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).

class schrodinger.protein.sequence.Sequence

Bases: object

__init__

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

class schrodinger.protein.sequence.SequenceProxy(seq)

Bases: schrodinger.models.json.JsonableClassMixin, schrodinger.protein.sequence.Sequence

A read-only wrapper for sequences. We use this to prevent users from directly modifying sequences which can corrupt undoability and residue anchoring.

MUTATION_METHODS = {'addGapsBeforeIndices', 'addGapsByIndices', 'append', 'extend', 'insert', 'mutate', 'removeAllGaps', 'removeElements', 'removeTerminalGaps', 'setStructure'}
__init__(seq)

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

__len__()
__contains__(item)
sequence_type

The class of the wrapped sequence.

Return type:type
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 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

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.

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
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 (residue.SequenceElement) – 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.SequenceElement

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

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

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
index(res)

Returns the index of the specified residue.

Parameters:res (schrodinger.structure._Residue) – The residue to find
Return type:int
Returns:The index of the residue
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)
getIdentity(reference, consider_gaps=True)

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

Parameters:
Returns:

The sequence identity score (between 0.0 and 1.0)

Return type:

float

getSimilarity(reference, consider_gaps=True)

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

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getConservation(reference, consider_gaps=True)

Return a float scoring the homology conservation between the sequence and a reference 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(reference)

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

Since the similarity with a gap will always be 0.0, there is no need to consider gaps.

Parameters:reference (schrodinger.protein.sequence.Sequence) – A sequence to compare against
Returns:The total sequence similarity score
Return type:float
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
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
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
iterResidues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(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))
insertElements(index, elements)

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

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
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.
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
removeAllGaps()

Remove gaps from the sequence

sanitize(start=0, end=None)

Remove gaps and unknown sequence elements from sequence

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.
clearAllCaching()

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

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

destroyed(self, QObject = None) [signal]

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

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

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

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

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

objectNameChanged(self, str) [signal]

parent(self) → QObject
property(self, str) → Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = -1) → str
class schrodinger.protein.sequence.AbstractSingleChainSequence(elements='', name='', origin=None, entry_id='', entry_name='', pdb_id='', chain='', structure_chain=None, title='')

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
disulfideBondsChanged
__init__(elements='', name='', origin=None, entry_id='', entry_name='', pdb_id='', chain='', structure_chain=None, title='')

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 iterable(str)) – An iterable of elements making up the sequence
  • name (basestring) – The name of the sequence
  • 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.
  • title (str) – The title for the sequence
Type:

str

Type:

str

Type:

str

Raises:

ValueError – If the unknown_res_type is None and an unrecognized character is encountered in the element list or elements is None

__len__()
__contains__(item)
origin
Returns:A piece of metadata indicating where the sequence came from
Rtype origin:Sequence.ORIGIN or None
getSummary()

Returns a friendly, readable summary of the sequence

Return type:basestring
Returns:A summary of the sequence
classmethod makeSeqElement(element)
Parameters:element (str or cls.ElementClass) – A sequence element or string representation thereof
Returns:sequence element
Return type:cls.ElementClass
Raises:ValueError – If an element is not in cls.alphabet and cls._unknown_res_type is not defined
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)
Return type:

Sequence

Returns:

A sequence

name
fullname
Returns:a formatted name + optional chain name for the sequence
Return type:str
index(res, ignore_gaps=False)

Returns the index of the specified residue

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

A Value error if the residue is not present or if the res is None

Return type:

int

Returns:

The index of the residue

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
insertElements(index, elements)

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

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
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.
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
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()
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))
visibility
AnnotationClass = None
ElementClass

alias of schrodinger.protein.residue.SequenceElement

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.
alphabet = {}
annotationTitleChanged
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
clearAllCaching()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

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

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

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

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

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(reference, consider_gaps=True)

Return a float scoring the homology conservation between the sequence and a reference 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(reference, consider_gaps=True)

Return a float scoring the identity between the sequence and a reference 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
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
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(reference, consider_gaps=True)

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

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(reference)

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

Since the similarity with a gap will always be 0.0, there is no need to consider gaps.

