schrodinger.protein.annotation module¶
Annotations for biological sequences
Copyright Schrodinger, LLC. All rights reserved.
-
class
schrodinger.protein.annotation.
BINDING_SITE
¶ Bases:
enum.Enum
An enumeration.
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CloseContact
= 1¶
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FarContact
= 2¶
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NoContact
= 3¶
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class
schrodinger.protein.annotation.
AntibodyCDRLabel
¶ Bases:
enum.Enum
An enumeration.
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H1
= 5¶
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H2
= 6¶
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H3
= 7¶
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L1
= 2¶
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L2
= 3¶
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L3
= 4¶
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NotCDR
= 1¶
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class
schrodinger.protein.annotation.
AntibodyCDR
(label, start, end)¶ Bases:
tuple
-
__contains__
¶ Return key in self.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
¶ Return len(self).
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count
(value) → integer -- return number of occurrences of value¶
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end
¶ Alias for field number 2
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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label
¶ Alias for field number 0
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start
¶ Alias for field number 1
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class
schrodinger.protein.annotation.
Domains
¶ Bases:
enum.Enum
An enumeration.
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Domain
= 1¶
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NoDomain
= 2¶
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class
schrodinger.protein.annotation.
Consensus
¶ Bases:
enum.Enum
An enumeration.
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not_conserved
= ' '¶
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fully_conserved
= '*'¶
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strongly_conserved
= ':'¶
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weakly_conserved
= '.'¶
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tooltip
¶
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class
schrodinger.protein.annotation.
TupleWithRange
¶ Bases:
tuple
-
range
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
__contains__
¶ Return key in self.
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
__len__
¶ Return len(self).
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count
(value) → integer -- return number of occurrences of value¶
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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class
schrodinger.protein.annotation.
AbstractSequenceAnnotations
(seq)¶ Bases:
PyQt5.QtCore.QObject
A base class for single-chain and combined-chain sequence annotations
Variables: titleChanged ( QtCore.pyqtSignal
) – A signal emitted after an annotation’s title (row header) changes.-
titleChanged
¶
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__init__
(seq)¶ Parameters: seq (sequence.Sequence) – The sequence to store annotations for.
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sequence
¶ A descriptor for an instance attribute that should be stored as a weakref. Unlike weakref.proxy, this descriptor allows the attribute to be hashed.
Note that the weakref is stored on the instance using the same name as the descriptor (which is stored on the class). Since this descriptor implements __set__, it will always take precedence over the value stored on the instance.
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blockSignals
(self, bool) → bool¶
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childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
connectNotify
(self, QMetaMethod)¶
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customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
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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]¶
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event
(self, QEvent) → bool¶
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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¶
-
installEventFilter
(self, QObject)¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
killTimer
(self, int)¶
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metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
parent
(self) → QObject¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
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sender
(self) → QObject¶
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senderSignalIndex
(self) → int¶
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setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
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setProperty
(self, str, Any) → bool¶
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signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
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staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
thread
(self) → QThread¶
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timerEvent
(self, QTimerEvent)¶
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tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
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class
schrodinger.protein.annotation.
AbstractProteinSequenceAnnotationsMixin
(*args, **kwargs)¶ Bases:
object
-
domainsChanged
¶
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invalidatedDomains
¶
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__init__
(*args, **kwargs)¶ Parameters: seq (sequence.Sequence) – The sequence to store annotations for.
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max_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
min_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
invalidateMaxMinBFactor
()¶
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getAntibodyCDR
(col, scheme)¶ Returns the antibody CDR information of the col’th index in the sequence under a given antibody CDR numbering scheme.
Parameters: - col (int) – index into the sequence
- scheme (
AntibodyCDRScheme
) – The antibody CDR numbering scheme to use
Returns: Antibody CDR label, start, and end positions
Return type: AntibodyCDR
, which is a named tuple of (AntibodyCDRLabel
, int, int) if col is in a CDR, otherwise (AntibodyCDRLabel.NotCDR, None, None)
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getAntibodyCDRs
(scheme)¶ Returns a list of antibody CDR information for the entire sequence.
