schrodinger.protein.sequence module¶
Implementation of ProteinSequence, Sequence, and StructureSequence class.
StructureSequence allows iteration over all sequences in a given protein CT, and iteration over residues of each (in sequence order).
-
schrodinger.protein.sequence.
guess_seq_type
(res_names)¶ Takes an iterable of residue names and returns the appropriate sequence class
Parameters: res_names (Iterable(str)) – An iterable of residue names. Note that all residue names must be uppercase. Returns: The appropriate class for the input sequence Return type: Type[AbstractSingleChainSequence] Note that we use a pretty simple heuristic here.
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schrodinger.protein.sequence.
make_sequence
(elements, *args, **kwargs)¶ Guesses the appropriates Sequence type from the names of residues and returns an instance with those residues.
Parameters: elements (list(str)) – A list of strings to examine Return type: protein.Sequence Returns: An instance of the appropriate type
-
class
schrodinger.protein.sequence.
Sequence
¶ Bases:
object
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
-
class
schrodinger.protein.sequence.
AbstractSequence
(*args, **kwargs)¶ Bases:
schrodinger.protein.sequence.Sequence
,PyQt5.QtCore.QObject
A base class for single-chain and combined-chain biological sequences.
Variables: - ORIGIN (enum.Enum) – Possible sequence origins
- AnnotationClass (annotation.SequenceAnnotations) – Class to use for annotations
- ElementClass (Type[residue.Residue]) – Class to use for elements
- ALPHABET (dict(str, residue.ElementType)) – A mapping of string representations of elements to element types
- _gap_chars (tuple(str)) – A tuple of permissible gap characters in the element list; the first item will be used for serialization.
- _unknown_res_type (residue.ElementType) – The type for an unknown residue
- residuesChanged (QtCore.pyqtSignal) – A signal emitted when sequence residues are changed. Emitted with the indices of the first and last changed residues.
- lengthAboutToChange (QtCore.pyqtSignal) – A signal emitted when the sequence length is about to change. Emitted with the old and new lengths.
- lengthChanged (QtCore.pyqtSignal) – A signal emitted when the sequence length is changed. Emitted with the old and new lengths.
- nameChanged (QtCore.pyqtSignal) – A signal emitted when the sequence name is changed.
- visibilityChanged (QtCore.pyqtSignal) – A signal emitted when the visibility is changed.
- structureChanged (QtCore.pyqtSignal) – A signal emitted when the structure changes.
- annotationTitleChanged (QtCore.pyqtSignal) – A signal emitted when an annotation title is changed.
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AnnotationClass
= None¶
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ElementClass
¶ alias of
schrodinger.protein.residue.Residue
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ALPHABET
= {}¶
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residuesRemoved
¶
-
residuesAdded
¶
-
residuesChanged
¶
-
lengthAboutToChange
¶
-
lengthChanged
¶
-
nameChanged
¶
-
visibilityChanged
¶
-
structureChanged
¶
-
annotationTitleChanged
¶
-
pfamChanged
¶
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__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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residues
()¶ Return an iterable of residues, ignoring gaps.
Returns: Iterable of residues Return type: iter(Residue)
-
getNextResidue
(res)¶ Return the next residue in the sequence (ignoring gaps) or None if this is the last residue.
Parameters: res (schrodinger.protein.residue.Residue) – A given residue in the sequence Returns: The previous residue in the sequence Return type: schrodinger.protein.residue.Residue
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getPreviousResidue
(res)¶ Return the previous residue in the sequence (ignoring gaps) or None if this is the first residue.
Parameters: res (schrodinger.protein.residue.Residue) – A given residue in the sequence Returns: The previous residue in the sequence Return type: schrodinger.protein.residue.Residue
-
iterNeighbors
()¶ Return an iterable of three element tuples consisting of (prev_res, curr_res, next_res), ignoring gaps.
None is used for neighbors of first and last residues in the sequence, and does not indicate gaps here.
Returns: Iterable of 3-tuples, each element of the each tuple being either a schrodinger.protein.residue.Residue
or NoneReturn type: iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
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index
(res)¶ Returns the index of the specified residue.
Parameters: res (residue.Residue) – The residue to find Returns: The index of the residue Return type: int
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indices
(residues)¶ Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)
Parameters: res (Iterable(residue.Residue)) – The residues to find indices of Returns: The indices of the residues Return type: list[int]
-
getRun
(res)¶ For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.
Parameters: res (residue.AbstractSequenceElement) – Residue to get the run of Reuturn: Set of residue indices in the run Return type: set(int)
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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
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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
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getSubsequence
(start, end)¶ Return a sequence containing a subset of the elements in this one
Parameters: - start (int) – The index at which the subsequence should start
- end (int) – The index at which the subsequence should end (exclusive)
Returns: The requested subsequence
Return type:
-
removeElements
(eles)¶ Remove elements from the sequence.
Parameters: eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence. Raises: ValueError – If any of the given elements are not in the sequence.
-
gap_char
¶
-
getGaplessLength
()¶ Returns: Length of this sequence ignoring gaps Return type: int
-
getGaps
()¶ Return type: list(residue.Gap) Returns: The gaps in the sequence.
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addGapsByIndices
(gap_idxs)¶ Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see
addGapsBeforeIndices
.Parameters: gap_idxs (list(int)) – A list of gap indices
-
validateGapIndices
(gap_idxs)¶ Make sure that the specified gap indices are valid input for
addGapsByIndices
. If the indices are invalid, aValueError
will be raised. Indices are considered invalid if:- they refer to a position that’s more than one residue past the end of the sequence
- they are negative
Parameters: gap_idxs (list[int]) – The gap indices to validate
-
addGapsBeforeIndices
(indices)¶ Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see
addGapsByIndices
.Parameters: indices (list(int)) – A list of indices to insert gaps before.
-
removeTerminalGaps
()¶ Remove gaps from the end of the sequence
-
getTerminalGaps
()¶ Return terminal gaps.
Returns: A list of terminal gaps (in ascending index order) Return type: list(residue.Gap)
-
getGapCount
()¶ Returns: the number of gaps in the sequence Return type: int
-
removeAllGaps
()¶ Remove gaps from the sequence
-
annotations
¶
-
getAnnotation
(index, annotation)¶ Returns the annotation at the specified index or None for a gap.
Raises: ValueError – if the annotation is not available
-
clearAllCaching
()¶ This method should be implemented in subclasses that cache any data.
-
setPfam
(new_pfam, pfam_name)¶
-
clearPfam
()¶
-
hasPfam
()¶
-
hasStructure
()¶ Returns: Whether this sequence has an associated structure. Return type: bool
-
getStructure
()¶ Returns: The associated structure. Will return None if there is no associated structure. Return type: schrodinger.structure.Structure or NoneType
-
setStructure
(struc)¶ Set the associated structure. Can only be used on sequences with an associated structure.
Parameters: struc (schrodinger.structure.Structure) – The new structure for this sequence Raises: RuntimeError – If there’s no structure associated with this sequence object.
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getIdentity
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence identity score (between 0.0 and 1.0)
Return type: float
-
getSimilarity
(other, consider_gaps=True, only_consider=None)¶ Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence similarity score (between 0.0 and 1.0)
Return type: float
-
getConservation
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.
The homology criterion is based on “side chain chemistry” descriptor matching.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence conservation score (between 0.0 and 1.0)
Return type: float
-
getSimilarityScore
(other, only_consider=None)¶ Return the total score of similarity between the sequence and a other 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: other (schrodinger.protein.sequence.Sequence) – A sequence to compare against Returns: The total sequence similarity score Return type: float
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blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
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connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
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disconnectNotify
(self, QMetaMethod)¶
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dumpObjectInfo
(self)¶
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dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
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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
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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]
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inherits
(self, str) → bool¶
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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.
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receivers
(self, PYQT_SIGNAL) → int¶
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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¶
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staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
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tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
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class
schrodinger.protein.sequence.
AbstractSingleChainSequence
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=None)¶ Bases:
schrodinger.protein.sequence.AbstractSequence
Base class for single-chain biological sequences
Note: Protein-specific functionality should go in ProteinSequence.
Variables: sequenceCopied (QtCore.pyqtSignal) – A signal emitted when this sequence is copied. Emitted with the sequence being copied and the newly created copy. This signal is used by the structure model to make sure that the newly created copy is kept in sync with the structure. -
sequenceCopied
¶
-
secondaryStructureChanged
¶
-
__init__
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=None)¶ Make a sequence object from a list of strings and/or
self.ElementClass
Strings are converted to
self.ElementClass
using a mapping of strings to element types.Parameters: - elements (iterable(self.ElementClass or None) or iterable(str or None)) – An iterable of elements making up the sequence. `None`s are interpretted as gaps.
- name (str) – The name of the sequence (possibly shortened), used for display purposes. For a FASTA sequence, this should be a short identifier such as the Uniprot ID.
- origin (Sequence.ORIGIN or None) – A piece of metadata indicating where the sequence came from
- entry_id – An entry associated with the sequence, if any
- entry_name – An entry name associated with the sequence, if any
- pdb_id – An id associated with the sequence, if any
- chain (str) – The chain to which the sequence belongs
- structure_chain (str) – The chain of the structure this sequence
is associated with. This is usually the same as
chain
if the sequence has a structure but isn’t necessarily. - long_name (str) – The full name of the sequence. For a FASTA sequence, this should be the full FASTA header.
- resnums (Iterable(int)) – Residue numbers to assign to
elements
. If not given, residues will be numbered starting from one. Regardless of what’s given here, no residue numbering will occur ifelements
is an iterable ofElementClass
and any element already has a residue number set. If this iterable is shorter thanelements
, additional numbers will be generated by incrementing the last number present.
Type: str
Type: str
Type: str
-
__len__
()¶
-
__contains__
(item)¶
-
classmethod
makeSeqElement
(element)¶ Parameters: element (str or cls.ElementClass) – A sequence element or string representation thereof Returns: sequence element Return type: cls.ElementClass
-
classmethod
isValid
(elements)¶ Parameters: elements (iterable(str) or str) – An iterable of string representations of elements making up the sequence Returns: Tuple indicating whether valid and a set of invalid characters, if any Return type: tuple(bool, set(str))
-
name
¶
-
fullname
¶ Returns: a formatted name + optional chain name for the sequence Return type: str
-
visibility
¶
-
index
(res, ignore_gaps=False)¶ Returns the index of the specified residue
Parameters: - res (residue.Residue) – The residue to find
- ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises: A ValueError if the residue is not present
Return type: int
Returns: The index of the residue
-
indices
(residues, ignore_gaps=False)¶ Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)
Parameters: - res (Iterable(residue.Residue)) – The residues to find indices of
- ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns: The indices of the residues
Return type: list[int]
-
insertElements
(index, elements)¶ Insert a list of elements or sequence element into this sequence.
Parameters: - index (int) – The index at which to insert elements
- elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
-
mutate
(start, end, elements)¶ Mutate sequence elements starting at the given index to the provided elements.
