valid and a set of invalid characters, if any
Return type:tuple(bool, set(str))
name
chain
fullname
Returns:a formatted name + optional chain name for the sequence
Return type:str
visibility
index(res, ignore_gaps=False)

Returns the index of the specified residue

Parameters:
  • res (residue.Residue) – The residue to find
  • ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises:

A ValueError if the residue is not present

Return type:

int

Returns:

The index of the residue

indices(residues, ignore_gaps=False)

Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)

Parameters:
  • res (Iterable(residue.Residue)) – The residues to find indices of
  • ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns:

The indices of the residues

Return type:

list[int]

insertElements(index, elements)

Insert a list of elements or sequence element into this sequence.

If elements is a string or iterable of strings, residue numbers will be automatically assigned.

Parameters:
  • index (int) – The index at which to insert elements
  • elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
mutate(start, end, elements)

Mutate sequence elements starting at the given index to the provided elements.

Parameters:
  • start (int) – The index at which to start mutating
  • end (int) – The index of the last mutated element (exclusive)
  • elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
append(element)

Appends an element to the sequence

Parameters:element – The element to append to this sequence
Type:element: self.ElementClass or basestring
extend(elements)

Extends the sequence with elements from an iterable

Parameters:elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
getSubsequence(start, end)

Return a sequence containing a subset of the elements in this one

Parameters:
  • start (int) – The index at which the subsequence should start
  • end (int) – The index at which the subsequence should end (exclusive)
Returns:

The requested subsequence

Return type:

AbstractSequence

removeElements(eles)

Remove elements from the sequence.

Parameters:eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence.
Raises:ValueError – If any of the given elements are not in the sequence.
getGaplessLength()
Returns:Length of this sequence ignoring gaps
Return type:int
addGapsByIndices(gap_idxs)

Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Parameters:gap_idxs (list(int)) – A list of gap indices
setSSA(new_ssa)
setSSAPredictions(pred)
setDisorderedRegionsPredictions(pred)
setDomainArrangementPredictions(pred)
setSolventAccessibilityPredictions(pred)
deletePrediction(prediction_type)
deleteAllPredictions()
origin
Returns:A piece of metadata indicating where the sequence came from
Rtype origin:Sequence.ORIGIN or None
hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
getStructure()
Returns:The associated structure. Will return None if there is no associated structure.
Return type:schrodinger.structure.Structure or NoneType
setStructure(struc)

Set the associated structure. Can only be used on sequences with an associated structure.

Parameters:struc (schrodinger.structure.Structure) – The new structure for this sequence
Raises:RuntimeError – If there’s no structure associated with this sequence object.
onStructureChanged()
setResidueMap(residue_map)

Set a new mapping between ResidueKey and structured residues.

Note: the only intended user of this method is schrodinger.application.msv.seqio.StructureConverter, where the ResidueKey is computed from the structure._Residue used to create the residue.Residue. If the sequence has a structure, the map can be generated using generateResidueMap.

Parameters:residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
generateResidueMap()

Create residue map based on current structured residues.

Note: this method requires self.hasStructure() to be True and self.entry_id to be set. If this sequence was produced by schrodinger.application.msv.seqio.StructureConverter, there should already be a residue map and this method does not need to be called.

Raises:RuntimeError – If sequence has no structure or entry id
getResByKey(res_key)
Parameters:res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode)
Returns:Residue matching key or None if no matching residue is found
Return type:residue.Residue or NoneType
Raises:RuntimeError – If sequence has no structure
getStructureResForRes(res)
Parameters:res (residue.Residue) – Residue to get structure residue for
Returns:Structure residue or None if no matching residue is found
Return type:schrodinger.structure._Residue or NoneType
ALPHABET = {}
AnnotationClass = None
ElementClass

alias of schrodinger.protein.residue.Residue

class ORIGIN

Bases: enum.Enum

An enumeration.

Maestro = 1
PyMOL = 2
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.

Parameters:indices (list(int)) – A list of indices to insert gaps before.
annotationTitleChanged
annotations
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → List[QObject]
clearAllCaching()

This method should be implemented in subclasses that cache any data.

clearDescriptors()
clearPfam()
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
descriptorsCleared
destroyed

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

gap_char
getAnnotation(index, annotation)

Returns the annotation at the specified index or None for a gap.

Raises:ValueError – if the annotation is not available
getConservation(other, consider_gaps=True, only_consider=None)

Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.

The homology criterion is based on “side chain chemistry” descriptor matching.

Parameters:
Returns:

The sequence conservation score (between 0.0 and 1.0)

Return type:

float

getGapCount()
Returns:the number of gaps in the sequence
Return type:int
getGaps()
Return type:list(residue.Gap)
Returns:The gaps in the sequence.
getIdentity(other, consider_gaps=True, only_consider=None)

Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)

Return type:

float

getNextResidue(res)

Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getNumAnnValues(ann)
getPreviousResidue(res)

Return the previous residue in the sequence (ignoring gaps) or None if this is the first residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getProperty(seq_prop)

Get the sequence’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the sequence property
Returns:The value of the sequence property
Return type:float or None
getRun(res)

For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.

Parameters:res (residue.AbstractSequenceElement) – Residue to get the run of
Reuturn:Set of residue indices in the run
Return type:set(int)
getSimilarity(other, consider_gaps=True, only_consider=None)

Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(other, consider_gaps=True, only_consider=None)

Return the total score of similarity between the sequence and a other sequence, assuming that they’re already aligned.

Parameters:
  • consider_gaps (bool) – Ignored because the similarity with a gap is 0.0
  • only_consider (set or None) – A set of residues to restrict attention to
  • other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:

The total sequence similarity score

Return type:

float

getTerminalGaps()

Return terminal gaps.

Returns:A list of terminal gaps (in ascending index order)
Return type:list(residue.Gap)
hasDescriptors()
hasPfam()
hasStructuredResidues()

Return whether this sequence has any structured residues. This method is equivalent to bool(seq.structuredResidueCount()) but doesn’t (typically) require iterating through the entire sequence.

Return type:bool
inherits(self, str) → bool
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
iterNeighbors()

Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.

None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.

Returns:Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue or None
Return type:iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
killTimer(self, int)
lengthAboutToChange
lengthChanged
metaObject(self) → QMetaObject
moveToThread(self, QThread)
nameChanged
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

parent(self) → QObject
pfamChanged
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()

Remove gaps from the sequence

removeEventFilter(self, QObject)
removeTerminalGaps()

Remove gaps from the end of the sequence

residues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
residuesAdded
residuesChanged
residuesRemoved
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setPfam(new_pfam, pfam_name)
setProperty(self, str, Any) → bool
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
structureChanged
structuredResidueCount()

Get the number of residues in this sequence with an associated structured residue. :rtype: int

thread(self) → QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = -1) → str
updateDescriptors(descriptors, property_source)

Updates the descriptor dicts with new descriptor values

Parameters:
  • descriptors (dict[str, float]) – A dict mapping descriptor names to their values
  • property_source (properties.PropertySource) – The source of the descriptors
validateGapIndices(gap_idxs)

Make sure that the specified gap indices are valid input for addGapsByIndices. If the indices are invalid, a ValueError will be raised. Indices are considered invalid if:

  • they refer to a position that’s more than one residue past the end of the sequence
  • they are negative
Parameters:gap_idxs (list[int]) – The gap indices to validate
visibilityChanged
class schrodinger.protein.sequence.AbstractProteinSequenceMixin(*args, **kwargs)

Bases: object

A mixin for code shared between split-chain and combined-chain protein sequences.

disulfideBondsCacheCleared
predictionsChanged
secondaryStructureChanged
__init__(*args, **kwargs)

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

disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.DisulfideBond)
secondary_structures

A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.

Returns:A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure.
Return type:list(_SecondaryStructure)
clearDisulfideBondsCache()
hasDisorderedRegionsPredictions()
hasDisulfideBondPredictions()
hasDomainArrangementPredictions()
hasSolventAccessibility()
hasSSAPredictions()
pred_secondary_structures
class schrodinger.protein.sequence.ProteinSequence(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)

Bases: schrodinger.models.json.JsonableClassMixin, schrodinger.protein.sequence.AbstractProteinSequenceMixin, schrodinger.protein.sequence.AbstractSingleChainSequence

A single-chain protein sequence.

Variables:secondaryStructureCacheCleared – A signal emitted when the secondary structure cache has been cleared. Used to keep the CombinedChainProteinSequence cache in sync. If listening for changes in the secondary structure values, use secondaryStructureChanged instead.
AnnotationClass