Parameters: scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use Returns: A list of Antibody CDR labels, starts, and end positions Return type: list(AntibodyCDR)
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isAntibodyChain
()¶ Returns: Whether the sequence described is an antibody chain Return type: bool
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binding_sites
¶
-
ligands
¶
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setLigandDistance
(distance)¶ Updates the ligand distance and invalidates the cache
-
domains
¶
-
getSSBondPartner
(index)¶ Return the residue’s intra-sequence disulfide bond partner, if any.
If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.
Parameters: index (int) – Index of the residue to check Returns: the other Residue in the disulfide bond or None Return type: schrodinger.protein.residue.Residue or None
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clearAllCaching
()¶
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class
schrodinger.protein.annotation.
SequenceAnnotations
(seq)¶ Bases:
schrodinger.protein.annotation.AbstractSequenceAnnotations
Knows how to annotate a single-chain sequence
Annotations can be set at the level of the sequence as a whole, or be per sequence element annotations. If an attribute is accessed on the SequenceAnnotations object, the attribute is first looked for on the object and if not found is assumed to be a per sequence element annotation. If the elements in the sequence lack the attribute, an AttributeError will be raised.
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__init__
(seq)¶ Parameters: seq (sequence.Sequence) – The sequence to store annotations for.
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blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
findChild
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶ findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject
-
findChildren
(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶ findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]
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inherits
(self, str) → bool¶
-
installEventFilter
(self, QObject)¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
killTimer
(self, int)¶
-
metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
parent
(self) → QObject¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
titleChanged
¶
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
-
class
schrodinger.protein.annotation.
ProteinSequenceAnnotations
(seq)¶ Bases:
schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin
,schrodinger.protein.annotation.SequenceAnnotations
Knows how to annotate a ProteinSequence
-
annotationInvalidated
¶
-
invalidatedLigandContacts
¶
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invalidatedMaxMinBFactor
¶
-
class
ANNOTATION_TYPES
¶ Bases:
schrodinger.models.json.JsonableClassMixin
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
alignment_set
= 2¶
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antibody_cdr
= 21¶
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b_factor
= 15¶
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beta_strand_propensity
= 7¶
-
binding_sites
= 19¶
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disulfide_bonds
= 5¶
-
domains
= 20¶
-
exposure_tendency
= 10¶
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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
-
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.
-
helix_propensity
= 6¶
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helix_termination_tendency
= 9¶
-
hydrophobicity
= 13¶
-
isoelectric_point
= 14¶
-
pairwise_constraints
= 1¶
-
pfam
= 23¶
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pred_accessibility
= 26¶
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pred_disordered
= 27¶
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pred_disulfide_bonds
= 24¶
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pred_domain_arr
= 28¶
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pred_secondary_structure
= 25¶
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rescode
= 4¶
-
resnum
= 3¶
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sasa
= 22¶
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secondary_structure
= 18¶
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side_chain_chem
= 12¶
-
steric_group
= 11¶
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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
-
turn_propensity
= 8¶
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window_hydrophobicity
= 16¶
-
window_isoelectric_point
= 17¶
-
-
RES_PROPENSITY_ANNOTATIONS
= {<ANNOTATION_TYPES.exposure_tendency: 10>, <ANNOTATION_TYPES.helix_termination_tendency: 9>, <ANNOTATION_TYPES.turn_propensity: 8>, <ANNOTATION_TYPES.steric_group: 11>, <ANNOTATION_TYPES.beta_strand_propensity: 7>, <ANNOTATION_TYPES.helix_propensity: 6>, <ANNOTATION_TYPES.side_chain_chem: 12>}¶
-
PRED_ANNOTATION_TYPES
= {<ANNOTATION_TYPES.pred_disulfide_bonds: 24>, <ANNOTATION_TYPES.pred_accessibility: 26>, <ANNOTATION_TYPES.pred_secondary_structure: 25>, <ANNOTATION_TYPES.pred_domain_arr: 28>, <ANNOTATION_TYPES.pred_disordered: 27>}¶
-
__init__
(seq)¶ Parameters: seq (sequence.Sequence) – The sequence to store annotations for.