Parameters: - start (int) – The index at which to start mutating
- end (int) – The index of the last mutated element (exclusive)
- elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
-
append
(element)¶ Appends an element to the sequence
Parameters: element – The element to append to this sequence Type: element: self.ElementClass or basestring
-
extend
(elements)¶ Extends the sequence with elements from an iterable
Parameters: elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
-
getSubsequence
(start, end)¶ Return a sequence containing a subset of the elements in this one
Parameters: - start (int) – The index at which the subsequence should start
- end (int) – The index at which the subsequence should end (exclusive)
Returns: The requested subsequence
Return type:
-
removeElements
(eles)¶ Remove elements from the sequence.
Parameters: eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence. Raises: ValueError – If any of the given elements are not in the sequence.
-
getGaplessLength
()¶ Returns: Length of this sequence ignoring gaps Return type: int
-
addGapsByIndices
(gap_idxs)¶ Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see
addGapsBeforeIndices
.Parameters: gap_idxs (list(int)) – A list of gap indices
-
setSSAPredictions
(pred)¶
-
setDisorderedRegionsPredictions
(pred)¶
-
setDomainArrangementPredictions
(pred)¶
-
setSolventAccessibilityPredictions
(pred)¶
-
deletePrediction
(prediction_type)¶
-
deleteAllPredictions
()¶
-
origin
¶ Returns: A piece of metadata indicating where the sequence came from Rtype origin: Sequence.ORIGIN
or None
-
hasStructure
()¶ Returns: Whether this sequence has an associated structure. Return type: bool
-
getStructure
()¶ Returns: The associated structure. Will return None if there is no associated structure. Return type: schrodinger.structure.Structure or NoneType
-
setStructure
(struc)¶ Set the associated structure. Can only be used on sequences with an associated structure.
Parameters: struc (schrodinger.structure.Structure) – The new structure for this sequence Raises: RuntimeError – If there’s no structure associated with this sequence object.
-
onStructureChanged
()¶
-
setResidueMap
(residue_map)¶ Set a new mapping between ResidueKey and structured residues.
Note: the only intended user of this method is
schrodinger.application.msv.seqio.StructureConverter
, where the ResidueKey is computed from thestructure._Residue
used to create theresidue.Residue
. If the sequence has a structure, the map can be generated usinggenerateResidueMap
.Parameters: residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
-
generateResidueMap
()¶ Create residue map based on current structured residues.
Note: this method requires
self.hasStructure()
to be True andself.entry_id
to be set. If this sequence was produced byschrodinger.application.msv.seqio.StructureConverter
, there should already be a residue map and this method does not need to be called.Raises: RuntimeError – If sequence has no structure or entry id
-
getResByKey
(res_key)¶ Parameters: res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode) Returns: Residue matching key or None if no matching residue is found Return type: residue.Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getStructureResForRes
(res)¶ Parameters: res (residue.Residue) – Residue to get structure residue for Returns: Structure residue or None if no matching residue is found Return type: schrodinger.structure._Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
ALPHABET
= {}¶
-
AnnotationClass
= None¶
-
ElementClass
¶ alias of
schrodinger.protein.residue.Residue
-
addGapsBeforeIndices
(indices)¶ Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see
addGapsByIndices
.Parameters: indices (list(int)) – A list of indices to insert gaps before.
-
annotationTitleChanged
¶
-
annotations
¶
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
clearAllCaching
()¶ This method should be implemented in subclasses that cache any data.
-
clearPfam
()¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
-
gap_char
¶
-
getAnnotation
(index, annotation)¶ Returns the annotation at the specified index or None for a gap.
Raises: ValueError – if the annotation is not available
-
getConservation
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.
The homology criterion is based on “side chain chemistry” descriptor matching.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence conservation score (between 0.0 and 1.0)
Return type: float
-
getGapCount
()¶ Returns: the number of gaps in the sequence Return type: int
-
getGaps
()¶ Return type: list(residue.Gap) Returns: The gaps in the sequence.
-
getIdentity
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
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
(other, consider_gaps=True, only_consider=None)¶ Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence similarity score (between 0.0 and 1.0)
Return type: float
-
getSimilarityScore
(other, only_consider=None)¶ Return the total score of similarity between the sequence and a other 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: other (schrodinger.protein.sequence.Sequence) – A sequence to compare against Returns: The total sequence similarity score Return type: float
-
getTerminalGaps
()¶ Return terminal gaps.
Returns: A list of terminal gaps (in ascending index order) Return type: list(residue.Gap)
-
hasPfam
()¶
-
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 NoneReturn type: iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
-
killTimer
(self, int)¶
-
lengthAboutToChange
¶
-
lengthChanged
¶
-
metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
nameChanged
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
parent
(self) → QObject¶
-
pfamChanged
¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeAllGaps
()¶ Remove gaps from the sequence
-
removeEventFilter
(self, QObject)¶
-
removeTerminalGaps
()¶ Remove gaps from the end of the sequence
-
residues
()¶ Return an iterable of residues, ignoring gaps.
Returns: Iterable of residues Return type: iter(Residue)
-
residuesAdded
¶
-
residuesChanged
¶
-
residuesRemoved
¶
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setPfam
(new_pfam, pfam_name)¶
-
setProperty
(self, str, Any) → bool¶
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
structureChanged
¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
validateGapIndices
(gap_idxs)¶ Make sure that the specified gap indices are valid input for
addGapsByIndices
. If the indices are invalid, aValueError
will be raised. Indices are considered invalid if:- they refer to a position that’s more than one residue past the end of the sequence
- they are negative
Parameters: gap_idxs (list[int]) – The gap indices to validate
-
visibilityChanged
¶
-
-
class
schrodinger.protein.sequence.
AbstractProteinSequenceMixin
(*args, **kwargs)¶ Bases:
object
A mixin for code shared between split-chain and combined-chain protein sequences.
-
disulfideBondsCacheCleared
¶
-
predictionsChanged
¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
disulfide_bonds
¶ Returns: A sorted tuple of the valid disulfide bonds. Return type: tuple(residue.DisulfideBond)
-
secondary_structures
¶ A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.
Returns: A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure. Return type: list(_SecondaryStructure)
-
clearDisulfideBondsCache
()¶
-
hasDisorderedRegionsPredictions
()¶
-
hasDisulfideBondPredictions
()¶
-
hasDomainArrangementPredictions
()¶
-
hasSolventAccessibility
()¶
-
hasSSAPredictions
()¶
-
pred_secondary_structures
¶
-
-
class
schrodinger.protein.sequence.
ProteinSequence
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)¶ Bases:
schrodinger.models.json.JsonableClassMixin
,schrodinger.protein.sequence.AbstractProteinSequenceMixin
,schrodinger.protein.sequence.AbstractSingleChainSequence
-
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=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)¶ See
AbstractSingleChainSequence
for additional documentation.Parameters: - disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via disulfide bonds.
- pred_disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via predicted disulfide bonds.
-
toJsonImplementation
()¶ Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.
Returns: A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
-
classmethod
fromJsonImplementation
(json_obj)¶ Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.
Parameters: json_dict (dict) – A dictionary loaded from a JSON string or file. Returns: An instance of the derived class. :rtype : cls
-
classmethod
adapter47007
(json_dict)¶
-
classmethod
adapter48002
(json_dict)¶
-
classmethod
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))
-
disulfide_bonds
¶ Returns: A sorted tuple of the valid disulfide bonds. Return type: tuple(residue.DisulfideBond)
-
pred_disulfide_bonds
¶
-
removeStructurelessResidues
(start=0, end=None)¶ Remove any structureless residues
Parameters: - start (int) – The index at which to start filtering structureless residues.
- end (int) – The index at which to end filtering
-
encodeForPatternSearch
(with_ss=False, with_flex=False, with_asa=False)¶ Convert to sequence dict expected by
find_generalized_pattern
.Parameters: - with_ss (bool) – Whether to include secondary structure information.
- with_flex (bool) – Whether to include flexibility information.
- with_asa (bool) – Whether to include accessible surface area information.
Return type: dict
Returns: dictionary of sequence data
-
clearAllCaching
()¶ This method should be implemented in subclasses that cache any data.
-
__contains__
(item)¶
-
__len__
()¶
-
addGapsBeforeIndices
(indices)¶ Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see
addGapsByIndices
.Parameters: indices (list(int)) – A list of indices to insert gaps before.
-
addGapsByIndices
(gap_idxs)¶ Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see
addGapsBeforeIndices
.Parameters: gap_idxs (list(int)) – A list of gap indices
-
annotationTitleChanged
¶
-
annotations
¶
-
append
(element)¶ Appends an element to the sequence
Parameters: element – The element to append to this sequence Type: element: self.ElementClass or basestring
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
clearDisulfideBondsCache
()¶
-
clearPfam
()¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteAllPredictions
()¶
-
deleteLater
(self)¶
-
deletePrediction
(prediction_type)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
disulfideBondsCacheCleared
¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
extend
(elements)¶ Extends the sequence with elements from an iterable
Parameters: elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
-
classmethod
fromJson
(json_obj)¶ A factory method which constructs a new object from a given dict loaded from a json string or file.
Parameters: json_obj (dict) – A json-loaded dictionary to create an object from. Returns: An instance of this class. :rtype : cls
-
fullname
¶ Returns: a formatted name + optional chain name for the sequence Return type: str
-
gap_char
¶
-
generateResidueMap
()¶ Create residue map based on current structured residues.
Note: this method requires
self.hasStructure()
to be True andself.entry_id
to be set. If this sequence was produced byschrodinger.application.msv.seqio.StructureConverter
, there should already be a residue map and this method does not need to be called.Raises: RuntimeError – If sequence has no structure or entry id
-
getAnnotation
(index, annotation)¶ Returns the annotation at the specified index or None for a gap.
Raises: ValueError – if the annotation is not available
-
getConservation
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.
The homology criterion is based on “side chain chemistry” descriptor matching.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence conservation score (between 0.0 and 1.0)
Return type: float
-
getGapCount
()¶ Returns: the number of gaps in the sequence Return type: int
-
getGaplessLength
()¶ Returns: Length of this sequence ignoring gaps Return type: int
-
getGaps
()¶ Return type: list(residue.Gap) Returns: The gaps in the sequence.
-
getIdentity
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
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
-
getResByKey
(res_key)¶ Parameters: res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode) Returns: Residue matching key or None if no matching residue is found Return type: residue.Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getRun
(res)¶ For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.