alias of schrodinger.protein.annotation.ProteinSequenceAnnotations

ElementClass

alias of schrodinger.protein.residue.Residue

ALPHABET = {'2AS': ResidueType('D', '2AS', 'Aspartic acid'), '3AH': ResidueType('H', '3AH', 'Histidine'), '5HP': ResidueType('E', '5HP', 'Glutamic acid'), 'A': ResidueType('A', 'ALA', 'Alanine'), 'ACE': ResidueType('X', 'ACE', 'Capping Group'), 'ACL': ResidueType('R', 'ACL', 'Arginine'), 'AGM': ResidueType('R', 'AGM', 'Arginine'), 'AIB': ResidueType('A', 'AIB', 'Alanine'), 'ALA': ResidueType('A', 'ALA', 'Alanine'), 'ALM': ResidueType('A', 'ALM', 'Alanine'), 'ALO': ResidueType('T', 'ALO', 'Threonine'), 'ALY': ResidueType('K', 'ALY', 'Lysine'), 'ANF': ResidueType('X', 'ANF', 'Capping Group'), 'ARG': ResidueType('R', 'ARG', 'Arginine'), 'ARM': ResidueType('R', 'ARM', 'Arginine'), 'ARN': ResidueType('R', 'ARN', 'Arginine'), 'ASA': ResidueType('D', 'ASA', 'Aspartic acid'), 'ASB': ResidueType('D', 'ASB', 'Aspartic acid'), 'ASH': ResidueType('D', 'ASH', 'Aspartic acid'), 'ASK': ResidueType('D', 'ASK', 'Aspartic acid'), 'ASL': ResidueType('D', 'ASL', 'Aspartic acid'), 'ASN': ResidueType('N', 'ASN', 'Asparagine'), 'ASP': ResidueType('D', 'ASP', 'Aspartic acid'), 'ASQ': ResidueType('D', 'ASQ', 'Aspartic acid'), 'AYA': ResidueType('A', 'AYA', 'Alanine'), 'BCS': ResidueType('X', 'BCS', 'Cysteine'), 'BHD': ResidueType('D', 'BHD', 'Aspartic acid'), 'BMT': ResidueType('T', 'BMT', 'Threonine'), 'BNN': ResidueType('A', 'BNN', 'Alanine'), 'BUC': ResidueType('C', 'BUC', 'Cysteine'), 'BUG': ResidueType('L', 'BUG', 'Leucine'), 'C': ResidueType('C', 'CYS', 'Cysteine'), 'C5C': ResidueType('C', 'C5C', 'Cysteine'), 'C6C': ResidueType('C', 'C6C', 'Cysteine'), 'CCS': ResidueType('C', 'CCS', 'Cysteine'), 'CEA': ResidueType('C', 'CEA', 'Cysteine'), 'CGU': ResidueType('E', 'CGU', 'Glutamic acid'), 'CHG': ResidueType('A', 'CHG', 'Alanine'), 'CLE': ResidueType('L', 'CLE', 'Leucine'), 'CME': ResidueType('C', 'CME', 'Cysteine'), 'CSD': ResidueType('A', 'CSD', 'Alanine'), 'CSO': ResidueType('C', 'CSO', 'Cysteine'), 'CSP': ResidueType('C', 'CSP', 'Cysteine'), 'CSS': ResidueType('C', 'CSS', 'Cysteine'), 'CSW': ResidueType('C', 'CSW', 'Cysteine'), 'CSX': ResidueType('C', 'CSX', 'Cysteine'), 'CXM': ResidueType('M', 'CXM', 'Methionine'), 'CY1': ResidueType('C', 'CY1', 'Cysteine'), 'CY3': ResidueType('C', 'CY3', 'Cysteine'), 'CYG': ResidueType('C', 'CYG', 'Cysteine'), 'CYM': ResidueType('C', 'CYM', 'Cysteine'), 'CYP': ResidueType('C', 'CYP', 'Cysteine'), 'CYQ': ResidueType('C', 'CYQ', 'Cysteine'), 'CYS': ResidueType('C', 'CYS', 'Cysteine'), 'CYX': ResidueType('C', 'CYX', 'Cysteine'), 'D': ResidueType('D', 'ASP', 'Aspartic acid'), 'DAH': ResidueType('F', 'DAH', 'Phenylalanine'), 'DAL': ResidueType('X', 'DAL', 'Alanine'), 'DAR': ResidueType('X', 'DAR', 'Arginine'), 'DAS': ResidueType('X', 'DAS', 'Aspartic acid'), 'DCY': ResidueType('X', 'DCY', 'Cysteine'), 'DGL': ResidueType('X', 'DGL', 'Glutamic acid'), 'DGN': ResidueType('X', 'DGN', 'Glutamine'), 'DHA': ResidueType('A', 'DHA', 'Alanine'), 'DHI': ResidueType('X', 'DHI', 'Histidine'), 'DIL': ResidueType('X', 'DIL', 'Isoleucine'), 'DIV': ResidueType('V', 'DIV', 'Valine'), 'DLE': ResidueType('X', 'DLE', 'Leucine'), 'DLY': ResidueType('X', 'DLY', 'Lysine'), 'DNP': ResidueType('A', 'DNP', 'Alanine'), 'DPN': ResidueType('X', 'DPN', 'Phenylalanine'), 'DPR': ResidueType('X', 'DPR', 'Proline'), 'DSG': ResidueType('X', 'DSG', 'Asparagine'), 'DSN': ResidueType('X', 'DSN', 'Serine'), 'DSP': ResidueType('D', 'DSP', 'Aspartic acid'), 'DTH': ResidueType('X', 'DTH', 'Threonine'), 'DTR': ResidueType('X', 'DTR', 'Tryptophan'), 'DTY': ResidueType('X', 'DTY', 'Tyrosine'), 'DVA': ResidueType('X', 'DVA', 'Valine'), 'E': ResidueType('E', 'GLU', 'Glutamic acid'), 'EFC': ResidueType('C', 'EFC', 'Cysteine'), 'F': ResidueType('F', 'PHE', 'Phenylalanine'), 'FCO': ResidueType('X', 'FCO', 'Capping Group'), 'FLA': ResidueType('A', 'FLA', 'Alanine'), 'FME': ResidueType('M', 'FME', 'Methionine'), 'G': ResidueType('G', 'GLY', 'Glycine'), 'GGL': ResidueType('E', 'GGL', 'Glutamic acid'), 'GL3': ResidueType('G', 'GL3', 'Glycine'), 'GLH': ResidueType('E', 'GLH', 'Glutamic acid'), 'GLN': ResidueType('Q', 'GLN', 'Glutamine'), 'GLU': ResidueType('E', 'GLU', 'Glutamic acid'), 'GLY': ResidueType('G', 'GLY', 'Glycine'), 'GLZ': ResidueType('G', 'GLZ', 'Glycine'), 'GMA': ResidueType('E', 'GMA', 'Glutamic acid'), 'GSC': ResidueType('G', 'GSC', 'Glycine'), 'H': ResidueType('H', 'HIS', 'Histidine'), 'HAC': ResidueType('A', 'HAC', 'Alanine'), 'HAR': ResidueType('R', 'HAR', 'Arginine'), 'HIC': ResidueType('H', 'HIC', 'Histidine'), 'HID': ResidueType('H', 'HID', 'Histidine'), 'HIE': ResidueType('H', 'HIE', 'Histidine'), 'HIP': ResidueType('H', 'HIP', 'Histidine'), 'HIS': ResidueType('H', 'HIS', 'Histidine'), 'HMR': ResidueType('R', 'HMR', 'Arginine'), 'HPQ': ResidueType('F', 'HPQ', 'Phenylalanine'), 'HSD': ResidueType('H', 'HSD', 'Histidine'), 'HSE': ResidueType('H', 'HSE', 'Histidine'), 'HSP': ResidueType('H', 'HSP', 'Histidine'), 'HTR': ResidueType('W', 'HTR', 'Tryptophan'), 'HYP': ResidueType('X', 'HYP', 'Proline'), 'I': ResidueType('I', 'ILE', 'Isoleucine'), 'IIL': ResidueType('I', 'IIL', 'Isoleucine'), 'ILE': ResidueType('I', 'ILE', 'Isoleucine'), 'IND': ResidueType('X', 'IND', 'Capping Group'), 'IYR': ResidueType('Y', 'IYR', 'Tyrosine'), 'K': ResidueType('K', 'LYS', 'Lysine'), 'KCX': ResidueType('K', 'KCX', 'Lysine'), 'L': ResidueType('L', 'LEU', 'Leucine'), 'LEU': ResidueType('L', 'LEU', 'Leucine'), 'LLP': ResidueType('K', 'LLP', 'Lysine'), 'LLY': ResidueType('K', 'LLY', 'Lysine'), 'LTR': ResidueType('W', 'LTR', 'Tryptophan'), 'LYM': ResidueType('K', 'LYM', 'Lysine'), 'LYN': ResidueType('K', 'LYN', 'Lysine'), 'LYS': ResidueType('K', 'LYS', 'Lysine'), 'LYZ': ResidueType('K', 'LYZ', 'Lysine'), 'M': ResidueType('M', 'MET', 'Methionine'), 'MAA': ResidueType('A', 'MAA', 'Alanine'), 'MEN': ResidueType('N', 'MEN', 'Asparagine'), 'MET': ResidueType('M', 'MET', 'Methionine'), 'MHS': ResidueType('H', 'MHS', 'Histidine'), 'MIS': ResidueType('S', 'MIS', 'Serine'), 'MLE': ResidueType('L', 'MLE', 'Leucine'), 'MMO': ResidueType('R', 'MMO', 'Arginine'), 'MPA': ResidueType('X', 'MPA', 'Capping Group'), 'MPQ': ResidueType('G', 'MPQ', 'Glycine'), 'MSA': ResidueType('G', 'MSA', 'Glycine'), 'MSE': ResidueType('M', 'MSE', 'Methionine'), 'MVA': ResidueType('V', 'MVA', 'Valine'), 'N': ResidueType('N', 'ASN', 'Asparagine'), 'NCO': ResidueType('X', 'NCO', 'Capping Group'), 'NEM': ResidueType('H', 'NEM', 'Histidine'), 'NEP': ResidueType('H', 'NEP', 'Histidine'), 'NH2': ResidueType('X', 'NH2', 'Capping Group'), 'NLE': ResidueType('X', 'NLE', 'Leucine'), 'NLN': ResidueType('L', 'NLN', 'Leucine'), 'NLP': ResidueType('L', 'NLP', 'Leucine'), 'NMA': ResidueType('X', 'NMA', 'Capping Group'), 'NMC': ResidueType('G', 'NMC', 'Glycine'), 'OAS': ResidueType('S', 'OAS', 'Serine'), 'OCS': ResidueType('C', 'OCS', 'Cysteine'), 'OMT': ResidueType('M', 'OMT', 'Methionine'), 'P': ResidueType('P', 'PRO', 'Proline'), 'PAQ': ResidueType('Y', 'PAQ', 'Tyrosine'), 'PCA': ResidueType('E', 'PCA', 'Glutamic acid'), 'PEC': ResidueType('C', 'PEC', 'Cysteine'), 'PHE': ResidueType('F', 'PHE', 'Phenylalanine'), 'PHI': ResidueType('F', 'PHI', 'Phenylalanine'), 'PHL': ResidueType('F', 'PHL', 'Phenylalanine'), 'PR3': ResidueType('C', 'PR3', 'Cysteine'), 'PRO': ResidueType('P', 'PRO', 'Proline'), 'PRR': ResidueType('A', 'PRR', 'Alanine'), 'PTR': ResidueType('y', 'PTR', 'Tyrosine'), 'Q': ResidueType('Q', 'GLN', 'Glutamine'), 'R': ResidueType('R', 'ARG', 'Arginine'), 'S': ResidueType('S', 'SER', 'Serine'), 'SAC': ResidueType('S', 'SAC', 'Serine'), 'SAR': ResidueType('G', 'SAR', 'Glycine'), 'SCH': ResidueType('C', 'SCH', 'Cysteine'), 'SCS': ResidueType('C', 'SCS', 'Cysteine'), 'SCY': ResidueType('C', 'SCY', 'Cysteine'), 'SEL': ResidueType('S', 'SEL', 'Serine'), 'SEP': ResidueType('X', 'SEP', 'Serine'), 'SER': ResidueType('S', 'SER', 'Serine'), 'SET': ResidueType('S', 'SET', 'Serine'), 'SHC': ResidueType('C', 'SHC', 'Cysteine'), 'SHR': ResidueType('K', 'SHR', 'Lysine'), 'SMC': ResidueType('C', 'SMC', 'Cysteine'), 'SOC': ResidueType('C', 'SOC', 'Cysteine'), 'STY': ResidueType('Y', 'STY', 'Tyrosine'), 'SVA': ResidueType('S', 'SVA', 'Serine'), 'T': ResidueType('T', 'THR', 'Threonine'), 'THO': ResidueType('T', 'THO', 'Threonine'), 'THR': ResidueType('T', 'THR', 'Threonine'), 'TIH': ResidueType('A', 'TIH', 'Alanine'), 'TOSG': ResidueType('X', 'TOSG', 'Capping Group'), 'TPL': ResidueType('W', 'TPL', 'Tryptophan'), 'TPO': ResidueType('t', 'TPO', 'Threonine'), 'TPQ': ResidueType('A', 'TPQ', 'Alanine'), 'TRG': ResidueType('K', 'TRG', 'Lysine'), 'TRO': ResidueType('W', 'TRO', 'Tryptophan'), 'TRP': ResidueType('W', 'TRP', 'Tryptophan'), 'TYB': ResidueType('Y', 'TYB', 'Tyrosine'), 'TYM': ResidueType('Y', 'TYM', 'Tyrosine'), 'TYO': ResidueType('Y', 'TYO', 'Tyrosine'), 'TYQ': ResidueType('Y', 'TYQ', 'Tyrosine'), 'TYR': ResidueType('Y', 'TYR', 'Tyrosine'), 'TYS': ResidueType('Y', 'TYS', 'Tyrosine'), 'TYY': ResidueType('Y', 'TYY', 'Tyrosine'), 'UNK': ResidueType('X', 'UNK', 'Unknown'), 'V': ResidueType('V', 'VAL', 'Valine'), 'VAL': ResidueType('V', 'VAL', 'Valine'), 'W': ResidueType('W', 'TRP', 'Tryptophan'), 'Y': ResidueType('Y', 'TYR', 'Tyrosine')}
secondaryStructureCacheCleared
__init__(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)

See AbstractSingleChainSequence for additional documentation.

Parameters:
  • disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via disulfide bonds.
  • pred_disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via predicted disulfide bonds.
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

classmethod adapter47007(json_dict)
classmethod adapter48002(json_dict)
classmethod adapter52065(json_dict)
classmethod isValid(elements)
Parameters:elements (iterable(str) or str) – An iterable of string representations of elements making up the sequence
Returns:Tuple indicating whether valid and a set of invalid characters, if any
Return type:tuple(bool, set(str))
renumberResidues(new_rescode_map)

Renumber residues in this sequence given a dictionary mapping old rescodes to the new desired rescodes.

disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.DisulfideBond)
pred_disulfide_bonds
removeStructurelessResidues(start=0, end=None)

Remove any structureless residues

Parameters:
  • start (int) – The index at which to start filtering structureless residues.
  • end (int) – The index at which to end filtering
encodeForPatternSearch(with_ss=False, with_flex=False, with_asa=False)

Convert to sequence dict expected by find_generalized_pattern.