-
invalidateMaxMinBFactor
()¶
-
window_hydrophobicity
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
hydrophobicity_window_padding
¶
-
isoelectric_point_window_padding
¶
-
invalidateWindowHydrophobicity
()¶ Invalidate the cached window hydrophobicity data. Note that this method is also called from the sequence when the window size changes.
-
window_isoelectric_point
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
invalidateWindowIsoelectricPoint
()¶ Invalidate the cached window isoelectric point data. Note that this method is also called from the sequence when the window size changes.
-
sasa
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
getAntibodyCDR
(col, scheme)¶ Returns the antibody CDR information of the col’th index in the sequence under a given antibody CDR numbering scheme.
Parameters: - col (int) – index into the sequence
- scheme (
AntibodyCDRScheme
) – The antibody CDR numbering scheme to use
Returns: Antibody CDR label, start, and end positions
Return type: AntibodyCDR
, which is a named tuple of (AntibodyCDRLabel
, int, int) if col is in a CDR, otherwise (AntibodyCDRLabel.NotCDR, None, None)
-
getAntibodyCDRs
(scheme)¶ Returns a list of antibody CDR information for the entire sequence.
Parameters: scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use Returns: A list of Antibody CDR labels, starts, and end positions Return type: list(AntibodyCDR)
-
isAntibodyChain
()¶ Returns: Whether the sequence described is an antibody chain Return type: bool
-
getSparseRescodes
(modulo)¶
-
onStructureChanged
()¶
-
setLigandDistance
(distance)¶ Updates the ligand distance and invalidates the cache
-
parseDomains
(filename)¶ Parse XML file from UniProt database to get domain information.
Parameters: filename (str) – the XML file to parse for domain information Returns: a list of the domains (names) for the sequence in order Return type: list(str)
-
resetAnnotation
(ann)¶ Force a reset of an annotation’s cache.
-
clearAllCaching
()¶
-
inscode
¶
-
resnum
¶
-
binding_sites
¶
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
domains
¶
-
domainsChanged
¶
-
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]
-
getSSBondPartner
(index)¶ Return the residue’s intra-sequence disulfide bond partner, if any.
If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.
Parameters: index (int) – Index of the residue to check Returns: the other Residue in the disulfide bond or None Return type: schrodinger.protein.residue.Residue or None
-
inherits
(self, str) → bool¶
-
installEventFilter
(self, QObject)¶
-
invalidatedDomains
¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
killTimer
(self, int)¶
-
ligands
¶
-
max_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
metaObject
(self) → QMetaObject¶
-
min_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
moveToThread
(self, QThread)¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
parent
(self) → QObject¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
titleChanged
¶
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
-
class
schrodinger.protein.annotation.
NucleicAcidSequenceAnnotations
(seq)¶ Bases:
schrodinger.protein.annotation.ProteinSequenceAnnotations
-
class
ANNOTATION_TYPES
¶ Bases:
schrodinger.models.json.JsonableClassMixin
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
alignment_set
= 2¶
-
antibody_cdr
= 21¶
-
b_factor
= 15¶
-
beta_strand_propensity
= 7¶
-
binding_sites
= 19¶
-
disulfide_bonds
= 5¶
-
domains
= 20¶
-
exposure_tendency
= 10¶
-
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
-
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.
-
helix_propensity
= 6¶
-
helix_termination_tendency
= 9¶
-
hydrophobicity
= 13¶
-
isoelectric_point
= 14¶
-
pairwise_constraints
= 1¶
-
pfam
= 23¶
-
pred_accessibility
= 26¶
-
pred_disordered
= 27¶
-
pred_disulfide_bonds
= 24¶
-
pred_domain_arr
= 28¶
-
pred_secondary_structure
= 25¶
-
rescode
= 4¶
-
resnum
= 3¶
-
sasa
= 22¶
-
secondary_structure
= 18¶
-
side_chain_chem
= 12¶
-
steric_group
= 11¶
-
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
-
turn_propensity
= 8¶
-
window_hydrophobicity
= 16¶
-
window_isoelectric_point
= 17¶
-
-
PRED_ANNOTATION_TYPES
= {<ANNOTATION_TYPES.pred_disulfide_bonds: 24>, <ANNOTATION_TYPES.pred_accessibility: 26>, <ANNOTATION_TYPES.pred_secondary_structure: 25>, <ANNOTATION_TYPES.pred_domain_arr: 28>, <ANNOTATION_TYPES.pred_disordered: 27>}¶
-
RES_PROPENSITY_ANNOTATIONS
= {<ANNOTATION_TYPES.exposure_tendency: 10>, <ANNOTATION_TYPES.helix_termination_tendency: 9>, <ANNOTATION_TYPES.turn_propensity: 8>, <ANNOTATION_TYPES.steric_group: 11>, <ANNOTATION_TYPES.beta_strand_propensity: 7>, <ANNOTATION_TYPES.helix_propensity: 6>, <ANNOTATION_TYPES.side_chain_chem: 12>}¶
-
__init__
(seq)¶ Parameters: seq (sequence.Sequence) – The sequence to store annotations for.
