schrodinger.protein.annotation module

Implementation of Multiple Sequence Viewer Annotation class.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.annotation.BINDING_SITE

Bases: enum.Enum

An enumeration.

CLOSE_CONTACT = 1
FAR_CONTACT = 2
NO_CONTACT = 3
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('CLOSE_CONTACT', <BINDING_SITE.CLOSE_CONTACT: 1>), ('FAR_CONTACT', <BINDING_SITE.FAR_CONTACT: 2>), ('NO_CONTACT', <BINDING_SITE.NO_CONTACT: 3>)]))
__module__ = 'schrodinger.protein.annotation'
class schrodinger.protein.annotation.AntibodyCDRLabel

Bases: enum.Enum

An enumeration.

H1 = 5
H2 = 6
H3 = 7
L1 = 2
L2 = 3
L3 = 4
NotCDR = 1
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('NotCDR', <AntibodyCDRLabel.NotCDR: 1>), ('L1', <AntibodyCDRLabel.L1: 2>), ('L2', <AntibodyCDRLabel.L2: 3>), ('L3', <AntibodyCDRLabel.L3: 4>), ('H1', <AntibodyCDRLabel.H1: 5>), ('H2', <AntibodyCDRLabel.H2: 6>), ('H3', <AntibodyCDRLabel.H3: 7>)]))
__module__ = 'schrodinger.protein.annotation'
class schrodinger.protein.annotation.AntibodyCDR(label, start, end)

Bases: tuple

__add__

Return self+value.

__class__

alias of builtins.type

__contains__

Return key in self.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__

Return self[key].

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__iter__

Implement iter(self).

__le__

Return self<=value.

__len__

Return len(self).

__lt__

Return self<value.

__module__ = 'schrodinger.protein.annotation'
__mul__

Return self*value.n

__ne__

Return self!=value.

static __new__(_cls, label, start, end)

Create new instance of AntibodyCDR(label, start, end)

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__()

Return a nicely formatted representation string

__rmul__

Return self*value.

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

count(value) → integer -- return number of occurrences of value
end

Alias for field number 2

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

label

Alias for field number 0

start

Alias for field number 1

class schrodinger.protein.annotation.Consensus

Bases: enum.Enum

An enumeration.

not_conserved = ' '
fully_conserved = '*'
strongly_conserved = ':'
weakly_conserved = '.'
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('not_conserved', <Consensus.not_conserved: ' '>), ('fully_conserved', <Consensus.fully_conserved: '*'>), ('strongly_conserved', <Consensus.strongly_conserved: ':'>), ('weakly_conserved', <Consensus.weakly_conserved: '.'>)]))
__module__ = 'schrodinger.protein.annotation'
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
__init__(seq)
Parameters:seq (sequence.Sequence) – The sequence to store annotations for.
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.

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.annotation', '__doc__': "\n A base class for single-chain and combined-chain sequence annotations\n\n :ivar titleChanged: A signal emitted after an annotation's title (row header)\n changes.\n :vartype titleChanged: `QtCore.pyqtSignal`\n ", 'titleChanged': <unbound PYQT_SIGNAL AbstractSequenceAnnotations.titleChanged[]>, 'sequence': <schrodinger.infra.util.WeakRefAttribute object>, '__init__': <function AbstractSequenceAnnotations.__init__>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.annotation'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

destroyed(self, QObject = None) [signal]

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

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

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

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

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

objectNameChanged(self, str) [signal]

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

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = -1) → str
class schrodinger.protein.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.

__getattr__(attr)

Returns a list of annotations, one for each residue in the sequence.

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.annotation', '__doc__': '\n Knows how to annotate a single-chain sequence\n\n Annotations can be set at the level of the sequence as a whole, or be per\n sequence element annotations. If an attribute is accessed on the\n SequenceAnnotations object, the attribute is first looked for on the object\n and if not found is assumed to be a per sequence element annotation. If the\n elements in the sequence lack the attribute, an AttributeError will be\n raised.\n ', '_getSequenceLengthAnnotation': <function SequenceAnnotations._getSequenceLengthAnnotation>, '_setSequenceLengthAnnotation': <function SequenceAnnotations._setSequenceLengthAnnotation>, '_lengthCheck': <function SequenceAnnotations._lengthCheck>, '__getattr__': <function SequenceAnnotations.__getattr__>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(seq)
Parameters:seq (sequence.Sequence) – The sequence to store annotations for.
__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.annotation'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

destroyed(self, QObject = None) [signal]

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

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

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

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

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

objectNameChanged(self, str) [signal]

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

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
titleChanged
tr(self, str, disambiguation: str = None, n: int = -1) → str
class schrodinger.protein.annotation.ProteinSequenceAnnotations(seq)