Parameters: res (residue.AbstractSequenceElement) – Residue to get the run of Reuturn: Set of residue indices in the run Return type: set(int)
-
getSimilarity
(other, consider_gaps=True, only_consider=None)¶ Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence similarity score (between 0.0 and 1.0)
Return type: float
-
getSimilarityScore
(other, only_consider=None)¶ Return the total score of similarity between the sequence and a other 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: other (schrodinger.protein.sequence.Sequence) – A sequence to compare against Returns: The total sequence similarity score Return type: float
-
getStructure
()¶ Returns: The associated structure. Will return None if there is no associated structure. Return type: schrodinger.structure.Structure or NoneType
-
getStructureResForRes
(res)¶ Parameters: res (residue.Residue) – Residue to get structure residue for Returns: Structure residue or None if no matching residue is found Return type: schrodinger.structure._Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getSubsequence
(start, end)¶ Return a sequence containing a subset of the elements in this one
Parameters: - start (int) – The index at which the subsequence should start
- end (int) – The index at which the subsequence should end (exclusive)
Returns: The requested subsequence
Return type:
-
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.
-
hasDisorderedRegionsPredictions
()¶
-
hasDisulfideBondPredictions
()¶
-
hasDomainArrangementPredictions
()¶
-
hasPfam
()¶
-
hasSSAPredictions
()¶
-
hasSolventAccessibility
()¶
-
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 (residue.Residue) – The residue to find
- ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises: A ValueError if the residue is not present
Return type: int
Returns: The index of the residue
-
indices
(residues, ignore_gaps=False)¶ Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)
Parameters: - res (Iterable(residue.Residue)) – The residues to find indices of
- ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns: The indices of the residues
Return type: list[int]
-
inherits
(self, str) → bool¶
-
insertElements
(index, elements)¶ Insert a list of elements or sequence element into this sequence.
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 NoneReturn type: iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
-
killTimer
(self, int)¶
-
lengthAboutToChange
¶
-
lengthChanged
¶
-
classmethod
makeSeqElement
(element)¶ Parameters: element (str or cls.ElementClass) – A sequence element or string representation thereof Returns: sequence element Return type: cls.ElementClass
-
metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
mutate
(start, end, elements)¶ Mutate sequence elements starting at the given index to the provided elements.
Parameters: - start (int) – The index at which to start mutating
- end (int) – The index of the last mutated element (exclusive)
- elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
-
name
¶
-
nameChanged
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
onStructureChanged
()¶
-
origin
¶ Returns: A piece of metadata indicating where the sequence came from Rtype origin: Sequence.ORIGIN
or None
-
parent
(self) → QObject¶
-
pfamChanged
¶
-
pred_secondary_structures
¶
-
predictionsChanged
¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeAllGaps
()¶ Remove gaps from the sequence
-
removeElements
(eles)¶ Remove elements from the sequence.
Parameters: eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence. Raises: ValueError – If any of the given elements are not in the sequence.
-
removeEventFilter
(self, QObject)¶
-
removeTerminalGaps
()¶ Remove gaps from the end of the sequence
-
residues
()¶ Return an iterable of residues, ignoring gaps.
Returns: Iterable of residues Return type: iter(Residue)
-
residuesAdded
¶
-
residuesChanged
¶
-
residuesRemoved
¶
-
secondaryStructureChanged
¶
-
secondary_structures
¶ A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.
Returns: A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure. Return type: list(_SecondaryStructure)
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
sequenceCopied
¶
-
setDisorderedRegionsPredictions
(pred)¶
-
setDomainArrangementPredictions
(pred)¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setPfam
(new_pfam, pfam_name)¶
-
setProperty
(self, str, Any) → bool¶
-
setResidueMap
(residue_map)¶ Set a new mapping between ResidueKey and structured residues.
Note: the only intended user of this method is
schrodinger.application.msv.seqio.StructureConverter
, where the ResidueKey is computed from thestructure._Residue
used to create theresidue.Residue
. If the sequence has a structure, the map can be generated usinggenerateResidueMap
.Parameters: residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
-
setSSAPredictions
(pred)¶
-
setSolventAccessibilityPredictions
(pred)¶
-
setStructure
(struc)¶ Set the associated structure. Can only be used on sequences with an associated structure.
Parameters: struc (schrodinger.structure.Structure) – The new structure for this sequence Raises: RuntimeError – If there’s no structure associated with this sequence object.
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
structureChanged
¶
-
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¶
-
validateGapIndices
(gap_idxs)¶ Make sure that the specified gap indices are valid input for
addGapsByIndices
. If the indices are invalid, aValueError
will be raised. Indices are considered invalid if:- they refer to a position that’s more than one residue past the end of the sequence
- they are negative
Parameters: gap_idxs (list[int]) – The gap indices to validate
-
visibility
¶
-
visibilityChanged
¶
-
-
class
schrodinger.protein.sequence.
NucleicAcidSequence
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)¶ Bases:
schrodinger.protein.sequence.ProteinSequence
-
AnnotationClass
¶ alias of
schrodinger.protein.annotation.NucleicAcidSequenceAnnotations
-
ElementClass
¶
-
ALPHABET
= None¶
-
getTranslation
()¶ Get a translated sequence. This method uses BioPython’s translate method to convert a nucleic acid sequence into an amino acid sequence
Returns: A translated protein sequence. The name and chain from the nucleic acid sequence are copied over Return type: ProteinSequence
-
__contains__
(item)¶
-
__init__
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)¶ See
AbstractSingleChainSequence
for additional documentation.Parameters: - disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via disulfide bonds.
- pred_disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via predicted disulfide bonds.
-
__len__
()¶
-
classmethod
adapter47007
(json_dict)¶
-
classmethod
adapter48002
(json_dict)¶
-
addGapsBeforeIndices
(indices)¶ Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see
addGapsByIndices
.Parameters: indices (list(int)) – A list of indices to insert gaps before.
-
addGapsByIndices
(gap_idxs)¶ Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see
addGapsBeforeIndices
.Parameters: gap_idxs (list(int)) – A list of gap indices
-
annotationTitleChanged
¶
-
annotations
¶
-
append
(element)¶ Appends an element to the sequence
Parameters: element – The element to append to this sequence Type: element: self.ElementClass or basestring
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
clearAllCaching
()¶ This method should be implemented in subclasses that cache any data.
-
clearDisulfideBondsCache
()¶
-
clearPfam
()¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteAllPredictions
()¶
-
deleteLater
(self)¶
-
deletePrediction
(prediction_type)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
disulfideBondsCacheCleared
¶
-
disulfide_bonds
¶ Returns: A sorted tuple of the valid disulfide bonds. Return type: tuple(residue.DisulfideBond)
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
encodeForPatternSearch
(with_ss=False, with_flex=False, with_asa=False)¶ Convert to sequence dict expected by
find_generalized_pattern
.Parameters: - with_ss (bool) – Whether to include secondary structure information.
- with_flex (bool) – Whether to include flexibility information.
- with_asa (bool) – Whether to include accessible surface area information.
Return type: dict
Returns: dictionary of sequence data
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
extend
(elements)¶ Extends the sequence with elements from an iterable
Parameters: elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
-
classmethod
fromJson
(json_obj)¶ A factory method which constructs a new object from a given dict loaded from a json string or file.
Parameters: json_obj (dict) – A json-loaded dictionary to create an object from. Returns: An instance of this class. :rtype : cls
-
classmethod
fromJsonImplementation
(json_obj)¶ Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.
Parameters: json_dict (dict) – A dictionary loaded from a JSON string or file. Returns: An instance of the derived class. :rtype : cls
-
fullname
¶ Returns: a formatted name + optional chain name for the sequence Return type: str
-
gap_char
¶
-
generateResidueMap
()¶ Create residue map based on current structured residues.
Note: this method requires
self.hasStructure()
to be True andself.entry_id
to be set. If this sequence was produced byschrodinger.application.msv.seqio.StructureConverter
, there should already be a residue map and this method does not need to be called.Raises: RuntimeError – If sequence has no structure or entry id
-
getAnnotation
(index, annotation)¶ Returns the annotation at the specified index or None for a gap.
Raises: ValueError – if the annotation is not available
-
getConservation
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.
The homology criterion is based on “side chain chemistry” descriptor matching.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence conservation score (between 0.0 and 1.0)
Return type: float
-
getGapCount
()¶ Returns: the number of gaps in the sequence Return type: int
-
getGaplessLength
()¶ Returns: Length of this sequence ignoring gaps Return type: int
-
getGaps
()¶ Return type: list(residue.Gap) Returns: The gaps in the sequence.
-
getIdentity
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
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
-
getResByKey
(res_key)¶ Parameters: res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode) Returns: Residue matching key or None if no matching residue is found Return type: residue.Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getRun
(res)¶ For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.
Parameters: res (residue.AbstractSequenceElement) – Residue to get the run of Reuturn: Set of residue indices in the run Return type: set(int)
-
getSimilarity
(other, consider_gaps=True, only_consider=None)¶ Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence similarity score (between 0.0 and 1.0)
Return type: float
-
getSimilarityScore
(other, only_consider=None)¶ Return the total score of similarity between the sequence and a other 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: other (schrodinger.protein.sequence.Sequence) – A sequence to compare against Returns: The total sequence similarity score Return type: float
-
getStructure
()¶ Returns: The associated structure. Will return None if there is no associated structure. Return type: schrodinger.structure.Structure or NoneType
-
getStructureResForRes
(res)¶ Parameters: res (residue.Residue) – Residue to get structure residue for Returns: Structure residue or None if no matching residue is found Return type: schrodinger.structure._Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getSubsequence
(start, end)¶ Return a sequence containing a subset of the elements in this one
Parameters: - start (int) – The index at which the subsequence should start
- end (int) – The index at which the subsequence should end (exclusive)
Returns: The requested subsequence
Return type:
-
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.
-
hasDisorderedRegionsPredictions
()¶
-
hasDisulfideBondPredictions
()¶
-
hasDomainArrangementPredictions
()¶
-
hasPfam
()¶
-
hasSSAPredictions
()¶
-
hasSolventAccessibility
()¶
-
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 (residue.Residue) – The residue to find
- ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises: A ValueError if the residue is not present
Return type: int
Returns: The index of the residue
-
indices
(residues, ignore_gaps=False)¶ Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)
Parameters: - res (Iterable(residue.Residue)) – The residues to find indices of
- ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns: The indices of the residues
Return type: list[int]
-
inherits
(self, str) → bool¶
-
insertElements
(index, elements)¶ Insert a list of elements or sequence element into this sequence.
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 NoneReturn type: iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
-
killTimer
(self, int)¶
-
lengthAboutToChange
¶
-
lengthChanged
¶
-
classmethod
makeSeqElement
(element)¶ Parameters: element (str or cls.ElementClass) – A sequence element or string representation thereof Returns: sequence element Return type: cls.ElementClass
-
metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
mutate
(start, end, elements)¶ Mutate sequence elements starting at the given index to the provided elements.
Parameters: - start (int) – The index at which to start mutating
- end (int) – The index of the last mutated element (exclusive)
- elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
-
name
¶
-
nameChanged
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
onStructureChanged
()¶
-
origin
¶ Returns: A piece of metadata indicating where the sequence came from Rtype origin: Sequence.ORIGIN
or None
-
parent
(self) → QObject¶
-
pfamChanged
¶
-
pred_disulfide_bonds
¶
-
pred_secondary_structures
¶
-
predictionsChanged
¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeAllGaps
()¶ Remove gaps from the sequence
-
removeElements
(eles)¶ Remove elements from the sequence.