-
annotationInvalidated
¶
-
binding_sites
¶
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
clearAllCaching
()¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
domains
¶
-
domainsChanged
¶
-
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]
-
getAntibodyCDR
(col, scheme)¶ Returns the antibody CDR information of the col’th index in the sequence under a given antibody CDR numbering scheme.
Parameters: - col (int) – index into the sequence
- scheme (
AntibodyCDRScheme
) – The antibody CDR numbering scheme to use
Returns: Antibody CDR label, start, and end positions
Return type: AntibodyCDR
, which is a named tuple of (AntibodyCDRLabel
, int, int) if col is in a CDR, otherwise (AntibodyCDRLabel.NotCDR, None, None)
-
getAntibodyCDRs
(scheme)¶ Returns a list of antibody CDR information for the entire sequence.
Parameters: scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use Returns: A list of Antibody CDR labels, starts, and end positions Return type: list(AntibodyCDR)
-
getSSBondPartner
(index)¶ Return the residue’s intra-sequence disulfide bond partner, if any.
If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.
Parameters: index (int) – Index of the residue to check Returns: the other Residue in the disulfide bond or None Return type: schrodinger.protein.residue.Residue or None
-
getSparseRescodes
(modulo)¶
-
hydrophobicity_window_padding
¶
-
inherits
(self, str) → bool¶
-
inscode
¶
-
installEventFilter
(self, QObject)¶
-
invalidateMaxMinBFactor
()¶
-
invalidateWindowHydrophobicity
()¶ Invalidate the cached window hydrophobicity data. Note that this method is also called from the sequence when the window size changes.
-
invalidateWindowIsoelectricPoint
()¶ Invalidate the cached window isoelectric point data. Note that this method is also called from the sequence when the window size changes.
-
invalidatedDomains
¶
-
invalidatedLigandContacts
¶
-
invalidatedMaxMinBFactor
¶
-
isAntibodyChain
()¶ Returns: Whether the sequence described is an antibody chain Return type: bool
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
isoelectric_point_window_padding
¶
-
killTimer
(self, int)¶
-
ligands
¶
-
max_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
metaObject
(self) → QMetaObject¶
-
min_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
moveToThread
(self, QThread)¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
onStructureChanged
()¶
-
parent
(self) → QObject¶
-
parseDomains
(filename)¶ Parse XML file from UniProt database to get domain information.
Parameters: filename (str) – the XML file to parse for domain information Returns: a list of the domains (names) for the sequence in order Return type: list(str)
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
resetAnnotation
(ann)¶ Force a reset of an annotation’s cache.
-
resnum
¶
-
sasa
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setLigandDistance
(distance)¶ Updates the ligand distance and invalidates the cache
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
titleChanged
¶
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
window_hydrophobicity
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
window_isoelectric_point
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
class
-
class
schrodinger.protein.annotation.
ProteinAlignmentAnnotations
(aln)¶ Bases:
object
Knows how to annotate an alignment (a collection of aligned sequences)
-
class
ANNOTATION_TYPES
¶ Bases:
schrodinger.models.json.JsonableClassMixin
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
consensus_freq
= 6¶
-
consensus_seq
= 5¶
-
consensus_symbols
= 4¶
-
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
-
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.