Parameters:
  • with_ss (bool) – Whether to include secondary structure information.
  • with_flex (bool) – Whether to include flexibility information.
  • with_asa (bool) – Whether to include accessible surface area information.
Return type:

dict

Returns:

dictionary of sequence data

clearAllCaching()

This method should be implemented in subclasses that cache any data.

class ORIGIN

Bases: enum.Enum

An enumeration.

Maestro = 1
PyMOL = 2
__contains__(item)
__len__()
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.

Parameters:indices (list(int)) – A list of indices to insert gaps before.
addGapsByIndices(gap_idxs)

Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Parameters:gap_idxs (list(int)) – A list of gap indices
annotationTitleChanged
annotations
append(element)

Appends an element to the sequence

Parameters:element – The element to append to this sequence
Type:element: self.ElementClass or basestring
blockSignals(self, bool) → bool
chain
childEvent(self, QChildEvent)
children(self) → List[QObject]
clearDescriptors()
clearDisulfideBondsCache()
clearPfam()
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteAllPredictions()
deleteLater(self)
deletePrediction(prediction_type)
descriptorsCleared
destroyed

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfideBondsCacheCleared
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
extend(elements)

Extends the sequence with elements from an iterable

Parameters:elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
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

fullname
Returns:a formatted name + optional chain name for the sequence
Return type:str
gap_char
generateResidueMap()

Create residue map based on current structured residues.

Note: this method requires self.hasStructure() to be True and self.entry_id to be set. If this sequence was produced by schrodinger.application.msv.seqio.StructureConverter, there should already be a residue map and this method does not need to be called.

Raises:RuntimeError – If sequence has no structure or entry id
getAnnotation(index, annotation)

Returns the annotation at the specified index or None for a gap.

Raises:ValueError – if the annotation is not available
getConservation(other, consider_gaps=True, only_consider=None)

Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.

The homology criterion is based on “side chain chemistry” descriptor matching.

Parameters:
Returns:

The sequence conservation score (between 0.0 and 1.0)

Return type:

float

getGapCount()
Returns:the number of gaps in the sequence
Return type:int
getGaplessLength()
Returns:Length of this sequence ignoring gaps
Return type:int
getGaps()
Return type:list(residue.Gap)
Returns:The gaps in the sequence.
getIdentity(other, consider_gaps=True, only_consider=None)

Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)

Return type:

float

getNextResidue(res)

Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getNumAnnValues(ann)
getPreviousResidue(res)

Return the previous residue in the sequence (ignoring gaps) or None if this is the first residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getProperty(seq_prop)

Get the sequence’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the sequence property
Returns:The value of the sequence property
Return type:float or None
getResByKey(res_key)
Parameters:res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode)
Returns:Residue matching key or None if no matching residue is found
Return type:residue.Residue or NoneType
Raises:RuntimeError – If sequence has no structure
getRun(res)

For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.

Parameters:res (residue.AbstractSequenceElement) – Residue to get the run of
Reuturn:Set of residue indices in the run
Return type:set(int)
getSimilarity(other, consider_gaps=True, only_consider=None)

Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(other, consider_gaps=True, only_consider=None)

Return the total score of similarity between the sequence and a other sequence, assuming that they’re already aligned.

Parameters:
  • consider_gaps (bool) – Ignored because the similarity with a gap is 0.0
  • only_consider (set or None) – A set of residues to restrict attention to
  • other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:

The total sequence similarity score

Return type:

float

getStructure()
Returns:The associated structure. Will return None if there is no associated structure.
Return type:schrodinger.structure.Structure or NoneType
getStructureResForRes(res)
Parameters:res (residue.Residue) – Residue to get structure residue for
Returns:Structure residue or None if no matching residue is found
Return type:schrodinger.structure._Residue or NoneType
getSubsequence(start, end)

Return a sequence containing a subset of the elements in this one

Parameters:
  • start (int) – The index at which the subsequence should start
  • end (int) – The index at which the subsequence should end (exclusive)
Returns:

The requested subsequence

Return type:

AbstractSequence

getTerminalGaps()

Return terminal gaps.

Returns:A list of terminal gaps (in ascending index order)
Return type:list(residue.Gap)
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.

hasDescriptors()
hasDisorderedRegionsPredictions()
hasDisulfideBondPredictions()
hasDomainArrangementPredictions()
hasPfam()
hasSSAPredictions()
hasSolventAccessibility()
hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
hasStructuredResidues()

Return whether this sequence has any structured residues. This method is equivalent to bool(seq.structuredResidueCount()) but doesn’t (typically) require iterating through the entire sequence.

Return type:bool
index(res, ignore_gaps=False)

Returns the index of the specified residue

Parameters:
  • res (residue.Residue) – The residue to find
  • ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises:

A ValueError if the residue is not present

Return type:

int

Returns:

The index of the residue

indices(residues, ignore_gaps=False)

Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)

Parameters:
  • res (Iterable(residue.Residue)) – The residues to find indices of
  • ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns:

The indices of the residues

Return type:

list[int]

inherits(self, str) → bool
insertElements(index, elements)

Insert a list of elements or sequence element into this sequence.

If elements is a string or iterable of strings, residue numbers will be automatically assigned.

Parameters:
  • index (int) – The index at which to insert elements
  • elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
iterNeighbors()

Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.

None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.

Returns:Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue or None
Return type:iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
killTimer(self, int)
lengthAboutToChange
lengthChanged
classmethod makeSeqElement(element)
Parameters:element (str or cls.ElementClass) – A sequence element or string representation thereof
Returns:sequence element
Return type:cls.ElementClass
metaObject(self) → QMetaObject
moveToThread(self, QThread)
mutate(start, end, elements)

Mutate sequence elements starting at the given index to the provided elements.

Parameters:
  • start (int) – The index at which to start mutating
  • end (int) – The index of the last mutated element (exclusive)
  • elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
name
nameChanged
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

onStructureChanged()
origin
Returns:A piece of metadata indicating where the sequence came from
Rtype origin:Sequence.ORIGIN or None
parent(self) → QObject
pfamChanged
pred_secondary_structures
predictionsChanged
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()

Remove gaps from the sequence

removeElements(eles)

Remove elements from the sequence.

Parameters:eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence.
Raises:ValueError – If any of the given elements are not in the sequence.
removeEventFilter(self, QObject)
removeTerminalGaps()

Remove gaps from the end of the sequence

residues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
residuesAdded
residuesChanged
residuesRemoved
secondaryStructureChanged
secondary_structures

A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.

Returns:A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure.
Return type:list(_SecondaryStructure)
sender(self) → QObject
senderSignalIndex(self) → int
sequenceCopied
setDisorderedRegionsPredictions(pred)
setDomainArrangementPredictions(pred)
setObjectName(self, str)
setParent(self, QObject)
setPfam(new_pfam, pfam_name)
setProperty(self, str, Any) → bool
setResidueMap(residue_map)

Set a new mapping between ResidueKey and structured residues.

Note: the only intended user of this method is schrodinger.application.msv.seqio.StructureConverter, where the ResidueKey is computed from the structure._Residue used to create the residue.Residue. If the sequence has a structure, the map can be generated using generateResidueMap.

Parameters:residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
setSSA(new_ssa)
setSSAPredictions(pred)
setSolventAccessibilityPredictions(pred)
setStructure(struc)

Set the associated structure. Can only be used on sequences with an associated structure.

Parameters:struc (schrodinger.structure.Structure) – The new structure for this sequence
Raises:RuntimeError – If there’s no structure associated with this sequence object.
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
structureChanged
structuredResidueCount()

Get the number of residues in this sequence with an associated structured residue. :rtype: int

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
updateDescriptors(descriptors, property_source)

Updates the descriptor dicts with new descriptor values

Parameters:
  • descriptors (dict[str, float]) – A dict mapping descriptor names to their values
  • property_source (properties.PropertySource) – The source of the descriptors
validateGapIndices(gap_idxs)

Make sure that the specified gap indices are valid input for addGapsByIndices. If the indices are invalid, a ValueError will be raised. Indices are considered invalid if:

  • they refer to a position that’s more than one residue past the end of the sequence
  • they are negative
Parameters:gap_idxs (list[int]) – The gap indices to validate
visibility
visibilityChanged
class schrodinger.protein.sequence.NucleicAcidSequence(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)

Bases: schrodinger.protein.sequence.ProteinSequence

AnnotationClass

alias of schrodinger.protein.annotation.NucleicAcidSequenceAnnotations

ElementClass

alias of schrodinger.protein.residue.Nucleotide

ALPHABET = None
getTranslation()

Get a translated sequence. This method uses BioPython’s translate method to convert a nucleic acid sequence into an amino acid sequence

Returns:A translated protein sequence. The name and chain from the nucleic acid sequence are copied over
Return type:ProteinSequence
class ORIGIN

Bases: enum.Enum

An enumeration.

Maestro = 1
PyMOL = 2
__contains__(item)
__init__(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)

See AbstractSingleChainSequence for additional documentation.

Parameters:
  • disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via disulfide bonds.
  • pred_disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via predicted disulfide bonds.
__len__()
classmethod adapter47007(json_dict)
classmethod adapter48002(json_dict)
classmethod adapter52065(json_dict)
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.

Parameters:indices (list(int)) – A list of indices to insert gaps before.
addGapsByIndices(gap_idxs)

Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Parameters:gap_idxs (list(int)) – A list of gap indices
annotationTitleChanged
annotations
append(element)

Appends an element to the sequence

Parameters:element – The element to append to this sequence
Type:element: self.ElementClass or basestring
blockSignals(self, bool) → bool
chain
childEvent(self, QChildEvent)
children(self) → List[QObject]
clearAllCaching()

This method should be implemented in subclasses that cache any data.

clearDescriptors()
clearDisulfideBondsCache()
clearPfam()
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteAllPredictions()
deleteLater(self)
deletePrediction(prediction_type)
descriptorsCleared
destroyed

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfideBondsCacheCleared
disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.DisulfideBond)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
encodeForPatternSearch(with_ss=False, with_flex=False, with_asa=False)

Convert to sequence dict expected by find_generalized_pattern.

Parameters:
  • with_ss (bool) – Whether to include secondary structure information.
  • with_flex (bool) – Whether to include flexibility information.
  • with_asa (bool) – Whether to include accessible surface area information.
Return type:

dict

Returns:

dictionary of sequence data

event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
extend(elements)

Extends the sequence with elements from an iterable

Parameters:elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
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

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

fullname
Returns:a formatted name + optional chain name for the sequence
Return type:str
gap_char
generateResidueMap()

Create residue map based on current structured residues.

Note: this method requires self.hasStructure() to be True and self.entry_id to be set. If this sequence was produced by schrodinger.application.msv.seqio.StructureConverter, there should already be a residue map and this method does not need to be called.

Raises:RuntimeError – If sequence has no structure or entry id
getAnnotation(index, annotation)

Returns the annotation at the specified index or None for a gap.

Raises:ValueError – if the annotation is not available
getConservation(other, consider_gaps=True, only_consider=None)

Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.

The homology criterion is based on “side chain chemistry” descriptor matching.

Parameters:
Returns:

The sequence conservation score (between 0.0 and 1.0)

Return type:

float

getGapCount()
Returns:the number of gaps in the sequence
Return type:int
getGaplessLength()
Returns:Length of this sequence ignoring gaps
Return type:int
getGaps()
Return type:list(residue.Gap)
Returns:The gaps in the sequence.
getIdentity(other, consider_gaps=True, only_consider=None)

Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)

Return type:

float

getNextResidue(res)

Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getNumAnnValues(ann)
getPreviousResidue(res)

Return the previous residue in the sequence (ignoring gaps) or None if this is the first residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getProperty(seq_prop)

Get the sequence’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the sequence property
Returns:The value of the sequence property
Return type:float or None
getResByKey(res_key)
Parameters:res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode)
Returns:Residue matching key or None if no matching residue is found
Return type:residue.Residue or NoneType
Raises:RuntimeError – If sequence has no structure
getRun(res)

For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.