Parameters:reference (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)
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))
iterResidues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
killTimer(self, int)
lengthAboutToChange
lengthChanged
metaObject(self) → QMetaObject
moveToThread(self, QThread)
nameChanged
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
removeAllGaps()

Remove gaps from the sequence

removeEventFilter(self, QObject)
removeTerminalGaps()

Remove gaps from the end of the sequence

residuesAdded
residuesChanged
residuesRemoved
sanitize(start=0, end=None)

Remove gaps and unknown sequence elements from sequence

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>
structureChanged
thread(self) → QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = -1) → str
visibilityChanged
class schrodinger.protein.sequence.ProteinSequence(elements='', name='', origin=None, entry_id='', entry_name='', pdb_id='', chain='', structure_chain=None, title='')

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

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')}
__init__(elements='', name='', origin=None, entry_id='', entry_name='', pdb_id='', chain='', structure_chain=None, title='')

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 iterable(str)) – An iterable of elements making up the sequence
  • name (basestring) – The name of the sequence
  • entry_id (str) – An entry associated with the sequence, if any
  • entry_name (str) – An entry name associated with the sequence, if any
  • pdb_id (str) – 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.
  • title (str) – The title for the sequence
Raises:

ValueError – If the unknown_res_type is None and an unrecognized character is encountered in the element list

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

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(namedtuple(int, (int,int)))
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

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

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfideBondsChanged
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
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
getAnnotation(index, annotation)

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

Raises:ValueError – if the annotation is not available
getConservation(reference, consider_gaps=True)

Return a float scoring the homology conservation between the sequence and a reference 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(reference, consider_gaps=True)

Return a float scoring the identity between the sequence and a reference 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
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
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(reference, consider_gaps=True)

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

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(reference)

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

Since the similarity with a gap will always be 0.0, there is no need to consider gaps.

Parameters:reference (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
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)
Return type:

Sequence

Returns:

A sequence

getSummary()

Returns a friendly, readable summary of the sequence

Return type:basestring
Returns:A summary of the sequence
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.

hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
index(res, ignore_gaps=False)

Returns the index of the specified residue

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

A Value error if the residue is not present or if the res is None

Return type:

int

Returns:

The index of the residue

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

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

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))
iterResidues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
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
Raises:ValueError – If an element is not in cls.alphabet and cls._unknown_res_type is not defined
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
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

residuesAdded
residuesChanged
residuesRemoved
sanitize(start=0, end=None)

Remove gaps and unknown sequence elements from sequence

sender(self) → QObject
senderSignalIndex(self) → int
sequenceCopied
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
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
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
visibility
visibilityChanged
class schrodinger.protein.sequence.NucleicAcidSequence(elements='', name='', origin=None, entry_id='', entry_name='', pdb_id='', chain='', structure_chain=None, title='')

Bases: schrodinger.protein.sequence.ProteinSequence

AnnotationClass

alias of schrodinger.protein.annotation.NucleicAcidSequenceAnnotations

ElementClass

alias of schrodinger.protein.residue.Nucleotide

alphabet = {'1CC': NucleotideType('C', '1CC', 'Cytosine'), '1MA': NucleotideType('A', '1MA', 'Adenine'), '1MG': NucleotideType('G', '1MG', 'Guanine'), '2MG': NucleotideType('G', '2MG', 'Guanine'), '5FC': NucleotideType('C', '5FC', 'Cytosine'), '5HC': NucleotideType('C', '5HC', 'Cytosine'), '5MC': NucleotideType('C', '5MC', 'Cytosine'), '5MU': NucleotideType('U', '5MU', 'Uracil'), '6MA': NucleotideType('A', '6MA', 'Adenine'), '7MG': NucleotideType('G', '7MG', 'Guanine'), 'A': NucleotideType('A', 'A', 'Adenine'), 'ADP': NucleotideType('A', 'ADP', 'Adenine'), 'AMP': NucleotideType('A', 'AMP', 'Adenine'), 'ATP': NucleotideType('A', 'ATP', 'Adenine'), 'C': NucleotideType('C', 'C', 'Cytosine'), 'CDP': NucleotideType('C', 'CDP', 'Cytosine'), 'CMP': NucleotideType('C', 'CMP', 'Cytosine'), 'CTP': NucleotideType('C', 'CTP', 'Cytosine'), 'DA': NucleotideType('A', 'DA', 'Adenine'), 'DC': NucleotideType('C', 'DC', 'Cytosine'), 'DG': NucleotideType('G', 'DG', 'Guanine'), 'DI': ResidueType('DI', 'DI', 'Unknown'), 'DT': NucleotideType('T', 'DT', 'Thymine'), 'DU': NucleotideType('U', 'DU', 'Uracil'), 'G': NucleotideType('G', 'G', 'Guanine'), 'GDP': NucleotideType('G', 'GDP', 'Guanine'), 'GMP': NucleotideType('G', 'GMP', 'Guanine'), 'GTP': NucleotideType('G', 'GTP', 'Guanine'), 'H2U': NucleotideType('U', 'H2U', 'Uracil'), 'I': ResidueType('I', 'I', 'Unknown'), 'M2G': NucleotideType('G', 'M2G', 'Guanine'), 'OMC': NucleotideType('C', 'OMC', 'Cytosine'), 'OMG': NucleotideType('G', 'OMG', 'Guanine'), 'PSU': NucleotideType('Ψ', 'PSU', 'Uracil'), 'TDP': NucleotideType('T', 'TDP', 'Thymine'), 'TMP': NucleotideType('T', 'TMP', 'Thymine'), 'TTP': NucleotideType('T', 'TTP', 'Thymine'), 'U': NucleotideType('U', 'U', 'Uracil'), 'UDP': NucleotideType('U', 'UDP', 'Uracil'), 'UMP': NucleotideType('U', 'UMP', 'Uracil'), 'UTP': NucleotideType('U', 'UTP', 'Uracil'), 'YYG': ResidueType('X', 'YYG', 'Unknown')}
class ORIGIN

Bases: enum.Enum

An enumeration.