Parameters: eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence. Raises: ValueError – If any of the given elements are not in the sequence.
-
removeEventFilter
(self, QObject)¶
-
removeStructurelessResidues
(start=0, end=None)¶ Remove any structureless residues
Parameters: - start (int) – The index at which to start filtering structureless residues.
- end (int) – The index at which to end filtering
-
removeTerminalGaps
()¶ Remove gaps from the end of the sequence
-
residues
()¶ Return an iterable of residues, ignoring gaps.
Returns: Iterable of residues Return type: iter(Residue)
-
residuesAdded
¶
-
residuesChanged
¶
-
residuesRemoved
¶
-
secondaryStructureChanged
¶
-
secondary_structures
¶ A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.
Returns: A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure. Return type: list(_SecondaryStructure)
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
sequenceCopied
¶
-
setDisorderedRegionsPredictions
(pred)¶
-
setDomainArrangementPredictions
(pred)¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setPfam
(new_pfam, pfam_name)¶
-
setProperty
(self, str, Any) → bool¶
-
setResidueMap
(residue_map)¶ Set a new mapping between ResidueKey and structured residues.
Note: the only intended user of this method is
schrodinger.application.msv.seqio.StructureConverter
, where the ResidueKey is computed from thestructure._Residue
used to create theresidue.Residue
. If the sequence has a structure, the map can be generated usinggenerateResidueMap
.Parameters: residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
-
setSSAPredictions
(pred)¶
-
setSolventAccessibilityPredictions
(pred)¶
-
setStructure
(struc)¶ Set the associated structure. Can only be used on sequences with an associated structure.
Parameters: struc (schrodinger.structure.Structure) – The new structure for this sequence Raises: RuntimeError – If there’s no structure associated with this sequence object.
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
structureChanged
¶
-
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¶
-
validateGapIndices
(gap_idxs)¶ Make sure that the specified gap indices are valid input for
addGapsByIndices
. If the indices are invalid, aValueError
will be raised. Indices are considered invalid if:- they refer to a position that’s more than one residue past the end of the sequence
- they are negative
Parameters: gap_idxs (list[int]) – The gap indices to validate
-
visibility
¶
-
visibilityChanged
¶
-
-
class
schrodinger.protein.sequence.
DNASequence
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)¶ Bases:
schrodinger.protein.sequence.NucleicAcidSequence
-
ALPHABET
= {'A': NucleotideType('A', 'DA', 'Adenine'), 'C': NucleotideType('C', 'DC', 'Cytosine'), 'DA': NucleotideType('A', 'DA', 'Adenine'), 'DC': NucleotideType('C', 'DC', 'Cytosine'), 'DG': NucleotideType('G', 'DG', 'Guanine'), 'DT': NucleotideType('T', 'DT', 'Thymine'), 'G': NucleotideType('G', 'DG', 'Guanine'), 'T': NucleotideType('T', 'DT', 'Thymine')}¶
-
AnnotationClass
¶ alias of
schrodinger.protein.annotation.NucleicAcidSequenceAnnotations
-
ElementClass
¶
-
__contains__
(item)¶
-
__init__
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)¶ See
AbstractSingleChainSequence
for additional documentation.Parameters: - disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via disulfide bonds.
- pred_disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via predicted disulfide bonds.
-
__len__
()¶
-
classmethod
adapter47007
(json_dict)¶
-
classmethod
adapter48002
(json_dict)¶
-
addGapsBeforeIndices
(indices)¶ Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see
addGapsByIndices
.Parameters: indices (list(int)) – A list of indices to insert gaps before.
-
addGapsByIndices
(gap_idxs)¶ Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see
addGapsBeforeIndices
.Parameters: gap_idxs (list(int)) – A list of gap indices
-
annotationTitleChanged
¶
-
annotations
¶
-
append
(element)¶ Appends an element to the sequence
Parameters: element – The element to append to this sequence Type: element: self.ElementClass or basestring
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
clearAllCaching
()¶ This method should be implemented in subclasses that cache any data.
-
clearDisulfideBondsCache
()¶
-
clearPfam
()¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteAllPredictions
()¶
-
deleteLater
(self)¶
-
deletePrediction
(prediction_type)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
disulfideBondsCacheCleared
¶
-
disulfide_bonds
¶ Returns: A sorted tuple of the valid disulfide bonds. Return type: tuple(residue.DisulfideBond)
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
encodeForPatternSearch
(with_ss=False, with_flex=False, with_asa=False)¶ Convert to sequence dict expected by
find_generalized_pattern
.Parameters: - with_ss (bool) – Whether to include secondary structure information.
- with_flex (bool) – Whether to include flexibility information.
- with_asa (bool) – Whether to include accessible surface area information.
Return type: dict
Returns: dictionary of sequence data
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
extend
(elements)¶ Extends the sequence with elements from an iterable
Parameters: elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
-
classmethod
fromJson
(json_obj)¶ A factory method which constructs a new object from a given dict loaded from a json string or file.
Parameters: json_obj (dict) – A json-loaded dictionary to create an object from. Returns: An instance of this class. :rtype : cls
-
classmethod
fromJsonImplementation
(json_obj)¶ Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.
Parameters: json_dict (dict) – A dictionary loaded from a JSON string or file. Returns: An instance of the derived class. :rtype : cls
-
fullname
¶ Returns: a formatted name + optional chain name for the sequence Return type: str
-
gap_char
¶
-
generateResidueMap
()¶ Create residue map based on current structured residues.
Note: this method requires
self.hasStructure()
to be True andself.entry_id
to be set. If this sequence was produced byschrodinger.application.msv.seqio.StructureConverter
, there should already be a residue map and this method does not need to be called.Raises: RuntimeError – If sequence has no structure or entry id
-
getAnnotation
(index, annotation)¶ Returns the annotation at the specified index or None for a gap.
Raises: ValueError – if the annotation is not available
-
getConservation
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.
The homology criterion is based on “side chain chemistry” descriptor matching.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence conservation score (between 0.0 and 1.0)
Return type: float
-
getGapCount
()¶ Returns: the number of gaps in the sequence Return type: int
-
getGaplessLength
()¶ Returns: Length of this sequence ignoring gaps Return type: int
-
getGaps
()¶ Return type: list(residue.Gap) Returns: The gaps in the sequence.
-
getIdentity
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
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
-
getResByKey
(res_key)¶ Parameters: res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode) Returns: Residue matching key or None if no matching residue is found Return type: residue.Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getRun
(res)¶ For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.
Parameters: res (residue.AbstractSequenceElement) – Residue to get the run of Reuturn: Set of residue indices in the run Return type: set(int)
-
getSimilarity
(other, consider_gaps=True, only_consider=None)¶ Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence similarity score (between 0.0 and 1.0)
Return type: float
-
getSimilarityScore
(other, only_consider=None)¶ Return the total score of similarity between the sequence and a other 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: other (schrodinger.protein.sequence.Sequence) – A sequence to compare against Returns: The total sequence similarity score Return type: float
-
getStructure
()¶ Returns: The associated structure. Will return None if there is no associated structure. Return type: schrodinger.structure.Structure or NoneType
-
getStructureResForRes
(res)¶ Parameters: res (residue.Residue) – Residue to get structure residue for Returns: Structure residue or None if no matching residue is found Return type: schrodinger.structure._Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getSubsequence
(start, end)¶ Return a sequence containing a subset of the elements in this one
Parameters: - start (int) – The index at which the subsequence should start
- end (int) – The index at which the subsequence should end (exclusive)
Returns: The requested subsequence
Return type:
-
getTerminalGaps
()¶ Return terminal gaps.
Returns: A list of terminal gaps (in ascending index order) Return type: list(residue.Gap)
-
getTranslation
()¶ Get a translated sequence. This method uses BioPython’s translate method to convert a nucleic acid sequence into an amino acid sequence
Returns: A translated protein sequence. The name and chain from the nucleic acid sequence are copied over Return type: ProteinSequence
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
hasDisorderedRegionsPredictions
()¶
-
hasDisulfideBondPredictions
()¶
-
hasDomainArrangementPredictions
()¶
-
hasPfam
()¶
-
hasSSAPredictions
()¶
-
hasSolventAccessibility
()¶
-
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 (residue.Residue) – The residue to find
- ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises: A ValueError if the residue is not present
Return type: int
Returns: The index of the residue
-
indices
(residues, ignore_gaps=False)¶ Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)
Parameters: - res (Iterable(residue.Residue)) – The residues to find indices of
- ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns: The indices of the residues
Return type: list[int]
-
inherits
(self, str) → bool¶
-
insertElements
(index, elements)¶ Insert a list of elements or sequence element into this sequence.
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 NoneReturn type: iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
-
killTimer
(self, int)¶
-
lengthAboutToChange
¶
-
lengthChanged
¶
-
classmethod
makeSeqElement
(element)¶ Parameters: element (str or cls.ElementClass) – A sequence element or string representation thereof Returns: sequence element Return type: cls.ElementClass
-
metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
mutate
(start, end, elements)¶ Mutate sequence elements starting at the given index to the provided elements.
Parameters: - start (int) – The index at which to start mutating
- end (int) – The index of the last mutated element (exclusive)
- elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
-
name
¶
-
nameChanged
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
onStructureChanged
()¶
-
origin
¶ Returns: A piece of metadata indicating where the sequence came from Rtype origin: Sequence.ORIGIN
or None
-
parent
(self) → QObject¶
-
pfamChanged
¶
-
pred_disulfide_bonds
¶
-
pred_secondary_structures
¶
-
predictionsChanged
¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeAllGaps
()¶ Remove gaps from the sequence
-
removeElements
(eles)¶ Remove elements from the sequence.
Parameters: eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence. Raises: ValueError – If any of the given elements are not in the sequence.
-
removeEventFilter
(self, QObject)¶
-
removeStructurelessResidues
(start=0, end=None)¶ Remove any structureless residues
Parameters: - start (int) – The index at which to start filtering structureless residues.
- end (int) – The index at which to end filtering
-
removeTerminalGaps
()¶ Remove gaps from the end of the sequence
-
residues
()¶ Return an iterable of residues, ignoring gaps.
Returns: Iterable of residues Return type: iter(Residue)
-
residuesAdded
¶
-
residuesChanged
¶
-
residuesRemoved
¶
-
secondaryStructureChanged
¶
-
secondary_structures
¶ A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.
Returns: A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure. Return type: list(_SecondaryStructure)
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
sequenceCopied
¶
-
setDisorderedRegionsPredictions
(pred)¶
-
setDomainArrangementPredictions
(pred)¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setPfam
(new_pfam, pfam_name)¶
-
setProperty
(self, str, Any) → bool¶
-
setResidueMap
(residue_map)¶ Set a new mapping between ResidueKey and structured residues.