Parameters:res (residue.AbstractSequenceElement) – Residue to get the run of
Reuturn:Set of residue indices in the run
Return type:set(int)
getSimilarity(other, consider_gaps=True, only_consider=None)

Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(other, consider_gaps=True, only_consider=None)

Return the total score of similarity between the sequence and a other sequence, assuming that they’re already aligned.

Parameters:
  • consider_gaps (bool) – Ignored because the similarity with a gap is 0.0
  • only_consider (set or None) – A set of residues to restrict attention to
  • other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:

The total sequence similarity score

Return type:

float

getStructure()
Returns:The associated structure. Will return None if there is no associated structure.
Return type:schrodinger.structure.Structure or NoneType
getStructureResForRes(res)
Parameters:res (residue.Residue) – Residue to get structure residue for
Returns:Structure residue or None if no matching residue is found
Return type:schrodinger.structure._Residue or NoneType
getSubsequence(start, end)

Return a sequence containing a subset of the elements in this one

Parameters:
  • start (int) – The index at which the subsequence should start
  • end (int) – The index at which the subsequence should end (exclusive)
Returns:

The requested subsequence

Return type:

AbstractSequence

getTerminalGaps()

Return terminal gaps.

Returns:A list of terminal gaps (in ascending index order)
Return type:list(residue.Gap)
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.

hasDescriptors()
hasDisorderedRegionsPredictions()
hasDisulfideBondPredictions()
hasDomainArrangementPredictions()
hasPfam()
hasSSAPredictions()
hasSolventAccessibility()
hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
hasStructuredResidues()

Return whether this sequence has any structured residues. This method is equivalent to bool(seq.structuredResidueCount()) but doesn’t (typically) require iterating through the entire sequence.

Return type:bool
index(res, ignore_gaps=False)

Returns the index of the specified residue

Parameters:
  • res (residue.Residue) – The residue to find
  • ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises:

A ValueError if the residue is not present

Return type:

int

Returns:

The index of the residue

indices(residues, ignore_gaps=False)

Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)

Parameters:
  • res (Iterable(residue.Residue)) – The residues to find indices of
  • ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns:

The indices of the residues

Return type:

list[int]

inherits(self, str) → bool
insertElements(index, elements)

Insert a list of elements or sequence element into this sequence.

If elements is a string or iterable of strings, residue numbers will be automatically assigned.

Parameters:
  • index (int) – The index at which to insert elements
  • elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
classmethod isValid(elements)
Parameters:elements (iterable(str) or str) – An iterable of string representations of elements making up the sequence
Returns:Tuple indicating whether valid and a set of invalid characters, if any
Return type:tuple(bool, set(str))
isWidgetType(self) → bool
isWindowType(self) → bool
iterNeighbors()

Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.

None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.

Returns:Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue or None
Return type:iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
killTimer(self, int)
lengthAboutToChange
lengthChanged
classmethod makeSeqElement(element)
Parameters:element (str or cls.ElementClass) – A sequence element or string representation thereof
Returns:sequence element
Return type:cls.ElementClass
metaObject(self) → QMetaObject
moveToThread(self, QThread)
mutate(start, end, elements)

Mutate sequence elements starting at the given index to the provided elements.

Parameters:
  • start (int) – The index at which to start mutating
  • end (int) – The index of the last mutated element (exclusive)
  • elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
name
nameChanged
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

onStructureChanged()
origin
Returns:A piece of metadata indicating where the sequence came from
Rtype origin:Sequence.ORIGIN or None
parent(self) → QObject
pfamChanged
pred_disulfide_bonds
pred_secondary_structures
predictionsChanged
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()

Remove gaps from the sequence

removeElements(eles)

Remove elements from the sequence.

Parameters:eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence.
Raises:ValueError – If any of the given elements are not in the sequence.
removeEventFilter(self, QObject)
removeStructurelessResidues(start=0, end=None)

Remove any structureless residues

Parameters:
  • start (int) – The index at which to start filtering structureless residues.
  • end (int) – The index at which to end filtering
removeTerminalGaps()

Remove gaps from the end of the sequence

renumberResidues(new_rescode_map)

Renumber residues in this sequence given a dictionary mapping old rescodes to the new desired rescodes.

residues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
residuesAdded
residuesChanged
residuesRemoved
secondaryStructureCacheCleared
secondaryStructureChanged
secondary_structures

A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.

Returns:A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure.
Return type:list(_SecondaryStructure)
sender(self) → QObject
senderSignalIndex(self) → int
sequenceCopied
setDisorderedRegionsPredictions(pred)
setDomainArrangementPredictions(pred)
setObjectName(self, str)
setParent(self, QObject)
setPfam(new_pfam, pfam_name)
setProperty(self, str, Any) → bool
setResidueMap(residue_map)

Set a new mapping between ResidueKey and structured residues.

Note: the only intended user of this method is schrodinger.application.msv.seqio.StructureConverter, where the ResidueKey is computed from the structure._Residue used to create the residue.Residue. If the sequence has a structure, the map can be generated using generateResidueMap.

Parameters:residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
setSSA(new_ssa)
setSSAPredictions(pred)
setSolventAccessibilityPredictions(pred)
setStructure(struc)

Set the associated structure. Can only be used on sequences with an associated structure.

Parameters:struc (schrodinger.structure.Structure) – The new structure for this sequence
Raises:RuntimeError – If there’s no structure associated with this sequence object.
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
structureChanged
structuredResidueCount()

Get the number of residues in this sequence with an associated structured residue. :rtype: int

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
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
tr(self, str, disambiguation: str = None, n: int = -1) → str
updateDescriptors(descriptors, property_source)

Updates the descriptor dicts with new descriptor values

Parameters:
  • descriptors (dict[str, float]) – A dict mapping descriptor names to their values
  • property_source (properties.PropertySource) – The source of the descriptors
validateGapIndices(gap_idxs)

Make sure that the specified gap indices are valid input for addGapsByIndices. If the indices are invalid, a ValueError will be raised. Indices are considered invalid if:

  • they refer to a position that’s more than one residue past the end of the sequence
  • they are negative
Parameters:gap_idxs (list[int]) – The gap indices to validate
visibility
visibilityChanged
class schrodinger.protein.sequence.DNASequence(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)

Bases: schrodinger.protein.sequence.NucleicAcidSequence

ALPHABET = {'A': DeoxyribonucleotideType('A', 'DA', 'Adenine'), 'C': DeoxyribonucleotideType('C', 'DC', 'Cytosine'), 'DA': DeoxyribonucleotideType('A', 'DA', 'Adenine'), 'DC': DeoxyribonucleotideType('C', 'DC', 'Cytosine'), 'DG': DeoxyribonucleotideType('G', 'DG', 'Guanine'), 'DT': DeoxyribonucleotideType('T', 'DT', 'Thymine'), 'G': DeoxyribonucleotideType('G', 'DG', 'Guanine'), 'T': DeoxyribonucleotideType('T', 'DT', 'Thymine')}
AnnotationClass

alias of schrodinger.protein.annotation.NucleicAcidSequenceAnnotations

ElementClass

alias of schrodinger.protein.residue.Nucleotide

class ORIGIN

Bases: enum.Enum

An enumeration.

Maestro = 1
PyMOL = 2
__contains__(item)
__init__(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)

See AbstractSingleChainSequence for additional documentation.

Parameters:
  • disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via disulfide bonds.
  • pred_disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via predicted disulfide bonds.
__len__()
classmethod adapter47007(json_dict)
classmethod adapter48002(json_dict)
classmethod adapter52065(json_dict)
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.

Parameters:indices (list(int)) – A list of indices to insert gaps before.
addGapsByIndices(gap_idxs)

Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Parameters:gap_idxs (list(int)) – A list of gap indices
annotationTitleChanged
annotations
append(element)

Appends an element to the sequence

Parameters:element – The element to append to this sequence
Type:element: self.ElementClass or basestring
blockSignals(self, bool) → bool
chain
childEvent(self, QChildEvent)
children(self) → List[QObject]
clearAllCaching()

This method should be implemented in subclasses that cache any data.

clearDescriptors()
clearDisulfideBondsCache()
clearPfam()
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteAllPredictions()
deleteLater(self)
deletePrediction(prediction_type)
descriptorsCleared
destroyed

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfideBondsCacheCleared
disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.DisulfideBond)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
encodeForPatternSearch(with_ss=False, with_flex=False, with_asa=False)

Convert to sequence dict expected by find_generalized_pattern.

Parameters:
  • with_ss (bool) – Whether to include secondary structure information.
  • with_flex (bool) – Whether to include flexibility information.
  • with_asa (bool) – Whether to include accessible surface area information.
Return type:

dict

Returns:

dictionary of sequence data

event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
extend(elements)

Extends the sequence with elements from an iterable

Parameters:elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
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

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

fullname
Returns:a formatted name + optional chain name for the sequence
Return type:str
gap_char
generateResidueMap()

Create residue map based on current structured residues.

Note: this method requires self.hasStructure() to be True and self.entry_id to be set. If this sequence was produced by schrodinger.application.msv.seqio.StructureConverter, there should already be a residue map and this method does not need to be called.

Raises:RuntimeError – If sequence has no structure or entry id
getAnnotation(index, annotation)

Returns the annotation at the specified index or None for a gap.

Raises:ValueError – if the annotation is not available
getConservation(other, consider_gaps=True, only_consider=None)

Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.

The homology criterion is based on “side chain chemistry” descriptor matching.

Parameters:
Returns:

The sequence conservation score (between 0.0 and 1.0)

Return type:

float

getGapCount()
Returns:the number of gaps in the sequence
Return type:int
getGaplessLength()
Returns:Length of this sequence ignoring gaps
Return type:int
getGaps()
Return type:list(residue.Gap)
Returns:The gaps in the sequence.
getIdentity(other, consider_gaps=True, only_consider=None)

Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)

Return type:

float

getNextResidue(res)

Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getNumAnnValues(ann)
getPreviousResidue(res)

Return the previous residue in the sequence (ignoring gaps) or None if this is the first residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getProperty(seq_prop)

Get the sequence’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the sequence property
Returns:The value of the sequence property
Return type:float or None
getResByKey(res_key)
Parameters:res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode)
Returns:Residue matching key or None if no matching residue is found
Return type:residue.Residue or NoneType
Raises:RuntimeError – If sequence has no structure
getRun(res)

For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.

Parameters:res (residue.AbstractSequenceElement) – Residue to get the run of
Reuturn:Set of residue indices in the run
Return type:set(int)
getSimilarity(other, consider_gaps=True, only_consider=None)

Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(other, consider_gaps=True, only_consider=None)

Return the total score of similarity between the sequence and a other sequence, assuming that they’re already aligned.

Parameters:
  • consider_gaps (bool) – Ignored because the similarity with a gap is 0.0
  • only_consider (set or None) – A set of residues to restrict attention to
  • other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:

The total sequence similarity score

Return type:

float

getStructure()
Returns:The associated structure. Will return None if there is no associated structure.
Return type:schrodinger.structure.Structure or NoneType
getStructureResForRes(res)
Parameters:res (residue.Residue) – Residue to get structure residue for
Returns:Structure residue or None if no matching residue is found
Return type:schrodinger.structure._Residue or NoneType
getSubsequence(start, end)

Return a sequence containing a subset of the elements in this one

Parameters:
  • start (int) – The index at which the subsequence should start
  • end (int) – The index at which the subsequence should end (exclusive)
Returns:

The requested subsequence

Return type:

AbstractSequence

getTerminalGaps()

Return terminal gaps.

Returns:A list of terminal gaps (in ascending index order)
Return type:list(residue.Gap)
getTranslation()

Get a translated sequence. This method uses BioPython’s translate method to convert a nucleic acid sequence into an amino acid sequence

Returns:A translated protein sequence. The name and chain from the nucleic acid sequence are copied over
Return type:ProteinSequence
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.

hasDescriptors()
hasDisorderedRegionsPredictions()
hasDisulfideBondPredictions()
hasDomainArrangementPredictions()
hasPfam()
hasSSAPredictions()
hasSolventAccessibility()
hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
hasStructuredResidues()

Return whether this sequence has any structured residues. This method is equivalent to bool(seq.structuredResidueCount()) but doesn’t (typically) require iterating through the entire sequence.