MAESTRO = 1
PYMOL = 2
__contains__(item)
__init__(elements='', name='', origin=None, entry_id='', entry_name='', pdb_id='', chain='', structure_chain=None, title='')

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 iterable(str)) – An iterable of elements making up the sequence
  • name (basestring) – The name of the sequence
  • entry_id (str) – An entry associated with the sequence, if any
  • entry_name (str) – An entry name associated with the sequence, if any
  • pdb_id (str) – 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.
  • title (str) – The title for the sequence
Raises:

ValueError – If the unknown_res_type is None and an unrecognized character is encountered in the element list

__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
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
childEvent(self, QChildEvent)
children(self) → object
clearAllCaching()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfideBondsChanged
disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.DisulfideBond)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
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
getAnnotation(index, annotation)

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

Raises:ValueError – if the annotation is not available
getConservation(reference, consider_gaps=True)

Return a float scoring the homology conservation between the sequence and a reference 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(reference, consider_gaps=True)

Return a float scoring the identity between the sequence and a reference 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
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
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(reference, consider_gaps=True)

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

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(reference)

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

Since the similarity with a gap will always be 0.0, there is no need to consider gaps.

Parameters:reference (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
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)
Return type:

Sequence

Returns:

A sequence

getSummary()

Returns a friendly, readable summary of the sequence

Return type:basestring
Returns:A summary of the sequence
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.

hasStructure()
Returns:Whether this sequence has an associated structure.
Return type:bool
index(res, ignore_gaps=False)

Returns the index of the specified residue

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

A Value error if the residue is not present or if the res is None

Return type:

int

Returns:

The index of the residue

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

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

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))
iterResidues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
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
Raises:ValueError – If an element is not in cls.alphabet and cls._unknown_res_type is not defined
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
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

residuesAdded
residuesChanged
residuesRemoved
sanitize(start=0, end=None)

Remove gaps and unknown sequence elements from sequence

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(namedtuple(int, (int,int)))
sender(self) → QObject
senderSignalIndex(self) → int
sequenceCopied
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
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
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
visibility
visibilityChanged
class schrodinger.protein.sequence.StructureSequence(st, atoms)

Bases: schrodinger.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.get_pairwise_sequence_similarity(chain1, chain2, consider_gap=True, method='clustalw')

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='clustalw')

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='clustalw')

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)

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.

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() → list

return a type’s method resolution order

class schrodinger.protein.sequence.CombinedChainProteinSequence(seqs)

Bases: 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__()
clearAllCaching()

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

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
fullname
chains
chain_offsets
disulfide_bonds
Returns:A sorted tuple of the valid disulfide bonds.
Return type:tuple(residue.CombinedChainDisulfideBond)
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
insertElements(index, elements)

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

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
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.
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.
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')}
annotationTitleChanged
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
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
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(reference, consider_gaps=True)

Return a float scoring the homology conservation between the sequence and a reference 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(reference, consider_gaps=True)

Return a float scoring the identity between the sequence and a reference 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
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
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(reference, consider_gaps=True)

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

Parameters:
Returns:

The sequence similarity score (between 0.0 and 1.0)

Return type:

float

getSimilarityScore(reference)

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

Since the similarity with a gap will always be 0.0, there is no need to consider gaps.

Parameters:reference (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)
hasStructure(*args, **kwargs)
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))
iterResidues()

Return an iterable of residues, ignoring gaps.

Returns:Iterable of residues
Return type:iter(Residue)
killTimer(self, int)
lengthAboutToChange
lengthChanged
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

origin
parent(self) → QObject
pdb_id
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

residuesAdded
residuesChanged
residuesRemoved
sanitize(start=0, end=None)

Remove gaps and unknown sequence elements from sequence

sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
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
thread(self) → QThread
timerEvent(self, QTimerEvent)
title
tr(self, str, disambiguation: str = None, n: int = -1) → str
visibility
visibilityChanged
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
index(res)

Returns the index of the specified residue

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

A Value error if the residue is not present or if the res is None

Return type:

int

Returns:

The index of the residue

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