Note: the only intended user of this method is
schrodinger.application.msv.seqio.StructureConverter
, where the ResidueKey is computed from thestructure._Residue
used to create theresidue.Residue
. If the sequence has a structure, the map can be generated usinggenerateResidueMap
.Parameters: residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
-
setSSAPredictions
(pred)¶
-
setSolventAccessibilityPredictions
(pred)¶
-
setStructure
(struc)¶ Set the associated structure. Can only be used on sequences with an associated structure.
Parameters: struc (schrodinger.structure.Structure) – The new structure for this sequence Raises: RuntimeError – If there’s no structure associated with this sequence object.
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
structureChanged
¶
-
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¶
-
validateGapIndices
(gap_idxs)¶ Make sure that the specified gap indices are valid input for
addGapsByIndices
. If the indices are invalid, aValueError
will be raised. Indices are considered invalid if:- they refer to a position that’s more than one residue past the end of the sequence
- they are negative
Parameters: gap_idxs (list[int]) – The gap indices to validate
-
visibility
¶
-
visibilityChanged
¶
-
-
class
schrodinger.protein.sequence.
RNASequence
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)¶ Bases:
schrodinger.protein.sequence.NucleicAcidSequence
-
ALPHABET
= {'A': NucleotideType('A', 'A', 'Adenine'), 'C': NucleotideType('C', 'C', 'Cytosine'), 'G': NucleotideType('G', 'G', 'Guanine'), 'U': NucleotideType('U', 'U', 'Uracil')}¶
-
AnnotationClass
¶ alias of
schrodinger.protein.annotation.NucleicAcidSequenceAnnotations
-
ElementClass
¶
-
__contains__
(item)¶
-
__init__
(elements='', name='', origin=None, entry_id=None, entry_name='', pdb_id='', chain='', structure_chain=None, long_name='', resnums=(), disulfide_bonds=None, pred_disulfide_bonds=None)¶ See
AbstractSingleChainSequence
for additional documentation.Parameters: - disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via disulfide bonds.
- pred_disulfide_bonds (Iterable(tuple(int, int))) – A list of pairs of residue indices to link via predicted disulfide bonds.
-
__len__
()¶
-
classmethod
adapter47007
(json_dict)¶
-
classmethod
adapter48002
(json_dict)¶
-
addGapsBeforeIndices
(indices)¶ Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see
addGapsByIndices
.Parameters: indices (list(int)) – A list of indices to insert gaps before.
-
addGapsByIndices
(gap_idxs)¶ Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see
addGapsBeforeIndices
.Parameters: gap_idxs (list(int)) – A list of gap indices
-
annotationTitleChanged
¶
-
annotations
¶
-
append
(element)¶ Appends an element to the sequence
Parameters: element – The element to append to this sequence Type: element: self.ElementClass or basestring
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
clearAllCaching
()¶ This method should be implemented in subclasses that cache any data.
-
clearDisulfideBondsCache
()¶
-
clearPfam
()¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteAllPredictions
()¶
-
deleteLater
(self)¶
-
deletePrediction
(prediction_type)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
disulfideBondsCacheCleared
¶
-
disulfide_bonds
¶ Returns: A sorted tuple of the valid disulfide bonds. Return type: tuple(residue.DisulfideBond)
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
encodeForPatternSearch
(with_ss=False, with_flex=False, with_asa=False)¶ Convert to sequence dict expected by
find_generalized_pattern
.Parameters: - with_ss (bool) – Whether to include secondary structure information.
- with_flex (bool) – Whether to include flexibility information.
- with_asa (bool) – Whether to include accessible surface area information.
Return type: dict
Returns: dictionary of sequence data
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
extend
(elements)¶ Extends the sequence with elements from an iterable
Parameters: elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
-
classmethod
fromJson
(json_obj)¶ A factory method which constructs a new object from a given dict loaded from a json string or file.
Parameters: json_obj (dict) – A json-loaded dictionary to create an object from. Returns: An instance of this class. :rtype : cls
-
classmethod
fromJsonImplementation
(json_obj)¶ Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.
Parameters: json_dict (dict) – A dictionary loaded from a JSON string or file. Returns: An instance of the derived class. :rtype : cls
-
fullname
¶ Returns: a formatted name + optional chain name for the sequence Return type: str
-
gap_char
¶
-
generateResidueMap
()¶ Create residue map based on current structured residues.
Note: this method requires
self.hasStructure()
to be True andself.entry_id
to be set. If this sequence was produced byschrodinger.application.msv.seqio.StructureConverter
, there should already be a residue map and this method does not need to be called.Raises: RuntimeError – If sequence has no structure or entry id
-
getAnnotation
(index, annotation)¶ Returns the annotation at the specified index or None for a gap.
Raises: ValueError – if the annotation is not available
-
getConservation
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.
The homology criterion is based on “side chain chemistry” descriptor matching.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence conservation score (between 0.0 and 1.0)
Return type: float
-
getGapCount
()¶ Returns: the number of gaps in the sequence Return type: int
-
getGaplessLength
()¶ Returns: Length of this sequence ignoring gaps Return type: int
-
getGaps
()¶ Return type: list(residue.Gap) Returns: The gaps in the sequence.
-
getIdentity
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
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
-
getResByKey
(res_key)¶ Parameters: res_key (residue.ResidueKey) – Residue key: (entry_id, chain, resnum, inscode) Returns: Residue matching key or None if no matching residue is found Return type: residue.Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getRun
(res)¶ For a given residue or gap, return a set of all adjacent element indices in the sequence that are also residues or gaps.
Parameters: res (residue.AbstractSequenceElement) – Residue to get the run of Reuturn: Set of residue indices in the run Return type: set(int)
-
getSimilarity
(other, consider_gaps=True, only_consider=None)¶ Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence similarity score (between 0.0 and 1.0)
Return type: float
-
getSimilarityScore
(other, only_consider=None)¶ Return the total score of similarity between the sequence and a other 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: other (schrodinger.protein.sequence.Sequence) – A sequence to compare against Returns: The total sequence similarity score Return type: float
-
getStructure
()¶ Returns: The associated structure. Will return None if there is no associated structure. Return type: schrodinger.structure.Structure or NoneType
-
getStructureResForRes
(res)¶ Parameters: res (residue.Residue) – Residue to get structure residue for Returns: Structure residue or None if no matching residue is found Return type: schrodinger.structure._Residue or NoneType Raises: RuntimeError – If sequence has no structure
-
getSubsequence
(start, end)¶ Return a sequence containing a subset of the elements in this one
Parameters: - start (int) – The index at which the subsequence should start
- end (int) – The index at which the subsequence should end (exclusive)
Returns: The requested subsequence
Return type:
-
getTerminalGaps
()¶ Return terminal gaps.
Returns: A list of terminal gaps (in ascending index order) Return type: list(residue.Gap)
-
getTranslation
()¶ Get a translated sequence. This method uses BioPython’s translate method to convert a nucleic acid sequence into an amino acid sequence
Returns: A translated protein sequence. The name and chain from the nucleic acid sequence are copied over Return type: ProteinSequence
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
hasDisorderedRegionsPredictions
()¶
-
hasDisulfideBondPredictions
()¶
-
hasDomainArrangementPredictions
()¶
-
hasPfam
()¶
-
hasSSAPredictions
()¶
-
hasSolventAccessibility
()¶
-
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 (residue.Residue) – The residue to find
- ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises: A ValueError if the residue is not present
Return type: int
Returns: The index of the residue
-
indices
(residues, ignore_gaps=False)¶ Returns the indices of all specified residues. Note that there is no guarantee that the returned integers will be in the same order as the input residues. (For combined-chain sequences, it’s highly likely that they won’t be.)
Parameters: - res (Iterable(residue.Residue)) – The residues to find indices of
- ignore_gaps (bool) – Whether the indices returned should ignore gaps in the sequence or not.
Returns: The indices of the residues
Return type: list[int]
-
inherits
(self, str) → bool¶
-
insertElements
(index, elements)¶ Insert a list of elements or sequence element into this sequence.
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 NoneReturn type: iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
-
killTimer
(self, int)¶
-
lengthAboutToChange
¶
-
lengthChanged
¶
-
classmethod
makeSeqElement
(element)¶ Parameters: element (str or cls.ElementClass) – A sequence element or string representation thereof Returns: sequence element Return type: cls.ElementClass
-
metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
mutate
(start, end, elements)¶ Mutate sequence elements starting at the given index to the provided elements.
Parameters: - start (int) – The index at which to start mutating
- end (int) – The index of the last mutated element (exclusive)
- elements (iterable(self.ElementClass) or iterable(str)) – The elements to which to mutate the sequence
-
name
¶
-
nameChanged
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
onStructureChanged
()¶
-
origin
¶ Returns: A piece of metadata indicating where the sequence came from Rtype origin: Sequence.ORIGIN
or None
-
parent
(self) → QObject¶
-
pfamChanged
¶
-
pred_disulfide_bonds
¶
-
pred_secondary_structures
¶
-
predictionsChanged
¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeAllGaps
()¶ Remove gaps from the sequence
-
removeElements
(eles)¶ Remove elements from the sequence.
Parameters: eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence. Raises: ValueError – If any of the given elements are not in the sequence.
-
removeEventFilter
(self, QObject)¶
-
removeStructurelessResidues
(start=0, end=None)¶ Remove any structureless residues
Parameters: - start (int) – The index at which to start filtering structureless residues.
- end (int) – The index at which to end filtering
-
removeTerminalGaps
()¶ Remove gaps from the end of the sequence
-
residues
()¶ Return an iterable of residues, ignoring gaps.
Returns: Iterable of residues Return type: iter(Residue)
-
residuesAdded
¶
-
residuesChanged
¶
-
residuesRemoved
¶
-
secondaryStructureChanged
¶
-
secondary_structures
¶ A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.
Returns: A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure. Return type: list(_SecondaryStructure)
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
sequenceCopied
¶
-
setDisorderedRegionsPredictions
(pred)¶
-
setDomainArrangementPredictions
(pred)¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setPfam
(new_pfam, pfam_name)¶
-
setProperty
(self, str, Any) → bool¶
-
setResidueMap
(residue_map)¶ Set a new mapping between ResidueKey and structured residues.
Note: the only intended user of this method is
schrodinger.application.msv.seqio.StructureConverter
, where the ResidueKey is computed from thestructure._Residue
used to create theresidue.Residue
. If the sequence has a structure, the map can be generated usinggenerateResidueMap
.Parameters: residue_map (dict(residue.ResidueKey, residue.Residue)) – Mapping between residue key and Residue
-
setSSAPredictions
(pred)¶
-
setSolventAccessibilityPredictions
(pred)¶
-
setStructure
(struc)¶ Set the associated structure. Can only be used on sequences with an associated structure.