Return type:bool
index(res, ignore_gaps=False)

Returns the index of the specified residue

Parameters:
  • res (residue.Residue) – The residue to find
  • ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises:

A ValueError if the residue is not present

Return type:

int

Returns:

The index of the residue

indices(residues, ignore_gaps=False)

Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)

Parameters:
  • res (Iterable(residue.Residue)) – The residues to find indices of
  • ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns:

The indices of the residues

Return type:

list[int]

inherits(self, str) → bool
insertElements(index, elements)

Insert a list of elements or sequence element into this sequence.

If elements is a string or iterable of strings, residue numbers will be automatically assigned.

Parameters:
  • index (int) – The index at which to insert elements
  • elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
classmethod isValid(elements)
Parameters:elements (iterable(str) or str) – An iterable of string representations of elements making up the sequence
Returns:Tuple indicating whether valid and a set of invalid characters, if any
Return type:tuple(bool, set(str))
isWidgetType(self) → bool
isWindowType(self) → bool
iterNeighbors()

Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.

None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.

Returns:Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue or None
Return type:iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
killTimer(self, int)
lengthAboutToChange
lengthChanged
classmethod makeSeqElement(element)
Parameters:element (str or cls.ElementClass) – A sequence element or string representation thereof
Returns:sequence element
Return type:cls.ElementClass
metaObject(self) → QMetaObject
moveToThread(self, QThread)
mutate(start, end, elements)

Mutate sequence elements starting at the given index to the provided elements.

Parameters:
  • start (int) – The index at which to start mutating
  • end (int) – The index of the last mutated element (exclusive)
  • elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
name
nameChanged
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

onStructureChanged()
origin
Returns:A piece of metadata indicating where the sequence came from
Rtype origin:Sequence.ORIGIN or None
parent(self) → QObject
pfamChanged
pred_disulfide_bonds
pred_secondary_structures
predictionsChanged
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()

Remove gaps from the sequence

removeElements(eles)

Remove elements from the sequence.

Parameters:eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence.
Raises:ValueError – If any of the given elements are not in the sequence.
removeEventFilter(self, QObject)
removeStructurelessResidues(start=0, end=None)

Remove any structureless residues

Parameters:
  • start (int) – The index at which to start filtering structureless residues.
  • end (int) – The index at which to end filtering
removeTerminalGaps()

Remove gaps from the end of the sequence

renumberResidues(new_rescode_map)

Renumber residues in this sequence given a dictionary mapping old rescodes to the new desired rescodes.

residues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
residuesAdded
residuesChanged
residuesRemoved
secondaryStructureCacheCleared
secondaryStructureChanged
secondary_structures

A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.

Returns:A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure.
Return type:list(_SecondaryStructure)
sender(self) → QObject
senderSignalIndex(self) → int
sequenceCopied
setDisorderedRegionsPredictions(pred)
setDomainArrangementPredictions(pred)
setObjectName(self, str)
setParent(self, QObject)
setPfam(new_pfam, pfam_name)
setProperty(self, str, Any) → bool
setResidueMap(residue_map)

Set a new mapping between ResidueKey and structured residues.

Note: the only intended user of this method is schrodinger.application.msv.seqio.StructureConverter, where the ResidueKey is computed from the structure._Residue used to create the residue.Residue. If the sequence has a structure, the map can be generated using generateResidueMap.

Parameters:residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
setSSA(new_ssa)
setSSAPredictions(pred)
setSolventAccessibilityPredictions(pred)
setStructure(struc)

Set the associated structure. Can only be used on sequences with an associated structure.

Parameters:struc (schrodinger.structure.Structure) – The new structure for this sequence
Raises:RuntimeError – If there’s no structure associated with this sequence object.
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
structureChanged
structuredResidueCount()

Get the number of residues in this sequence with an associated structured residue. :rtype: int

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
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
tr(self, str, disambiguation: str = None, n: int = -1) → str
updateDescriptors(descriptors, property_source)

Updates the descriptor dicts with new descriptor values

Parameters:
  • descriptors (dict[str, float]) – A dict mapping descriptor names to their values
  • property_source (properties.PropertySource) – The source of the descriptors
validateGapIndices(gap_idxs)

Make sure that the specified gap indices are valid input for addGapsByIndices. If the indices are invalid, a ValueError will be raised. Indices are considered invalid if:

  • they refer to a position that’s more than one residue past the end of the sequence
  • they are negative
Parameters:gap_idxs (list[int]) – The gap indices to validate
visibility
visibilityChanged
class schrodinger.protein.sequence.RNASequence(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)

Bases: schrodinger.protein.sequence.NucleicAcidSequence

ALPHABET = {'A': RibonucleotideType('A', 'A', 'Adenine'), 'C': RibonucleotideType('C', 'C', 'Cytosine'), 'G': RibonucleotideType('G', 'G', 'Guanine'), 'U': RibonucleotideType('U', 'U', 'Uracil')}
AnnotationClass

alias of schrodinger.protein.annotation.NucleicAcidSequenceAnnotations

ElementClass

alias of schrodinger.protein.residue.Nucleotide

class ORIGIN

Bases: enum.Enum

An enumeration.

Maestro = 1
PyMOL = 2
__contains__(item)
__init__(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)

See AbstractSingleChainSequence for additional documentation.

Parameters:
  • disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via disulfide bonds.
  • pred_disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via predicted disulfide bonds.
__len__()
classmethod adapter47007(json_dict)
classmethod adapter48002(json_dict)
classmethod adapter52065(json_dict)
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.

Parameters:indices (list(int)) – A list of indices to insert gaps before.
addGapsByIndices(gap_idxs)

Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Parameters:gap_idxs (list(int)) – A list of gap indices
annotationTitleChanged
annotations
append(element)

Appends an element to the sequence

Parameters:element – The element to append to this sequence
Type:element: self.ElementClass or basestring
blockSignals(self, bool) → bool
chain
childEvent(self, QChildEvent)
children(self) → List[QObject]
clearAllCaching()

This method should be implemented in subclasses that cache any data.

clearDescriptors()
clearDisulfideBondsCache()
clearPfam()
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteAllPredictions()
deleteLater(self)
deletePrediction(prediction_type)
descriptorsCleared
destroyed

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfideBondsCacheCleared
disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.DisulfideBond)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
encodeForPatternSearch(with_ss=False, with_flex=False, with_asa=False)

Convert to sequence dict expected by find_generalized_pattern.

Parameters:
  • with_ss (bool) – Whether to include secondary structure information.
  • with_flex (bool) – Whether to include flexibility information.
  • with_asa (bool) – Whether to include accessible surface area information.
Return type:

dict

Returns:

dictionary of sequence data

event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
extend(elements)

Extends the sequence with elements from an iterable

Parameters:elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
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

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

fullname
Returns:a formatted name + optional chain name for the sequence
Return type:str
gap_char
generateResidueMap()

Create residue map based on current structured residues.

Note: this method requires self.hasStructure() to be True and self.entry_id to be set. If this sequence was produced by schrodinger.application.msv.seqio.StructureConverter, there should already be a residue map and this method does not need to be called.

Raises:RuntimeError – If sequence has no structure or entry id
getAnnotation(index, annotation)

Returns the annotation at the specified index or None for a gap.

Raises:ValueError – if the annotation is not available
getConservation(other, consider_gaps=True, only_consider=None)

Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.

The homology criterion is based on “side chain chemistry” descriptor matching.

Parameters:
Returns:

The sequence conservation score (between 0.0 and 1.0)

Return type:

float

getGapCount()
Returns:the number of gaps in the sequence
Return type:int
getGaplessLength()
Returns:Length of this sequence ignoring gaps
Return type:int
getGaps()
Return type:list(residue.Gap)
Returns:The gaps in the sequence.
getIdentity(other, consider_gaps=True, only_consider=None)

Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)

Return type:

float

getNextResidue(res)

Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getNumAnnValues(ann)
getPreviousResidue(res)

Return the previous residue in the sequence (ignoring gaps) or None if this is the first residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getProperty(seq_prop)

Get the sequence’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the sequence property
Returns:The value of the sequence property
Return type:float or None
getResByKey(res_key)
Parameters:res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode)
Returns:Residue matching key or None if no matching residue is found
Return type:residue.Residue or NoneType
Raises:RuntimeError – If sequence has no structure
getRun(res)

For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.

Parameters:res (residue.AbstractSequenceElement) – Residue to get the run of
Reuturn:Set of residue indices in the run
Return type:set(int)
getSimilarity(other, consider_gaps=True, only_consider=None)

Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(other, consider_gaps=True, only_consider=None)

Return the total score of similarity between the sequence and a other sequence, assuming that they’re already aligned.

Parameters:
  • consider_gaps (bool) – Ignored because the similarity with a gap is 0.0
  • only_consider (set or None) – A set of residues to restrict attention to
  • other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:

The total sequence similarity score

Return type:

float

getStructure()
Returns:The associated structure. Will return None if there is no associated structure.
Return type:schrodinger.structure.Structure or NoneType
getStructureResForRes(res)
Parameters:res (residue.Residue) – Residue to get structure residue for
Returns:Structure residue or None if no matching residue is found
Return type:schrodinger.structure._Residue or NoneType
getSubsequence(start, end)

Return a sequence containing a subset of the elements in this one

Parameters:
  • start (int) – The index at which the subsequence should start
  • end (int) – The index at which the subsequence should end (exclusive)
Returns:

The requested subsequence

Return type:

AbstractSequence

getTerminalGaps()

Return terminal gaps.

Returns:A list of terminal gaps (in ascending index order)
Return type:list(residue.Gap)
getTranslation()

Get a translated sequence. This method uses BioPython’s translate method to convert a nucleic acid sequence into an amino acid sequence

Returns:A translated protein sequence. The name and chain from the nucleic acid sequence are copied over
Return type:ProteinSequence
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.

hasDescriptors()
hasDisorderedRegionsPredictions()
hasDisulfideBondPredictions()
hasDomainArrangementPredictions()
hasPfam()
hasSSAPredictions()
hasSolventAccessibility()
hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
hasStructuredResidues()

Return whether this sequence has any structured residues. This method is equivalent to bool(seq.structuredResidueCount()) but doesn’t (typically) require iterating through the entire sequence.

Return type:bool
index(res, ignore_gaps=False)

Returns the index of the specified residue

Parameters:
  • res (residue.Residue) – The residue to find
  • ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises:

A ValueError if the residue is not present

Return type:

int

Returns:

The index of the residue

indices(residues, ignore_gaps=False)

Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)

Parameters:
  • res (Iterable(residue.Residue)) – The residues to find indices of
  • ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns:

The indices of the residues

Return type:

list[int]

inherits(self, str) → bool
insertElements(index, elements)

Insert a list of elements or sequence element into this sequence.

If elements is a string or iterable of strings, residue numbers will be automatically assigned.

Parameters:
  • index (int) – The index at which to insert elements
  • elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
classmethod isValid(elements)
Parameters:elements (iterable(str) or str) – An iterable of string representations of elements making up the sequence
Returns:Tuple indicating whether valid and a set of invalid characters, if any
Return type:tuple(bool, set(str))
isWidgetType(self) → bool
isWindowType(self) → bool
iterNeighbors()

Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.

None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.

Returns:Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue or None
Return type:iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
killTimer(self, int)
lengthAboutToChange
lengthChanged
classmethod makeSeqElement(element)
Parameters:element (str or cls.ElementClass) – A sequence element or string representation thereof
Returns:sequence element
Return type:cls.ElementClass
metaObject(self) → QMetaObject
moveToThread(self, QThread)
mutate(start, end, elements)

Mutate sequence elements starting at the given index to the provided elements.