-
indices
= 1¶
-
mean_hydrophobicity
= 2¶
-
mean_isoelectric_point
= 3¶
-
sequence_logo
= 7¶
-
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
-
-
__init__
(aln)¶ Parameters: aln – alignment.Alignment
-
alignment
¶ A descriptor for an instance attribute that should be stored as a weakref. Unlike weakref.proxy, this descriptor allows the attribute to be hashed.
Note that the weakref is stored on the instance using the same name as the descriptor (which is stored on the class). Since this descriptor implements __set__, it will always take precedence over the value stored on the instance.
-
indices
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
mean_hydrophobicity
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
mean_isoelectric_point
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
consensus_seq
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
consensus_freq
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
consensus_symbols
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
sequence_logo
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
clearAllCaching
()¶
-
class
-
class
schrodinger.protein.annotation.
CombinedChainSequenceAnnotationMeta
¶ Bases:
schrodinger.application.msv.utils.QtDocstringWrapperMetaClass
The metaclass for
CombinedChainSequenceAnnotations
. This metaclass automatically wraps getters for all sequence annotations.-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
mro
() → list¶ return a type’s method resolution order
-
-
class
schrodinger.protein.annotation.
CombinedChainProteinSequenceAnnotations
(seq)¶ Bases:
schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin
,schrodinger.protein.annotation.AbstractSequenceAnnotations
Sequence annotations for a
sequence.CombinedChainProteinSequence
. Annotations will be fetched from theProteinSequenceAnnotations
objects for each split-chain sequence.-
sequence
¶ A descriptor for an instance attribute that should be stored as a weakref. Unlike weakref.proxy, this descriptor allows the attribute to be hashed.
Note that the weakref is stored on the instance using the same name as the descriptor (which is stored on the class). Since this descriptor implements __set__, it will always take precedence over the value stored on the instance.
-
__init__
(seq)¶ Parameters: seq (sequence.CombinedChainProteinSequence) – The sequence to store annotations for.
-
class
ANNOTATION_TYPES
¶ Bases:
schrodinger.models.json.JsonableClassMixin
-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
-
alignment_set
= 2¶
-
antibody_cdr
= 21¶
-
b_factor
= 15¶
-
beta_strand_propensity
= 7¶
-
binding_sites
= 19¶
-
disulfide_bonds
= 5¶
-
domains
= 20¶
-
exposure_tendency
= 10¶
-
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
-
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.
-
helix_propensity
= 6¶
-
helix_termination_tendency
= 9¶
-
hydrophobicity
= 13¶
-
isoelectric_point
= 14¶
-
pairwise_constraints
= 1¶
-
pfam
= 23¶
-
pred_accessibility
= 26¶
-
pred_disordered
= 27¶
-
pred_disulfide_bonds
= 24¶
-
pred_domain_arr
= 28¶
-
pred_secondary_structure
= 25¶
-
rescode
= 4¶
-
resnum
= 3¶
-
sasa
= 22¶
-
secondary_structure
= 18¶
-
side_chain_chem
= 12¶
-
steric_group
= 11¶
-
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
-
turn_propensity
= 8¶
-
window_hydrophobicity
= 16¶
-
window_isoelectric_point
= 17¶
-
-
PRED_ANNOTATION_TYPES
= {<ANNOTATION_TYPES.pred_disulfide_bonds: 24>, <ANNOTATION_TYPES.pred_accessibility: 26>, <ANNOTATION_TYPES.pred_secondary_structure: 25>, <ANNOTATION_TYPES.pred_domain_arr: 28>, <ANNOTATION_TYPES.pred_disordered: 27>}¶
-
RES_PROPENSITY_ANNOTATIONS
= {<ANNOTATION_TYPES.exposure_tendency: 10>, <ANNOTATION_TYPES.helix_termination_tendency: 9>, <ANNOTATION_TYPES.turn_propensity: 8>, <ANNOTATION_TYPES.steric_group: 11>, <ANNOTATION_TYPES.beta_strand_propensity: 7>, <ANNOTATION_TYPES.helix_propensity: 6>, <ANNOTATION_TYPES.side_chain_chem: 12>}¶
-
alignment_set
¶
-
antibody_cdr
¶
-
b_factor
¶
-
beta_strand_propensity
¶
-
binding_sites
¶
-
blockSignals
(self, bool) → bool¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
disulfide_bonds
¶
-
domains
¶
-
domainsChanged
¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exposure_tendency
¶
-
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]
-
getSSBondPartner
(index)¶ Return the residue’s intra-sequence disulfide bond partner, if any.