Parameters: struc (schrodinger.structure.Structure) – The new structure for this sequence Raises: RuntimeError – If there’s no structure associated with this sequence object.
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
structureChanged
¶
-
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¶
-
validateGapIndices
(gap_idxs)¶ Make sure that the specified gap indices are valid input for
addGapsByIndices
. If the indices are invalid, aValueError
will be raised. Indices are considered invalid if:- they refer to a position that’s more than one residue past the end of the sequence
- they are negative
Parameters: gap_idxs (list[int]) – The gap indices to validate
-
visibility
¶
-
visibilityChanged
¶
-
-
class
schrodinger.protein.sequence.
CombinedChainSequenceMeta
¶ Bases:
schrodinger.application.msv.utils.DocstringWrapperMetaClass
,sip.wrappertype
The metaclass for
CombinedChainProteinSequence
. This metaclass wraps the specified class attributes.-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
mro
() → list¶ return a type’s method resolution order
-
-
class
schrodinger.protein.sequence.
CombinedChainProteinSequence
(seqs)¶ Bases:
schrodinger.protein.sequence.AbstractProteinSequenceMixin
,schrodinger.protein.sequence.AbstractSequence
A sequence that contains multiple chains from the same protein. Instances of this class do not directly contain any residues themselves and instead wrap one or several
ProteinSequence
objects.Note: CombinedChainProteinSequence.visibility
properly reports entryinclusion state, but it may not correctly report entry visibility (e.g. partially visible vs. fully visible). The MSV structure icons only report inclusion state and the visibility of included entries isn’t reported anywhere in the panel, though, so this limitation doesn’t have any impact on functionality.
-
AnnotationClass
¶ alias of
schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations
-
__init__
(seqs)¶ Parameters: seqs (list(ProteinSequence)) – A list of the split-chain sequences to wrap.
-
__len__
()¶
-
fullname
¶
-
index
(res)¶ Returns the index of the specified residue
Parameters: - res (residue.Residue) – The residue to find
- ignore_gaps (bool) – Whether the index returned should ignore gaps in the sequence or not.
Raises: A ValueError if the residue is not present
Return type: int
Returns: The index of the residue
-
indices
(residues)¶ Returns the indices of all specified residues. Note that the returned integers will likely not be in the same order as the input residues.
Parameters: res (Iterable(residue.CombinedChainResidueWrapper)) – The residues to find indices of Returns: The indices of the residues Return type: list[int]
-
insertElements
(index, elements)¶ Insert a list of elements or sequence element into this sequence.
Parameters: - index (int) – The index at which to insert elements
- elements (iterable(self.ElementClass) or iterable(str)) – A list of elements to insert
-
mutate
(start, end, elements)¶ Mutate sequence elements. See parent class for additional method documentation.
Raises: MultipleChainsError – If the specified residue range spans multiple chains.
-
assertCanMutateResidues
(start, end)¶ Make sure that we can mutate the specified residues. If not, raise an exception.
Parameters: - start (int) – The index at which to start mutating
- end (int) – The index of the last mutated element (exclusive)
Raises: MultipleChainsError – If the specified residue range spans multiple chains.
-
append
(element)¶ Appends an element to the sequence
Parameters: element – The element to append to this sequence Type: element: self.ElementClass or basestring
-
extend
(elements)¶ Extends the sequence with elements from an iterable
Parameters: elements (iterable(self.ElementClass) or iterable(str)) – The iterable containing elements with which to extend this sequence
-
getSubsequence
(start, end)¶ Return a sequence containing a subset of the elements in this one. Note that the new sequence will be a split-chain sequence and will ignore any chain breaks present in the requested subset of elements.
Parameters: - start (int) – The index at which the subsequence should start
- end (int) – The index at which the subsequence should end (exclusive)
Returns: The requested subsequence
Return type:
-
removeElements
(eles)¶ Remove elements from the sequence.
Parameters: eles (list(residue.AbstractSequenceElement)) – A list of elements to remove from the sequence. Raises: ValueError – If any of the given elements are not in the sequence.
-
getGaplessLength
()¶ Returns: Length of this sequence ignoring gaps Return type: int
-
addGapsByIndices
(gap_idxs)¶ Add gaps to the sequence from a list of gap indices. Note that these indices are based on numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see
addGapsBeforeIndices
.Parameters: gap_idxs (list(int)) – A list of gap indices
-
addGapsToChainStartsAndEnds
(gaps)¶ Add the specified numbers of gaps to the starts and ends of each chain.
Parameters: gaps (list[tuple(int, int)]) – The numbers of gaps to add, formatted as gaps_to_add[chain_index] = (gaps to add to the start of the chain,
gaps to add to the end of the chain)
-
removeGapsFromChainStartsAndEnds
(gaps)¶ Remove the specified numbers of gaps from the starts and ends of each chain.
Parameters: gaps (list[tuple(int, int)]) – The numbers of gaps to remove, formatted as gaps_to_remove[chain_index] =
- (gaps to remove from the start of the chain,
- gaps to remove from the end of the chain)
-
validateGapsToRemoveFromChainStartAndEnds
(gaps)¶ Make sure that we can remove the specified numbers of gaps from the starts and ends of each chain.
Parameters: gaps (list[tuple(int, int)]) – The numbers of gaps to remove, formatted as gaps_to_remove[chain_index] =
- (gaps to remove from the start of the chain,
- gaps to remove from the end of the chain)
Raises: AssertionError – If some of the sequence elements to be removed aren’t actually gaps.
-
disulfide_bonds
¶ Returns: A sorted tuple of the valid disulfide bonds. Return type: tuple(residue.CombinedChainDisulfideBond)
-
pred_disulfide_bonds
¶
-
indexToSeqAndIndex
(index)¶ Convert a combined-chain residue index to a split-chain sequence and a residue index within the specified sequence.
Parameters: index (int) – A valid combined-chain residue index Returns: A tuple of - the split-chain sequence - residue index - the starting index of the split-chain sequence Return type: tuple(ProteinSequence, int, int)
-
chain
¶
-
chains
¶
-
chain_offsets
¶
-
hasChain
(chain_name)¶ Does this sequence contain a chain with the specified name?
Parameters: chain_name (str) – The chain name to check Return type: bool
-
addChain
(seq)¶ Add a new chain to this sequence.
Parameters: seq (ProteinSequence) – The chain to add
-
removeChain
(seq)¶ Remove a chain from this sequence. Note that you should not remove the last chain; instead, remove this sequence from the alignment.
Parameters: seq (ProteinSequence) – The chain to remove
-
removeChains
(seqs)¶ Remove multiple chains from this sequence. Note that you should not all chain from a combine-chain sequence; instead, remove the sequence from the alignment.
Parameters: seqs (list[ProteinSequence]) – The chains to remove
-
insertElementByChain
(index, chain, element)¶ Add the given element to the specified chain of a sequence.
Parameters: - index (int) – The index to insert the element at. Note that this is the index in the sequence, not the chain.
- chain (sequence.ProteinSequence) – The chain to insert into
- element (str or residue.AbstractSequenceElement) – The element to insert
-
offsetForChain
(chain)¶ Get the combined-chain residue index for the first residue of the specified chain.
Parameters: chain (ProteinSequence) – The chain Returns: The offset Return type: int
-
clearAllCaching
()¶ This method should be implemented in subclasses that cache any data.
-
ALPHABET