Parameters:
  • start (int) – The index at which to start mutating
  • end (int) – The index of the last mutated element (exclusive)
  • elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
name
nameChanged
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

onStructureChanged()
origin
Returns:A piece of metadata indicating where the sequence came from
Rtype origin:Sequence.ORIGIN or None
parent(self) → QObject
pfamChanged
pred_disulfide_bonds
pred_secondary_structures
predictionsChanged
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()

Remove gaps from the sequence

removeElements(eles)

Remove elements from the sequence.

Parameters:eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence.
Raises:ValueError – If any of the given elements are not in the sequence.
removeEventFilter(self, QObject)
removeStructurelessResidues(start=0, end=None)

Remove any structureless residues

Parameters:
  • start (int) – The index at which to start filtering structureless residues.
  • end (int) – The index at which to end filtering
removeTerminalGaps()

Remove gaps from the end of the sequence

renumberResidues(new_rescode_map)

Renumber residues in this sequence given a dictionary mapping old rescodes to the new desired rescodes.

residues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
residuesAdded
residuesChanged
residuesRemoved
secondaryStructureCacheCleared
secondaryStructureChanged
secondary_structures

A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.

Returns:A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure.
Return type:list(_SecondaryStructure)
sender(self) → QObject
senderSignalIndex(self) → int
sequenceCopied
setDisorderedRegionsPredictions(pred)
setDomainArrangementPredictions(pred)
setObjectName(self, str)
setParent(self, QObject)
setPfam(new_pfam, pfam_name)
setProperty(self, str, Any) → bool
setResidueMap(residue_map)

Set a new mapping between ResidueKey and structured residues.

Note: the only intended user of this method is schrodinger.application.msv.seqio.StructureConverter, where the ResidueKey is computed from the structure._Residue used to create the residue.Residue. If the sequence has a structure, the map can be generated using generateResidueMap.

Parameters:residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
setSSA(new_ssa)
setSSAPredictions(pred)
setSolventAccessibilityPredictions(pred)
setStructure(struc)

Set the associated structure. Can only be used on sequences with an associated structure.

Parameters:struc (schrodinger.structure.Structure) – The new structure for this sequence
Raises:RuntimeError – If there’s no structure associated with this sequence object.
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
structureChanged
structuredResidueCount()

Get the number of residues in this sequence with an associated structured residue. :rtype: int

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
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
tr(self, str, disambiguation: str = None, n: int = -1) → str
updateDescriptors(descriptors, property_source)

Updates the descriptor dicts with new descriptor values

Parameters:
  • descriptors (dict[str, float]) – A dict mapping descriptor names to their values
  • property_source (properties.PropertySource) – The source of the descriptors
validateGapIndices(gap_idxs)

Make sure that the specified gap indices are valid input for addGapsByIndices. If the indices are invalid, a ValueError will be raised. Indices are considered invalid if:

  • they refer to a position that’s more than one residue past the end of the sequence
  • they are negative
Parameters:gap_idxs (list[int]) – The gap indices to validate
visibility
visibilityChanged
class schrodinger.protein.sequence.CombinedChainSequenceMeta

Bases: schrodinger.application.msv.utils.DocstringWrapperMetaClass, sip.wrappertype

The metaclass for CombinedChainProteinSequence. This metaclass wraps the specified class attributes.

__init__

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

mro()

Return a type’s method resolution order.

class schrodinger.protein.sequence.CombinedChainProteinSequence(seqs)

Bases: schrodinger.protein.sequence.AbstractProteinSequenceMixin, schrodinger.protein.sequence.AbstractSequence

A sequence that contains multiple chains from the same protein. Instances of this class do not directly contain any residues themselves and instead wrap one or several ProteinSequence objects.

Note:CombinedChainProteinSequence.visibility properly reports entry

inclusion state, but it may not correctly report entry visibility (e.g. partially visible vs. fully visible). The MSV structure icons only report inclusion state and the visibility of included entries isn’t reported anywhere in the panel, though, so this limitation doesn’t have any impact on functionality.

AnnotationClass

alias of schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations

__init__(seqs)
Parameters:seqs (list(ProteinSequence)) – A list of the split-chain sequences to wrap.
__len__()
fullname
index(res)

Returns the index of the specified residue

Parameters:
  • res (residue.Residue) – The residue to find
  • ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises:

A ValueError if the residue is not present

Return type:

int

Returns:

The index of the residue

indices(residues)

Returns the indices of all specified residues. Note that the returned integers will likely not be in the same order as the input residues.

Parameters:res (Iterable(residue.CombinedChainResidueWrapper)) – The residues to find indices of
Returns:The indices of the residues
Return type:list[int]
insertElements(index, elements)

Insert a list of elements or sequence element into this sequence.

If elements is a string or iterable of strings, residue numbers will be automatically assigned.

Parameters:
  • index (int) – The index at which to insert elements
  • elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
mutate(start, end, elements)

Mutate sequence elements. See parent class for additional method documentation.

Raises:MultipleChainsError – If the specified residue range spans multiple chains.
assertCanMutateResidues(start, end)

Make sure that we can mutate the specified residues. If not, raise an exception.

Parameters:
  • start (int) – The index at which to start mutating
  • end (int) – The index of the last mutated element (exclusive)
Raises:

MultipleChainsError – If the specified residue range spans multiple chains.

append(element)

Appends an element to the sequence

Parameters:element – The element to append to this sequence
Type:element: self.ElementClass or basestring
extend(elements)

Extends the sequence with elements from an iterable

Parameters:elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
getSubsequence(start, end)

Return a sequence containing a subset of the elements in this one. Note that the new sequence will be a split-chain sequence and will ignore any chain breaks present in the requested subset of elements.

Parameters:
  • start (int) – The index at which the subsequence should start
  • end (int) – The index at which the subsequence should end (exclusive)
Returns:

The requested subsequence

Return type:

ProteinSequence

removeElements(eles)

Remove elements from the sequence.

Parameters:eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence.
Raises:ValueError – If any of the given elements are not in the sequence.
getStructureResForRes(res)
Parameters:res (residue.Residue) – Residue to get structure residue for
Returns:Structure residue or None if no matching residue is found
Return type:schrodinger.structure._Residue or NoneType
getGaplessLength()
Returns:Length of this sequence ignoring gaps
Return type:int
addGapsByIndices(gap_idxs)

Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.

Parameters:gap_idxs (list(int)) – A list of gap indices
addGapsToChainStartsAndEnds(gaps)

Add the specified numbers of gaps to the starts and ends of each chain.

Parameters:gaps (list[tuple(int, int)]) –

The numbers of gaps to add, formatted as gaps_to_add[chain_index] = (gaps to add to the start of the chain,

gaps to add to the end of the chain)
removeGapsFromChainStartsAndEnds(gaps)

Remove the specified numbers of gaps from the starts and ends of each chain.

Parameters:gaps (list[tuple(int, int)]) –

The numbers of gaps to remove, formatted as gaps_to_remove[chain_index] =

(gaps to remove from the start of the chain,
gaps to remove from the end of the chain)
validateGapsToRemoveFromChainStartAndEnds(gaps)

Make sure that we can remove the specified numbers of gaps from the starts and ends of each chain.

Parameters:gaps (list[tuple(int, int)]) –

The numbers of gaps to remove, formatted as gaps_to_remove[chain_index] =

(gaps to remove from the start of the chain,
gaps to remove from the end of the chain)
Raises:AssertionError – If some of the sequence elements to be removed aren’t actually gaps.
disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.CombinedChainDisulfideBond)
pred_disulfide_bonds
indexToSeqAndIndex(index)

Convert a combined-chain residue index to a split-chain sequence and a residue index within the specified sequence.

Parameters:index (int) – A valid combined-chain residue index
Returns:A tuple of - the split-chain sequence - residue index - the starting index of the split-chain sequence
Return type:tuple(ProteinSequence, int, int)
chain
chains
chain_offsets
hasChain(chain_name)

Does this sequence contain a chain with the specified name?

Parameters:chain_name (str) – The chain name to check
Return type:bool
addChain(seq)

Add a new chain to this sequence.

Parameters:seq (ProteinSequence) – The chain to add
removeChain(seq)

Remove a chain from this sequence. Note that you should not remove the last chain; instead, remove this sequence from the alignment.

Parameters:seq (ProteinSequence) – The chain to remove
removeChains(seqs)

Remove multiple chains from this sequence. Note that you should not all chain from a combine-chain sequence; instead, remove the sequence from the alignment.

Parameters:seqs (list[ProteinSequence]) – The chains to remove
insertElementByChain(index, chain, element)

Add the given element to the specified chain of a sequence.

Parameters:
offsetForChain(chain)

Get the combined-chain residue index for the first residue of the specified chain.

Parameters:chain (ProteinSequence) – The chain
Returns:The offset
Return type:int
clearAllCaching()

This method should be implemented in subclasses that cache any data.