If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.
Parameters: index (int) – Index of the residue to check Returns: the other Residue in the disulfide bond or None Return type: schrodinger.protein.residue.Residue or None
-
helix_propensity
¶
-
helix_termination_tendency
¶
-
hydrophobicity
¶
-
hydrophobicity_window_padding
¶
-
inherits
(self, str) → bool¶
-
installEventFilter
(self, QObject)¶
-
invalidateMaxMinBFactor
()¶
-
invalidatedDomains
¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
isoelectric_point
¶
-
isoelectric_point_window_padding
¶
-
killTimer
(self, int)¶
-
ligands
¶
-
max_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
metaObject
(self) → QMetaObject¶
-
min_b_factor
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
moveToThread
(self, QThread)¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
pairwise_constraints
¶
-
parent
(self) → QObject¶
-
pfam
¶
-
pred_accessibility
¶
-
pred_disordered
¶
-
pred_disulfide_bonds
¶
-
pred_domain_arr
¶
-
pred_secondary_structure
¶
-
property
(self, str) → Any¶
-
pyqtConfigure
(...)¶ Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
rescode
¶
-
resnum
¶
-
sasa
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
secondary_structure
¶
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
side_chain_chem
¶
-
signalsBlocked
(self) → bool¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
steric_group
¶
-
thread
(self) → QThread¶
-
timerEvent
(self, QTimerEvent)¶
-
titleChanged
¶
-
tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
-
turn_propensity
¶
-
window_hydrophobicity
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
window_isoelectric_point
¶ Decorator that converts a method with a single self argument into a property cached on the instance.
Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.
This class is based on code that is Copyright (c) Django Software Foundation
-
chainAdded
(chain)¶ Respond to a new chain being added to the sequence. The sequence is responsible for calling this method whenever a chain is added.
Parameters: chain (sequence.ProteinSequence) – The newly added chain.
-
chainRemoved
(chain)¶ Respond to a chain being removed from the sequence. The sequence is responsible for calling this method whenever a chain is removed.
Parameters: chain (sequence.ProteinSequence) – The removed chain.
-
getAntibodyCDR
(col, scheme)¶ Returns the antibody CDR information of the col’th index in the sequence under a given antibody CDR numbering scheme.
Parameters: - col (int) – index into the sequence
- scheme (
AntibodyCDRScheme
) – The antibody CDR numbering scheme to use
Returns: Antibody CDR label, start, and end positions
Return type: AntibodyCDR
, which is a named tuple of (AntibodyCDRLabel
, int, int) if col is in a CDR, otherwise (AntibodyCDRLabel.NotCDR, None, None)
-
getAntibodyCDRs
(scheme)¶ Returns a list of antibody CDR information for the entire sequence.
Parameters: scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use Returns: A list of Antibody CDR labels, starts, and end positions Return type: list(AntibodyCDR)
-
isAntibodyChain
()¶ Returns: Whether the sequence described is an antibody chain Return type: bool
-
setLigandDistance
(distance)¶ Updates the ligand distance and invalidates the cache
-
clearAllCaching
()¶
-
-
schrodinger.protein.annotation.
make_ligand_name_atom
(ct, atom_index)¶ Make a unique, human-readable name for a ligand identified by atom index.
Parameters: - ct (schrodinger.structure.Structure) – Structure the ligand belongs to
- atom_index (int) – the atom index of the ligand to make a name for
Returns: The name for the ligand
Return type: str
-
schrodinger.protein.annotation.
make_ligand_name
(ct, ligand)¶ Make a unique, human-readable name for a ligand. This name matches the ligand name in the structure hierarchy.
Parameters: - ct (schrodinger.structure.Structure) – Structure the ligand belongs to
- ligand (schrodinger.structutils.analyze.Ligand) – the ligand to make a name for
Returns: The name for the ligand
Return type: str