= {'2AS': ResidueType('D', '2AS', 'Aspartic acid'), '3AH': ResidueType('H', '3AH', 'Histidine'), '5HP': ResidueType('E', '5HP', 'Glutamic acid'), 'A': ResidueType('A', 'ALA', 'Alanine'), 'ACE': ResidueType('X', 'ACE', 'Capping Group'), 'ACL': ResidueType('R', 'ACL', 'Arginine'), 'AGM': ResidueType('R', 'AGM', 'Arginine'), 'AIB': ResidueType('A', 'AIB', 'Alanine'), 'ALA': ResidueType('A', 'ALA', 'Alanine'), 'ALM': ResidueType('A', 'ALM', 'Alanine'), 'ALO': ResidueType('T', 'ALO', 'Threonine'), 'ALY': ResidueType('K', 'ALY', 'Lysine'), 'ANF': ResidueType('X', 'ANF', 'Capping Group'), 'ARG': ResidueType('R', 'ARG', 'Arginine'), 'ARM': ResidueType('R', 'ARM', 'Arginine'), 'ARN': ResidueType('R', 'ARN', 'Arginine'), 'ASA': ResidueType('D', 'ASA', 'Aspartic acid'), 'ASB': ResidueType('D', 'ASB', 'Aspartic acid'), 'ASH': ResidueType('D', 'ASH', 'Aspartic acid'), 'ASK': ResidueType('D', 'ASK', 'Aspartic acid'), 'ASL': ResidueType('D', 'ASL', 'Aspartic acid'), 'ASN': ResidueType('N', 'ASN', 'Asparagine'), 'ASP': ResidueType('D', 'ASP', 'Aspartic acid'), 'ASQ': ResidueType('D', 'ASQ', 'Aspartic acid'), 'AYA': ResidueType('A', 'AYA', 'Alanine'), 'BCS': ResidueType('X', 'BCS', 'Cysteine'), 'BHD': ResidueType('D', 'BHD', 'Aspartic acid'), 'BMT': ResidueType('T', 'BMT', 'Threonine'), 'BNN': ResidueType('A', 'BNN', 'Alanine'), 'BUC': ResidueType('C', 'BUC', 'Cysteine'), 'BUG': ResidueType('L', 'BUG', 'Leucine'), 'C': ResidueType('C', 'CYS', 'Cysteine'), 'C5C': ResidueType('C', 'C5C', 'Cysteine'), 'C6C': ResidueType('C', 'C6C', 'Cysteine'), 'CCS': ResidueType('C', 'CCS', 'Cysteine'), 'CEA': ResidueType('C', 'CEA', 'Cysteine'), 'CGU': ResidueType('E', 'CGU', 'Glutamic acid'), 'CHG': ResidueType('A', 'CHG', 'Alanine'), 'CLE': ResidueType('L', 'CLE', 'Leucine'), 'CME': ResidueType('C', 'CME', 'Cysteine'), 'CSD': ResidueType('A', 'CSD', 'Alanine'), 'CSO': ResidueType('C', 'CSO', 'Cysteine'), 'CSP': ResidueType('C', 'CSP', 'Cysteine'), 'CSS': ResidueType('C', 'CSS', 'Cysteine'), 'CSW': ResidueType('C', 'CSW', 'Cysteine'), 'CSX': ResidueType('C', 'CSX', 'Cysteine'), 'CXM': ResidueType('M', 'CXM', 'Methionine'), 'CY1': ResidueType('C', 'CY1', 'Cysteine'), 'CY3': ResidueType('C', 'CY3', 'Cysteine'), 'CYG': ResidueType('C', 'CYG', 'Cysteine'), 'CYM': ResidueType('C', 'CYM', 'Cysteine'), 'CYP': ResidueType('C', 'CYP', 'Cysteine'), 'CYQ': ResidueType('C', 'CYQ', 'Cysteine'), 'CYS': ResidueType('C', 'CYS', 'Cysteine'), 'CYX': ResidueType('C', 'CYX', 'Cysteine'), 'D': ResidueType('D', 'ASP', 'Aspartic acid'), 'DAH': ResidueType('F', 'DAH', 'Phenylalanine'), 'DAL': ResidueType('X', 'DAL', 'Alanine'), 'DAR': ResidueType('X', 'DAR', 'Arginine'), 'DAS': ResidueType('X', 'DAS', 'Aspartic acid'), 'DCY': ResidueType('X', 'DCY', 'Cysteine'), 'DGL': ResidueType('X', 'DGL', 'Glutamic acid'), 'DGN': ResidueType('X', 'DGN', 'Glutamine'), 'DHA': ResidueType('A', 'DHA', 'Alanine'), 'DHI': ResidueType('X', 'DHI', 'Histidine'), 'DIL': ResidueType('X', 'DIL', 'Isoleucine'), 'DIV': ResidueType('V', 'DIV', 'Valine'), 'DLE': ResidueType('X', 'DLE', 'Leucine'), 'DLY': ResidueType('X', 'DLY', 'Lysine'), 'DNP': ResidueType('A', 'DNP', 'Alanine'), 'DPN': ResidueType('X', 'DPN', 'Phenylalanine'), 'DPR': ResidueType('X', 'DPR', 'Proline'), 'DSG': ResidueType('X', 'DSG', 'Asparagine'), 'DSN': ResidueType('X', 'DSN', 'Serine'), 'DSP': ResidueType('D', 'DSP', 'Aspartic acid'), 'DTH': ResidueType('X', 'DTH', 'Threonine'), 'DTR': ResidueType('X', 'DTR', 'Tryptophan'), 'DTY': ResidueType('X', 'DTY', 'Tyrosine'), 'DVA': ResidueType('X', 'DVA', 'Valine'), 'E': ResidueType('E', 'GLU', 'Glutamic acid'), 'EFC': ResidueType('C', 'EFC', 'Cysteine'), 'F': ResidueType('F', 'PHE', 'Phenylalanine'), 'FCO': ResidueType('X', 'FCO', 'Capping Group'), 'FLA': ResidueType('A', 'FLA', 'Alanine'), 'FME': ResidueType('M', 'FME', 'Methionine'), 'G': ResidueType('G', 'GLY', 'Glycine'), 'GGL': ResidueType('E', 'GGL', 'Glutamic acid'), 'GL3': ResidueType('G', 'GL3', 'Glycine'), 'GLH': ResidueType('E', 'GLH', 'Glutamic acid'), 'GLN': ResidueType('Q', 'GLN', 'Glutamine'), 'GLU': ResidueType('E', 'GLU', 'Glutamic acid'), 'GLY': ResidueType('G', 'GLY', 'Glycine'), 'GLZ': ResidueType('G', 'GLZ', 'Glycine'), 'GMA': ResidueType('E', 'GMA', 'Glutamic acid'), 'GSC': ResidueType('G', 'GSC', 'Glycine'), 'H': ResidueType('H', 'HIS', 'Histidine'), 'HAC': ResidueType('A', 'HAC', 'Alanine'), 'HAR': ResidueType('R', 'HAR', 'Arginine'), 'HIC': ResidueType('H', 'HIC', 'Histidine'), 'HID': ResidueType('H', 'HID', 'Histidine'), 'HIE': ResidueType('H', 'HIE', 'Histidine'), 'HIP': ResidueType('H', 'HIP', 'Histidine'), 'HIS': ResidueType('H', 'HIS', 'Histidine'), 'HMR': ResidueType('R', 'HMR', 'Arginine'), 'HPQ': ResidueType('F', 'HPQ', 'Phenylalanine'), 'HSD': ResidueType('H', 'HSD', 'Histidine'), 'HSE': ResidueType('H', 'HSE', 'Histidine'), 'HSP': ResidueType('H', 'HSP', 'Histidine'), 'HTR': ResidueType('W', 'HTR', 'Tryptophan'), 'HYP': ResidueType('X', 'HYP', 'Proline'), 'I': ResidueType('I', 'ILE', 'Isoleucine'), 'IIL': ResidueType('I', 'IIL', 'Isoleucine'), 'ILE': ResidueType('I', 'ILE', 'Isoleucine'), 'IND': ResidueType('X', 'IND', 'Capping Group'), 'IYR': ResidueType('Y', 'IYR', 'Tyrosine'), 'K': ResidueType('K', 'LYS', 'Lysine'), 'KCX': ResidueType('K', 'KCX', 'Lysine'), 'L': ResidueType('L', 'LEU', 'Leucine'), 'LEU': ResidueType('L', 'LEU', 'Leucine'), 'LLP': ResidueType('K', 'LLP', 'Lysine'), 'LLY': ResidueType('K', 'LLY', 'Lysine'), 'LTR': ResidueType('W', 'LTR', 'Tryptophan'), 'LYM': ResidueType('K', 'LYM', 'Lysine'), 'LYN': ResidueType('K', 'LYN', 'Lysine'), 'LYS': ResidueType('K', 'LYS', 'Lysine'), 'LYZ': ResidueType('K', 'LYZ', 'Lysine'), 'M': ResidueType('M', 'MET', 'Methionine'), 'MAA': ResidueType('A', 'MAA', 'Alanine'), 'MEN': ResidueType('N', 'MEN', 'Asparagine'), 'MET': ResidueType('M', 'MET', 'Methionine'), 'MHS': ResidueType('H', 'MHS', 'Histidine'), 'MIS': ResidueType('S', 'MIS', 'Serine'), 'MLE': ResidueType('L', 'MLE', 'Leucine'), 'MMO': ResidueType('R', 'MMO', 'Arginine'), 'MPA': ResidueType('X', 'MPA', 'Capping Group'), 'MPQ': ResidueType('G', 'MPQ', 'Glycine'), 'MSA': ResidueType('G', 'MSA', 'Glycine'), 'MSE': ResidueType('M', 'MSE', 'Methionine'), 'MVA': ResidueType('V', 'MVA', 'Valine'), 'N': ResidueType('N', 'ASN', 'Asparagine'), 'NCO': ResidueType('X', 'NCO', 'Capping Group'), 'NEM': ResidueType('H', 'NEM', 'Histidine'), 'NEP': ResidueType('H', 'NEP', 'Histidine'), 'NH2': ResidueType('X', 'NH2', 'Capping Group'), 'NLE': ResidueType('X', 'NLE', 'Leucine'), 'NLN': ResidueType('L', 'NLN', 'Leucine'), 'NLP': ResidueType('L', 'NLP', 'Leucine'), 'NMA': ResidueType('X', 'NMA', 'Capping Group'), 'NMC': ResidueType('G', 'NMC', 'Glycine'), 'OAS': ResidueType('S', 'OAS', 'Serine'), 'OCS': ResidueType('C', 'OCS', 'Cysteine'), 'OMT': ResidueType('M', 'OMT', 'Methionine'), 'P': ResidueType('P', 'PRO', 'Proline'), 'PAQ': ResidueType('Y', 'PAQ', 'Tyrosine'), 'PCA': ResidueType('E', 'PCA', 'Glutamic acid'), 'PEC': ResidueType('C', 'PEC', 'Cysteine'), 'PHE': ResidueType('F', 'PHE', 'Phenylalanine'), 'PHI': ResidueType('F', 'PHI', 'Phenylalanine'), 'PHL': ResidueType('F', 'PHL', 'Phenylalanine'), 'PR3': ResidueType('C', 'PR3', 'Cysteine'), 'PRO': ResidueType('P', 'PRO', 'Proline'), 'PRR': ResidueType('A', 'PRR', 'Alanine'), 'PTR': ResidueType('y', 'PTR', 'Tyrosine'), 'Q': ResidueType('Q', 'GLN', 'Glutamine'), 'R': ResidueType('R', 'ARG', 'Arginine'), 'S': ResidueType('S', 'SER', 'Serine'), 'SAC': ResidueType('S', 'SAC', 'Serine'), 'SAR': ResidueType('G', 'SAR', 'Glycine'), 'SCH': ResidueType('C', 'SCH', 'Cysteine'), 'SCS': ResidueType('C', 'SCS', 'Cysteine'), 'SCY': ResidueType('C', 'SCY', 'Cysteine'), 'SEL': ResidueType('S', 'SEL', 'Serine'), 'SEP': ResidueType('X', 'SEP', 'Serine'), 'SER': ResidueType('S', 'SER', 'Serine'), 'SET': ResidueType('S', 'SET', 'Serine'), 'SHC': ResidueType('C', 'SHC', 'Cysteine'), 'SHR': ResidueType('K', 'SHR', 'Lysine'), 'SMC': ResidueType('C', 'SMC', 'Cysteine'), 'SOC': ResidueType('C', 'SOC', 'Cysteine'), 'STY': ResidueType('Y', 'STY', 'Tyrosine'), 'SVA': ResidueType('S', 'SVA', 'Serine'), 'T': ResidueType('T', 'THR', 'Threonine'), 'THO': ResidueType('T', 'THO', 'Threonine'), 'THR': ResidueType('T', 'THR', 'Threonine'), 'TIH': ResidueType('A', 'TIH', 'Alanine'), 'TOSG': ResidueType('X', 'TOSG', 'Capping Group'), 'TPL': ResidueType('W', 'TPL', 'Tryptophan'), 'TPO': ResidueType('t', 'TPO', 'Threonine'), 'TPQ': ResidueType('A', 'TPQ', 'Alanine'), 'TRG': ResidueType('K', 'TRG', 'Lysine'), 'TRO': ResidueType('W', 'TRO', 'Tryptophan'), 'TRP': ResidueType('W', 'TRP', 'Tryptophan'), 'TYB': ResidueType('Y', 'TYB', 'Tyrosine'), 'TYM': ResidueType('Y', 'TYM', 'Tyrosine'), 'TYO': ResidueType('Y', 'TYO', 'Tyrosine'), 'TYQ': ResidueType('Y', 'TYQ', 'Tyrosine'), 'TYR': ResidueType('Y', 'TYR', 'Tyrosine'), 'TYS': ResidueType('Y', 'TYS', 'Tyrosine'), 'TYY': ResidueType('Y', 'TYY', 'Tyrosine'), 'UNK': ResidueType('X', 'UNK', 'Unknown'), 'V': ResidueType('V', 'VAL', 'Valine'), 'VAL': ResidueType('V', 'VAL', 'Valine'), 'W': ResidueType('W', 'TRP', 'Tryptophan'), 'Y': ResidueType('Y', 'TYR', 'Tyrosine')}¶
-
ElementClass
¶ alias of
schrodinger.protein.residue.Residue
-
addGapsBeforeIndices
(indices)¶ Add one gap to the alignment before each of the specified residue positions. Note that these indices are based on numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see
addGapsByIndices
.Parameters: indices (list(int)) – A list of indices to insert gaps before.