ALPHABET = {'2AS': ResidueType('D', '2AS', 'Aspartic acid'), '3AH': ResidueType('H', '3AH', 'Histidine'), '5HP': ResidueType('E', '5HP', 'Glutamic acid'), 'A': ResidueType('A', 'ALA', 'Alanine'), 'ACE': ResidueType('X', 'ACE', 'Capping Group'), 'ACL': ResidueType('R', 'ACL', 'Arginine'), 'AGM': ResidueType('R', 'AGM', 'Arginine'), 'AIB': ResidueType('A', 'AIB', 'Alanine'), 'ALA': ResidueType('A', 'ALA', 'Alanine'), 'ALM': ResidueType('A', 'ALM', 'Alanine'), 'ALO': ResidueType('T', 'ALO', 'Threonine'), 'ALY': ResidueType('K', 'ALY', 'Lysine'), 'ANF': ResidueType('X', 'ANF', 'Capping Group'), 'ARG': ResidueType('R', 'ARG', 'Arginine'), 'ARM': ResidueType('R', 'ARM', 'Arginine'), 'ARN': ResidueType('R', 'ARN', 'Arginine'), 'ASA': ResidueType('D', 'ASA', 'Aspartic acid'), 'ASB': ResidueType('D', 'ASB', 'Aspartic acid'), 'ASH': ResidueType('D', 'ASH', 'Aspartic acid'), 'ASK': ResidueType('D', 'ASK', 'Aspartic acid'), 'ASL': ResidueType('D', 'ASL', 'Aspartic acid'), 'ASN': ResidueType('N', 'ASN', 'Asparagine'), 'ASP': ResidueType('D', 'ASP', 'Aspartic acid'), 'ASQ': ResidueType('D', 'ASQ', 'Aspartic acid'), 'AYA': ResidueType('A', 'AYA', 'Alanine'), 'BCS': ResidueType('X', 'BCS', 'Cysteine'), 'BHD': ResidueType('D', 'BHD', 'Aspartic acid'), 'BMT': ResidueType('T', 'BMT', 'Threonine'), 'BNN': ResidueType('A', 'BNN', 'Alanine'), 'BUC': ResidueType('C', 'BUC', 'Cysteine'), 'BUG': ResidueType('L', 'BUG', 'Leucine'), 'C': ResidueType('C', 'CYS', 'Cysteine'), 'C5C': ResidueType('C', 'C5C', 'Cysteine'), 'C6C': ResidueType('C', 'C6C', 'Cysteine'), 'CCS': ResidueType('C', 'CCS', 'Cysteine'), 'CEA': ResidueType('C', 'CEA', 'Cysteine'), 'CGU': ResidueType('E', 'CGU', 'Glutamic acid'), 'CHG': ResidueType('A', 'CHG', 'Alanine'), 'CLE': ResidueType('L', 'CLE', 'Leucine'), 'CME': ResidueType('C', 'CME', 'Cysteine'), 'CSD': ResidueType('A', 'CSD', 'Alanine'), 'CSO': ResidueType('C', 'CSO', 'Cysteine'), 'CSP': ResidueType('C', 'CSP', 'Cysteine'), 'CSS': ResidueType('C', 'CSS', 'Cysteine'), 'CSW': ResidueType('C', 'CSW', 'Cysteine'), 'CSX': ResidueType('C', 'CSX', 'Cysteine'), 'CXM': ResidueType('M', 'CXM', 'Methionine'), 'CY1': ResidueType('C', 'CY1', 'Cysteine'), 'CY3': ResidueType('C', 'CY3', 'Cysteine'), 'CYG': ResidueType('C', 'CYG', 'Cysteine'), 'CYM': ResidueType('C', 'CYM', 'Cysteine'), 'CYP': ResidueType('C', 'CYP', 'Cysteine'), 'CYQ': ResidueType('C', 'CYQ', 'Cysteine'), 'CYS': ResidueType('C', 'CYS', 'Cysteine'), 'CYX': ResidueType('C', 'CYX', 'Cysteine'), 'D': ResidueType('D', 'ASP', 'Aspartic acid'), 'DAH': ResidueType('F', 'DAH', 'Phenylalanine'), 'DAL': ResidueType('X', 'DAL', 'Alanine'), 'DAR': ResidueType('X', 'DAR', 'Arginine'), 'DAS': ResidueType('X', 'DAS', 'Aspartic acid'), 'DCY': ResidueType('X', 'DCY', 'Cysteine'), 'DGL': ResidueType('X', 'DGL', 'Glutamic acid'), 'DGN': ResidueType('X', 'DGN', 'Glutamine'), 'DHA': ResidueType('A', 'DHA', 'Alanine'), 'DHI': ResidueType('X', 'DHI', 'Histidine'), 'DIL': ResidueType('X', 'DIL', 'Isoleucine'), 'DIV': ResidueType('V', 'DIV', 'Valine'), 'DLE': ResidueType('X', 'DLE', 'Leucine'), 'DLY': ResidueType('X', 'DLY', 'Lysine'), 'DNP': ResidueType('A', 'DNP', 'Alanine'), 'DPN': ResidueType('X', 'DPN', 'Phenylalanine'), 'DPR': ResidueType('X', 'DPR', 'Proline'), 'DSG': ResidueType('X', 'DSG', 'Asparagine'), 'DSN': ResidueType('X', 'DSN', 'Serine'), 'DSP': ResidueType('D', 'DSP', 'Aspartic acid'), 'DTH': ResidueType('X', 'DTH', 'Threonine'), 'DTR': ResidueType('X', 'DTR', 'Tryptophan'), 'DTY': ResidueType('X', 'DTY', 'Tyrosine'), 'DVA': ResidueType('X', 'DVA', 'Valine'), 'E': ResidueType('E', 'GLU', 'Glutamic acid'), 'EFC': ResidueType('C', 'EFC', 'Cysteine'), 'F': ResidueType('F', 'PHE', 'Phenylalanine'), 'FCO': ResidueType('X', 'FCO', 'Capping Group'), 'FLA': ResidueType('A', 'FLA', 'Alanine'), 'FME': ResidueType('M', 'FME', 'Methionine'), 'G': ResidueType('G', 'GLY', 'Glycine'), 'GGL': ResidueType('E', 'GGL', 'Glutamic acid'), 'GL3': ResidueType('G', 'GL3', 'Glycine'), 'GLH': ResidueType('E', 'GLH', 'Glutamic acid'), 'GLN': ResidueType('Q', 'GLN', 'Glutamine'), 'GLU': ResidueType('E', 'GLU', 'Glutamic acid'), 'GLY': ResidueType('G', 'GLY', 'Glycine'), 'GLZ': ResidueType('G', 'GLZ', 'Glycine'), 'GMA': ResidueType('E', 'GMA', 'Glutamic acid'), 'GSC': ResidueType('G', 'GSC', 'Glycine'), 'H': ResidueType('H', 'HIS', 'Histidine'), 'HAC': ResidueType('A', 'HAC', 'Alanine'), 'HAR': ResidueType('R', 'HAR', 'Arginine'), 'HIC': ResidueType('H', 'HIC', 'Histidine'), 'HID': ResidueType('H', 'HID', 'Histidine'), 'HIE': ResidueType('H', 'HIE', 'Histidine'), 'HIP': ResidueType('H', 'HIP', 'Histidine'), 'HIS': ResidueType('H', 'HIS', 'Histidine'), 'HMR': ResidueType('R', 'HMR', 'Arginine'), 'HPQ': ResidueType('F', 'HPQ', 'Phenylalanine'), 'HSD': ResidueType('H', 'HSD', 'Histidine'), 'HSE': ResidueType('H', 'HSE', 'Histidine'), 'HSP': ResidueType('H', 'HSP', 'Histidine'), 'HTR': ResidueType('W', 'HTR', 'Tryptophan'), 'HYP': ResidueType('X', 'HYP', 'Proline'), 'I': ResidueType('I', 'ILE', 'Isoleucine'), 'IIL': ResidueType('I', 'IIL', 'Isoleucine'), 'ILE': ResidueType('I', 'ILE', 'Isoleucine'), 'IND': ResidueType('X', 'IND', 'Capping Group'), 'IYR': ResidueType('Y', 'IYR', 'Tyrosine'), 'K': ResidueType('K', 'LYS', 'Lysine'), 'KCX': ResidueType('K', 'KCX', 'Lysine'), 'L': ResidueType('L', 'LEU', 'Leucine'), 'LEU': ResidueType('L', 'LEU', 'Leucine'), 'LLP': ResidueType('K', 'LLP', 'Lysine'), 'LLY': ResidueType('K', 'LLY', 'Lysine'), 'LTR': ResidueType('W', 'LTR', 'Tryptophan'), 'LYM': ResidueType('K', 'LYM', 'Lysine'), 'LYN': ResidueType('K', 'LYN', 'Lysine'), 'LYS': ResidueType('K', 'LYS', 'Lysine'), 'LYZ': ResidueType('K', 'LYZ', 'Lysine'), 'M': ResidueType('M', 'MET', 'Methionine'), 'MAA': ResidueType('A', 'MAA', 'Alanine'), 'MEN': ResidueType('N', 'MEN', 'Asparagine'), 'MET': ResidueType('M', 'MET', 'Methionine'), 'MHS': ResidueType('H', 'MHS', 'Histidine'), 'MIS': ResidueType('S', 'MIS', 'Serine'), 'MLE': ResidueType('L', 'MLE', 'Leucine'), 'MMO': ResidueType('R', 'MMO', 'Arginine'), 'MPA': ResidueType('X', 'MPA', 'Capping Group'), 'MPQ': ResidueType('G', 'MPQ', 'Glycine'), 'MSA': ResidueType('G', 'MSA', 'Glycine'), 'MSE': ResidueType('M', 'MSE', 'Methionine'), 'MVA': ResidueType('V', 'MVA', 'Valine'), 'N': ResidueType('N', 'ASN', 'Asparagine'), 'NCO': ResidueType('X', 'NCO', 'Capping Group'), 'NEM': ResidueType('H', 'NEM', 'Histidine'), 'NEP': ResidueType('H', 'NEP', 'Histidine'), 'NH2': ResidueType('X', 'NH2', 'Capping Group'), 'NLE': ResidueType('X', 'NLE', 'Leucine'), 'NLN': ResidueType('L', 'NLN', 'Leucine'), 'NLP': ResidueType('L', 'NLP', 'Leucine'), 'NMA': ResidueType('X', 'NMA', 'Capping Group'), 'NMC': ResidueType('G', 'NMC', 'Glycine'), 'OAS': ResidueType('S', 'OAS', 'Serine'), 'OCS': ResidueType('C', 'OCS', 'Cysteine'), 'OMT': ResidueType('M', 'OMT', 'Methionine'), 'P': ResidueType('P', 'PRO', 'Proline'), 'PAQ': ResidueType('Y', 'PAQ', 'Tyrosine'), 'PCA': ResidueType('E', 'PCA', 'Glutamic acid'), 'PEC': ResidueType('C', 'PEC', 'Cysteine'), 'PHE': ResidueType('F', 'PHE', 'Phenylalanine'), 'PHI': ResidueType('F', 'PHI', 'Phenylalanine'), 'PHL': ResidueType('F', 'PHL', 'Phenylalanine'), 'PR3': ResidueType('C', 'PR3', 'Cysteine'), 'PRO': ResidueType('P', 'PRO', 'Proline'), 'PRR': ResidueType('A', 'PRR', 'Alanine'), 'PTR': ResidueType('y', 'PTR', 'Tyrosine'), 'Q': ResidueType('Q', 'GLN', 'Glutamine'), 'R': ResidueType('R', 'ARG', 'Arginine'), 'S': ResidueType('S', 'SER', 'Serine'), 'SAC': ResidueType('S', 'SAC', 'Serine'), 'SAR': ResidueType('G', 'SAR', 'Glycine'), 'SCH': ResidueType('C', 'SCH', 'Cysteine'), 'SCS': ResidueType('C', 'SCS', 'Cysteine'), 'SCY': ResidueType('C', 'SCY', 'Cysteine'), 'SEL': ResidueType('S', 'SEL', 'Serine'), 'SEP': ResidueType('X', 'SEP', 'Serine'), 'SER': ResidueType('S', 'SER', 'Serine'), 'SET': ResidueType('S', 'SET', 'Serine'), 'SHC': ResidueType('C', 'SHC', 'Cysteine'), 'SHR': ResidueType('K', 'SHR', 'Lysine'), 'SMC': ResidueType('C', 'SMC', 'Cysteine'), 'SOC': ResidueType('C', 'SOC', 'Cysteine'), 'STY': ResidueType('Y', 'STY', 'Tyrosine'), 'SVA': ResidueType('S', 'SVA', 'Serine'), 'T': ResidueType('T', 'THR', 'Threonine'), 'THO': ResidueType('T', 'THO', 'Threonine'), 'THR': ResidueType('T', 'THR', 'Threonine'), 'TIH': ResidueType('A', 'TIH', 'Alanine'), 'TOSG': ResidueType('X', 'TOSG', 'Capping Group'), 'TPL': ResidueType('W', 'TPL', 'Tryptophan'), 'TPO': ResidueType('t', 'TPO', 'Threonine'), 'TPQ': ResidueType('A', 'TPQ', 'Alanine'), 'TRG': ResidueType('K', 'TRG', 'Lysine'), 'TRO': ResidueType('W', 'TRO', 'Tryptophan'), 'TRP': ResidueType('W', 'TRP', 'Tryptophan'), 'TYB': ResidueType('Y', 'TYB', 'Tyrosine'), 'TYM': ResidueType('Y', 'TYM', 'Tyrosine'), 'TYO': ResidueType('Y', 'TYO', 'Tyrosine'), 'TYQ': ResidueType('Y', 'TYQ', 'Tyrosine'), 'TYR': ResidueType('Y', 'TYR', 'Tyrosine'), 'TYS': ResidueType('Y', 'TYS', 'Tyrosine'), 'TYY': ResidueType('Y', 'TYY', 'Tyrosine'), 'UNK': ResidueType('X', 'UNK', 'Unknown'), 'V': ResidueType('V', 'VAL', 'Valine'), 'VAL': ResidueType('V', 'VAL', 'Valine'), 'W': ResidueType('W', 'TRP', 'Tryptophan'), 'Y': ResidueType('Y', 'TYR', 'Tyrosine')}
ElementClass

alias of schrodinger.protein.residue.Residue

class ORIGIN

Bases: enum.Enum

An enumeration.

Maestro = 1
PyMOL = 2
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.

Parameters:indices (list(int)) – A list of indices to insert gaps before.
annotationTitleChanged
annotations
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → List[QObject]
clearDescriptors()
clearDisulfideBondsCache()
clearPfam()
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
descriptorsCleared
destroyed

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

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfideBondsCacheCleared
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
entry_id
entry_name
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]

gap_char
getAnnotation(index, annotation)

Returns the annotation at the specified index or None for a gap.

Raises:ValueError – if the annotation is not available
getConservation(other, consider_gaps=True, only_consider=None)

Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.

The homology criterion is based on “side chain chemistry” descriptor matching.