-
annotationTitleChanged
¶
-
annotations
¶
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
clearDisulfideBondsCache
()¶
-
clearPfam
()¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
disulfideBondsCacheCleared
¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
entry_id
¶
-
entry_name
¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
-
gap_char
¶
-
getAnnotation
(index, annotation)¶ Returns the annotation at the specified index or None for a gap.
Raises: ValueError – if the annotation is not available
-
getConservation
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the homology conservation between the sequence and another sequence, assuming that they’re already aligned.
The homology criterion is based on “side chain chemistry” descriptor matching.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence conservation score (between 0.0 and 1.0)
Return type: float
-
getGapCount
()¶ Returns: the number of gaps in the sequence Return type: int
-
getGaps
()¶ Return type: list(residue.Gap) Returns: The gaps in the sequence.
-
getIdentity
(other, consider_gaps=True, only_consider=None)¶ Return a float scoring the identity between the sequence and another sequence, assuming that they’re already aligned
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
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
(other, consider_gaps=True, only_consider=None)¶ Return a float score of the similarity count between the sequence and another sequence, assuming that they’re already aligned.
Parameters: - other (schrodinger.protein.sequence.Sequence) – A sequence to compare against
- consider_gaps (bool) – Whether we should count gaps when we’re calculating the average score.
Returns: The sequence similarity score (between 0.0 and 1.0)
Return type: float
-
getSimilarityScore
(other, only_consider=None)¶ Return the total score of similarity between the sequence and a other 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: other (schrodinger.protein.sequence.Sequence) – A sequence to compare against Returns: The total sequence similarity score Return type: float
-
getStructure
(*args, **kwargs)¶
-
getTerminalGaps
()¶ Return terminal gaps.
Returns: A list of terminal gaps (in ascending index order) Return type: list(residue.Gap)
-
hasDisorderedRegionsPredictions
()¶
-
hasDisulfideBondPredictions
()¶
-
hasDomainArrangementPredictions
()¶
-
hasPfam
()¶
-
hasSSAPredictions
()¶
-
hasSolventAccessibility
()¶
-
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 NoneReturn type: iter(tuple(Residue or NoneType, Residue, Residue or NoneType))
-
killTimer
(self, int)¶
-
lengthAboutToChange
¶
-
lengthChanged
¶
-
long_name
¶
-
metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
origin
¶
-
parent
(self) → QObject¶
-
pdb_id
¶
-
pfamChanged
¶
-
pred_secondary_structures
¶
-
predictionsChanged
¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeAllGaps
()¶ Remove gaps from the sequence
-
removeEventFilter
(self, QObject)¶
-
removeTerminalGaps
()¶ Remove gaps from the end of the sequence
-
residues
()¶ Return an iterable of residues, ignoring gaps.
Returns: Iterable of residues Return type: iter(Residue)
-
residuesAdded
¶
-
residuesChanged
¶
-
residuesRemoved
¶
-
secondary_structures
¶ A list of _SecondaryStructure namedtuples containing the type of secondary structure and where the secondary structures begin and end.
Returns: A list of namedtuples containing an SS_TYPE from schrodinger.structure and the residue indexes marking the limits of the secondary structure. Return type: list(_SecondaryStructure)
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setPfam
(new_pfam, pfam_name)¶
-
setProperty
(self, str, Any) → bool¶
-
setStructure
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
structureChanged
¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
validateGapIndices
(gap_idxs)¶ Make sure that the specified gap indices are valid input for
addGapsByIndices
. If the indices are invalid, aValueError
will be raised. Indices are considered invalid if:- they refer to a position that’s more than one residue past the end of the sequence
- they are negative
Parameters: gap_idxs (list[int]) – The gap indices to validate
-
visibility
¶
-
visibilityChanged
¶
-
-
exception
schrodinger.protein.sequence.
MultipleChainsError
¶ Bases:
ValueError
An exception raised when the specified indices span multiple chains but the operation can only be carried out on a single chain.
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
args
¶
-
with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
-
-
class
schrodinger.protein.sequence.
StructureSequence
(st, atoms)¶ Bases:
schrodinger.structure.structure._AtomCollection
Class representing a sequence of protein residues.
-
residue
¶ Returns residue iterator for all residues in the sequence
-
__init__
(st, atoms)¶ Initialize self. See help(type(self)) for accurate signature.
-
__len__
()¶ Return number of atoms.
-
atom
¶ Iterate over all atoms. Also allows 1-based indexed access to the atoms.
-
extractStructure
(copy_props=False)¶ Return a new Structure containing only the atoms associated with this substructure. Structure properties, including the title, are inherited only if copy_props is set to True.
-
getAtomIndices
()¶ Return a list of atom indices for all atoms in this object.
Returns: List of atom indicies. Return type: list of ints
-
getAtomList
()¶ Deprecated. Use getAtomIndices() method instead.
-
structure
¶ Return the parent Structure object for this atom collection.
-
temperature_factor
¶ Average B (temperature) factor for all atoms that have it assigned. Setting this property will set the B factor to the given value for each atom.
-
-
schrodinger.protein.sequence.
get_structure_sequences
(st)¶ Iterates over all sequences in the given structure.
-
schrodinger.protein.sequence.
find_generalized_pattern
(sequence_list, pattern, validate_pattern=False)¶ Finds a generalized sequence pattern within specified sequences. NOTE: The search is performed in the forward direction only.
Parameters: - sequence_list – list of sequence dictionaries to search.
- pattern (str) –
Pattern defined using extended PROSITE syntax.
- standard IUPAC one-letter codes are used for all amino acids
- each element in a pattern is separated using ‘-‘ symbol
- symbol ‘x’ is used for position where any amino acid is accepted
- ambiguities are listed using the acceptable amino acids between square brackets, e.g. [ACT] means Ala, Cys or Thr
- amino acids not accepted for a given position are indicated by listing them between curly brackets, e.g. {GP} means ‘not Gly and not Pro’
- repetition is indicated using parentheses, e.g. A(3) means Ala-Ala-Ala, x(2,4) means between 2 to 4 any residues
- the following lowercase characters can be used as additional
flags:
- ’x’ means any amino acid
- ’a’ means acidic residue: [DE]
- ’b’ means basic residue: [KR]
- ’o’ means hydrophobic residue: [ACFILPWVY]
- ’p’ means aromatic residue: [WYF]
- ’s‘ means solvent exposed residue
- ’h’ means helical residue
- ’e’ means extended residue
- ’f’ means flexible residue
- Each position can optionally by followed by @<res_num> expression that will match the position with a given residue number.
- Entire pattern can be followed by :<index> expression that defines a ‘hotspot’ in the pattern. When the hotspot is defined, only a single residue corresponding to (pattern_match_start+index-1) will be returned as a match. The index is 1-based and can be used to place the hotspot outside of the pattern (can also be a negative number).
Pattern examples:
- N-{P}-[ST] : Asn-X-Ser or Thr (X != Pro)
- N[sf]-{P}[sf]-[ST][sf] : as above, but all residues flexible OR solvent exposed
- Nsf-{P}sf-[ST]sf : as above, but all residues flexible AND solvent exposed
- Ns{f} : Asn solvent exposed AND not in flexible region
- N[s{f}] : Asn solvent exposed OR not in flexible region
- [ab]{K}{s}f : acidic OR basic, with exception of Lys, flexible AND not solvent exposed
- Ahe : Ala helical AND extended - no match possible
- A[he] : Ala helical OR extended
- A{he} : Ala coiled chain conformation (not helical nor extended)
- [ST] : Ser OR Thr
- ST : Ser AND Thr - no match possible
- validate_pattern (boolean) – If True, the function will validate the pattern without performing the search (the sequences parameter will be ignored) and return True if the pattern is valid, or False otherwise. The default is False.
Return type: list of lists of integer tuples or False if the pattern is invalid
Returns: False if the specified input pattern was incorrect. Otherwise, it returns a list of lists of matches for each input sequence. Each match is a (start, end) tuple where start and end are matching sequence positions.
-
schrodinger.protein.sequence.
convert_structure_sequence_for_pattern_search
(seq, sasa_by_atom=None)¶ 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
- seq (
-
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.
- seq (
-
schrodinger.protein.sequence.
get_pairwise_sequence_similarity
(chain1, chain2, consider_gap=True, method='muscle')¶ Given two single chain sequences, align them, and return sequence similarity among them.
Parameters: - chain1 (
structure._Chain
) – The first sequence chain. - chain2 (
structure._Chain
) – The second sequence chain. - consider_gap (bool) – Whether or not to consider gaps in the alignment, default to true.
- method (string) – Which alignment method to use (‘muscle’ or ‘clustalw’)
Returns: Sequence similarity of the alignment of the two.
Return type: float, between 0.0 and 1.0
- chain1 (
-
schrodinger.protein.sequence.
create_alignment_from_chains
(chains)¶ Return
ProteinAlignment
object comprised of two chainsParameters: chains (iterable(structure._Chain)) – Chains to be aligned
-
schrodinger.protein.sequence.
align_alignment
(aln, second_aln=None, method='muscle')¶ Perform alignment from an ProteinAlignment object
Parameters: - aln (
ProteinAlignment
) – Alignment data - method (string) – Which method/program to use
Returns: Aligned sequences
Return type: ProteinAlignment
- aln (
-
schrodinger.protein.sequence.
align_from_chains
(chains, method='muscle')¶ Perform alignment on a series of chains
Parameters: - chains (iterable(structure._Chain)) – Chains to be aligned
- method (string) – Which method/program to use (choices ‘muscle’, ‘clustalw’)
Returns: Aligned sequences
Return type: ProteinAlignment
-
schrodinger.protein.sequence.
get_aligned_residues
(st1, st2, method='muscle')¶ This generator will yield 2 structure._Residue objects - one from each structure - for each position in aligned sequences.
Parameters: - st1 (
structure.Structure
) – First structure. - st2 (
structure.Structure
) – Second structure
Returns: Generates tuples of 2 residues that align at each position.
Return type: generator(structure._Residue or None, structure._Residue or None)
Raises: ValueError – if structures don’t have equivalent chains.
- st1 (
-
schrodinger.protein.sequence.
get_aligned_structure_residues
(sts, method='muscle')¶ This generator will yield 2 structure._Residue objects - one from each structure for each position in aligned sequences.
Parameters: sts (list(structure.Structure)) – Structures to align Returns: Generates lists of residues that align at each position. Return type: generator(list[structure._Residue or None])
-
schrodinger.protein.sequence.
offset_indices
(indices)¶ Offset insertion indices based on numbering before insertion to reflect numbering after insertion.
For example, [1, 1, 2, 3, 5, 8] would be changed to [1, 2, 4, 6, 9, 13]