Parameters:
Returns:

The sequence conservation score (between 0.0 and 1.0)

Return type:

float

getGapCount()
Returns:the number of gaps in the sequence
Return type:int
getGaps()
Return type:list(residue.Gap)
Returns:The gaps in the sequence.
getIdentity(other, consider_gaps=True, only_consider=None)

Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)

Return type:

float

getNextResidue(res)

Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getNumAnnValues(ann)
getPreviousResidue(res)

Return the previous residue in the sequence (ignoring gaps) or None if this is the first residue.

Parameters:res (schrodinger.protein.residue.Residue) – A given residue in the sequence
Returns:The previous residue in the sequence
Return type:schrodinger.protein.residue.Residue
getProperty(seq_prop)

Get the sequence’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the sequence property
Returns:The value of the sequence property
Return type:float or None
getRun(res)

For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.

Parameters:res (residue.AbstractSequenceElement) – Residue to get the run of
Reuturn:Set of residue indices in the run
Return type:set(int)
getSimilarity(other, consider_gaps=True, only_consider=None)

Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(other, consider_gaps=True, only_consider=None)

Return the total score of similarity between the sequence and a other sequence, assuming that they’re already aligned.

Parameters:
  • consider_gaps (bool) – Ignored because the similarity with a gap is 0.0
  • only_consider (set or None) – A set of residues to restrict attention to
  • other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:

The total sequence similarity score

Return type:

float

getStructure(*args, **kwargs)
getTerminalGaps()

Return terminal gaps.

Returns:A list of terminal gaps (in ascending index order)
Return type:list(residue.Gap)
hasDescriptors()
hasDisorderedRegionsPredictions()
hasDisulfideBondPredictions()
hasDomainArrangementPredictions()
hasPfam()
hasSSAPredictions()
hasSolventAccessibility()
hasStructure(*args, **kwargs)
hasStructuredResidues()

Return whether this sequence has any structured residues. This method is equivalent to bool(seq.structuredResidueCount()) but doesn’t (typically) require iterating through the entire sequence.

Return type:bool
inherits(self, str) → bool
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
iterNeighbors()

Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.

None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.

Returns:Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue or None
Return type:iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
killTimer(self, int)
lengthAboutToChange
lengthChanged
long_name
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

origin
parent(self) → QObject
pdb_id
pfamChanged
pred_secondary_structures
predictionsChanged
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()

Remove gaps from the sequence

removeEventFilter(self, QObject)
removeTerminalGaps()

Remove gaps from the end of the sequence

residues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
residuesAdded
residuesChanged
residuesRemoved
secondaryStructureChanged
secondary_structures

A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.

Returns:A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure.
Return type:list(_SecondaryStructure)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setPfam(new_pfam, pfam_name)
setProperty(self, str, Any) → bool
setStructure(*args, **kwargs)
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
structureChanged
structuredResidueCount()

Get the number of residues in this sequence with an associated structured residue. :rtype: int

thread(self) → QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = -1) → str
updateDescriptors(descriptors, property_source)

Updates the descriptor dicts with new descriptor values

Parameters:
  • descriptors (dict[str, float]) – A dict mapping descriptor names to their values
  • property_source (properties.PropertySource) – The source of the descriptors
validateGapIndices(gap_idxs)

Make sure that the specified gap indices are valid input for addGapsByIndices. If the indices are invalid, a ValueError will be raised. Indices are considered invalid if:

  • they refer to a position that’s more than one residue past the end of the sequence
  • they are negative
Parameters:gap_idxs (list[int]) – The gap indices to validate
visibility
visibilityChanged
exception schrodinger.protein.sequence.MultipleChainsError

Bases: ValueError

An exception raised when the specified indices span multiple chains but the operation can only be carried out on a single chain.

__init__

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

args
with_traceback()

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

class schrodinger.protein.sequence.StructureSequence(st, atoms)

Bases: schrodinger.structure._structure._AtomCollection

Class representing a sequence of protein residues.

residue

Returns residue iterator for all residues in the sequence

__init__(st, atoms)

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

__len__()

Return number of atoms.

atom

Iterate over all atoms. Also allows 1-based indexed access to the atoms.

extractStructure(copy_props=False)

Return a new Structure containing only the atoms associated with this substructure. Structure properties, including the title, are inherited only if copy_props is set to True.

getAtomIndices()

Return a list of atom indices for all atoms in this object.

Returns:List of atom indicies.
Return type:list of ints
getAtomList()

Deprecated. Use getAtomIndices() method instead.

structure

Return the parent Structure object for this atom collection.

temperature_factor

Average B (temperature) factor for all atoms that have it assigned. Setting this property will set the B factor to the given value for each atom.

schrodinger.protein.sequence.get_structure_sequences(st)

Iterates over all sequences in the given structure.

schrodinger.protein.sequence.find_generalized_pattern(sequence_list, pattern, validate_pattern=False)

Finds a generalized sequence pattern within specified sequences. NOTE: The search is performed in the forward direction only.

Parameters:
  • sequence_list – list of sequence dictionaries to search.
  • pattern (str) –

    Pattern defined using extended PROSITE syntax.

    • standard IUPAC one-letter codes are used for all amino acids
    • each element in a pattern is separated using ‘-‘ symbol
    • symbol ‘x’ is used for position where any amino acid is accepted
    • ambiguities are listed using the acceptable amino acids between square brackets, e.g. [ACT] means Ala, Cys or Thr
    • amino acids not accepted for a given position are indicated by listing them between curly brackets, e.g. {GP} means ‘not Gly and not Pro’
    • repetition is indicated using parentheses, e.g. A(3) means Ala-Ala-Ala, x(2,4) means between 2 to 4 any residues
    • the following lowercase characters can be used as additional flags:
      • ’x’ means any amino acid
      • ’a’ means acidic residue: [DE]
      • ’b’ means basic residue: [KR]
      • ’o’ means hydrophobic residue: [ACFILPWVY]
      • ’p’ means aromatic residue: [WYF]
      • ’s‘ means solvent exposed residue
      • ’h’ means helical residue
      • ’e’ means extended residue
      • ’f’ means flexible residue
    • Each position can optionally by followed by @<res_num> expression that will match the position with a given residue number.
    • Entire pattern can be followed by :<index> expression that defines a ‘hotspot’ in the pattern. When the hotspot is defined, only a single residue corresponding to (pattern_match_start+index-1) will be returned as a match. The index is 1-based and can be used to place the hotspot outside of the pattern (can also be a negative number).

    Pattern examples:

    • N-{P}-[ST] : Asn-X-Ser or Thr (X != Pro)
    • N[sf]-{P}[sf]-[ST][sf] : as above, but all residues flexible OR solvent exposed
    • Nsf-{P}sf-[ST]sf : as above, but all residues flexible AND solvent exposed
    • Ns{f} : Asn solvent exposed AND not in flexible region
    • N[s{f}] : Asn solvent exposed OR not in flexible region
    • [ab]{K}{s}f : acidic OR basic, with exception of Lys, flexible AND not solvent exposed
    • Ahe : Ala helical AND extended - no match possible
    • A[he] : Ala helical OR extended
    • A{he} : Ala coiled chain conformation (not helical nor extended)
    • [ST] : Ser OR Thr
    • ST : Ser AND Thr - no match possible
  • validate_pattern (boolean) – If True, the function will validate the pattern without performing the search (the sequences parameter will be ignored) and return True if the pattern is valid, or False otherwise. The default is False.
Return type:

list of lists of integer tuples or False if the pattern is invalid

Returns:

False if the specified input pattern was incorrect. Otherwise, it returns a list of lists of matches for each input sequence. Each match is a (start, end) tuple where start and end are matching sequence positions.

Converts a StructureSequence object to dictionary required by find_generalized_pattern function. Because the conversion can be time consuming, it should be done once per sequence.

Optionally a list of atom SASAs for each atom in the CT can be specified. If it’s not specified, it will get calculated by calling analyze.calculate_sasa_by_atom().

Parameters:
  • seq (StructureSequence) – StructureSequence object
  • sasa_by_atom (list) – list of atom SASAs
Return type:

dict

Returns:

Dictionary of sequence information

schrodinger.protein.sequence.find_pattern(seq, pattern)

Find pattern matches in a specified StructureSequence object. Returns a list of matching positions.

Parameters:
  • seq (StructureSequence) – StructureSequence object
  • pattern (string) – Sequence pattern. The syntax is described in find_generalized_pattern.
Return type:

list of lists of integer tuples or None

Returns:

None if the specified input pattern was incorrect. Otherwise, it returns a list of lists of matches for each residue position in the input structure. Each match is a (start, end) tuple where start and end are matching sequence positions. If ‘hotspot’ is specified then start = end.

schrodinger.protein.sequence.assign_residue_numbers(residues, start_res=None, end_res=None)

Assign residue numbers to the given residues based on the residues before and after

Parameters:
  • residues (list[residue.Residue]) – Residues that need numbering. Will be modified in-place.
  • start_res (residue.Residue or NoneType) – Previous residue. Pass None if the residues are N-terminal
  • end_res (residue.Residue or NoneType) – Next residue. Pass None if the residues are C-terminal
schrodinger.protein.sequence.gen_resnums_and_inscodes(start_resnum, start_inscode, end_resnum, end_inscode)

Create a list of all residue numbers/insertion code combinations possible between the given endpoints. If the ending residue number and insertion code are less than or equal to the starting residue number and insertion code, then an empty list will be returned.

Parameters:
  • start_resnum (int) – The starting residue number.
  • start_inscode (str) – The starting insertion code.
  • end_resnum (int) – The ending residue number.
  • end_inscode (str) – The ending insertion code.
Returns:

A list of residue numbers and insertion codes

Return type:

list[tuple[int, str]]

schrodinger.protein.sequence.get_pairwise_sequence_similarity(chain1, chain2, consider_gap=True, method='muscle')

Given two single chain sequences, align them, and return sequence similarity among them.

Parameters:
  • chain1 (structure._Chain) – The first sequence chain.
  • chain2 (structure._Chain) – The second sequence chain.
  • consider_gap (bool) – Whether or not to consider gaps in the alignment, default to true.
  • method (string) – Which alignment method to use (‘muscle’ or ‘clustalw’)
Returns:

Sequence similarity of the alignment of the two.

Return type:

float, between 0.0 and 1.0

schrodinger.protein.sequence.create_alignment_from_chains(chains)

Return ProteinAlignment object comprised of two chains

Parameters:chains (iterable(structure._Chain)) – Chains to be aligned
schrodinger.protein.sequence.align_alignment(aln, second_aln=None, method='muscle')

Perform alignment from an ProteinAlignment object

Parameters:
  • aln (ProteinAlignment) – Alignment data
  • method (string) – Which method/program to use
Returns:

Aligned sequences

Return type:

ProteinAlignment

schrodinger.protein.sequence.align_from_chains(chains, method='muscle')

Perform alignment on a series of chains

Parameters:
  • chains (iterable(structure._Chain)) – Chains to be aligned
  • method (string) – Which method/program to use (choices ‘muscle’, ‘clustalw’)
Returns:

Aligned sequences

Return type:

ProteinAlignment

schrodinger.protein.sequence.get_aligned_residues(st1, st2, method='muscle')

This generator will yield 2 structure._Residue objects - one from each structure - for each position in aligned sequences.

Parameters:
  • st1 (structure.Structure) – First structure.
  • st2 (structure.Structure) – Second structure
Returns:

Generates tuples of 2 residues that align at each position.

Return type:

generator(structure._Residue or None, structure._Residue or None)

Raises:

ValueError – if structures don’t have equivalent chains.

schrodinger.protein.sequence.get_aligned_structure_residues(sts, method='muscle')

This generator will yield 2 structure._Residue objects - one from each structure for each position in aligned sequences.

Parameters:sts (list(structure.Structure)) – Structures to align
Returns:Generates lists of residues that align at each position.
Return type:generator(list[structure._Residue or None])
schrodinger.protein.sequence.offset_indices(indices)

Offset insertion indices based on numbering before insertion to reflect numbering after insertion.

For example, [1, 1, 2, 3, 5, 8] would be changed to [1, 2, 4, 6, 9, 13]