Bases: schrodinger.protein.annotation.SequenceAnnotations

Knows how to annotate a ProteinSequence

class ANNOTATION_TYPES

Bases: object

__class__

alias of enum_speedup.<locals>.meta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'resnum': <ANNOTATION_TYPES.resnum: 1>, 'rescode': <ANNOTATION_TYPES.rescode: 2>, 'disulfide_bonds': <ANNOTATION_TYPES.disulfide_bonds: 3>, 'helix_propensity': <ANNOTATION_TYPES.helix_propensity: 4>, 'beta_strand_propensity': <ANNOTATION_TYPES.beta_strand_propensity: 5>, 'turn_propensity': <ANNOTATION_TYPES.turn_propensity: 6>, 'helix_termination_tendency': <ANNOTATION_TYPES.helix_termination_tendency: 7>, 'exposure_tendency': <ANNOTATION_TYPES.exposure_tendency: 8>, 'steric_group': <ANNOTATION_TYPES.steric_group: 9>, 'side_chain_chem': <ANNOTATION_TYPES.side_chain_chem: 10>, 'hydrophobicity': <ANNOTATION_TYPES.hydrophobicity: 11>, 'isoelectric_point': <ANNOTATION_TYPES.isoelectric_point: 12>, 'b_factor': <ANNOTATION_TYPES.b_factor: 13>, 'window_hydrophobicity': <ANNOTATION_TYPES.window_hydrophobicity: 14>, 'window_isoelectric_point': <ANNOTATION_TYPES.window_isoelectric_point: 15>, 'secondary_structure': <ANNOTATION_TYPES.secondary_structure: 16>, 'binding_sites': <ANNOTATION_TYPES.binding_sites: 17>, 'antibody_cdr': <ANNOTATION_TYPES.antibody_cdr: 18>, 'sasa': <ANNOTATION_TYPES.sasa: 19>, '__module__': 'schrodinger.infra.util', '__dict__': <attribute '__dict__' of 'ANNOTATION_TYPES' objects>, '__weakref__': <attribute '__weakref__' of 'ANNOTATION_TYPES' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.infra.util'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

antibody_cdr = 18
b_factor = 13
beta_strand_propensity = 5
binding_sites = 17
disulfide_bonds = 3
exposure_tendency = 8
helix_propensity = 4
helix_termination_tendency = 7
hydrophobicity = 11
isoelectric_point = 12
rescode = 2
resnum = 1
sasa = 19
secondary_structure = 16
side_chain_chem = 10
steric_group = 9
turn_propensity = 6
window_hydrophobicity = 14
window_isoelectric_point = 15
RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.turn_propensity: 6>, <ANNOTATION_TYPES.steric_group: 9>, <ANNOTATION_TYPES.helix_propensity: 4>, <ANNOTATION_TYPES.side_chain_chem: 10>, <ANNOTATION_TYPES.helix_termination_tendency: 7>, <ANNOTATION_TYPES.exposure_tendency: 8>, <ANNOTATION_TYPES.beta_strand_propensity: 5>}
__init__(seq)
Parameters:seq (sequence.Sequence) – The sequence to store annotations for.
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

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)
binding_sites
ligands
onStructureChanged()
setLigandDistance(distance)

Updates the ligand distance and invalidates the cache

resetAnnotation(ann)

Force a reset of an annotation’s cache.

clearAllCaching()
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
inscode
resnum
__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.annotation', '__doc__': '\n Knows how to annotate a ProteinSequence\n ', 'ANNOTATION_TYPES': <class 'schrodinger.infra.util.ANNOTATION_TYPES'>, 'RES_PROPENSITY_ANNOTATIONS': {<ANNOTATION_TYPES.turn_propensity: 6>, <ANNOTATION_TYPES.steric_group: 9>, <ANNOTATION_TYPES.helix_propensity: 4>, <ANNOTATION_TYPES.side_chain_chem: 10>, <ANNOTATION_TYPES.helix_termination_tendency: 7>, <ANNOTATION_TYPES.exposure_tendency: 8>, <ANNOTATION_TYPES.beta_strand_propensity: 5>}, '__init__': <function ProteinSequenceAnnotations.__init__>, 'window_hydrophobicity': <schrodinger.infra.util.cached_property object>, 'invalidateWindowHydrophobicity': <function ProteinSequenceAnnotations.invalidateWindowHydrophobicity>, 'window_isoelectric_point': <schrodinger.infra.util.cached_property object>, 'invalidateWindowIsoelectricPoint': <function ProteinSequenceAnnotations.invalidateWindowIsoelectricPoint>, 'sasa': <schrodinger.infra.util.cached_property object>, '_invalidateSASA': <function ProteinSequenceAnnotations._invalidateSASA>, '_getWindowAvgAnnotation': <function ProteinSequenceAnnotations._getWindowAvgAnnotation>, 'getAntibodyCDR': <function ProteinSequenceAnnotations.getAntibodyCDR>, 'getAntibodyCDRs': <function ProteinSequenceAnnotations.getAntibodyCDRs>, 'isAntibodyChain': <function ProteinSequenceAnnotations.isAntibodyChain>, '_invalidateAntibodyCDRSlot': <function ProteinSequenceAnnotations._invalidateAntibodyCDRSlot>, '_invalidateAntibodyCDRs': <function ProteinSequenceAnnotations._invalidateAntibodyCDRs>, 'getSparseRescodes': <function ProteinSequenceAnnotations.getSparseRescodes>, 'binding_sites': <property object>, 'ligands': <property object>, 'onStructureChanged': <function ProteinSequenceAnnotations.onStructureChanged>, 'setLigandDistance': <function ProteinSequenceAnnotations.setLigandDistance>, '_invalidateLigandContacts': <function ProteinSequenceAnnotations._invalidateLigandContacts>, '_updateLigandContacts': <function ProteinSequenceAnnotations._updateLigandContacts>, 'resetAnnotation': <function ProteinSequenceAnnotations.resetAnnotation>, 'clearAllCaching': <function ProteinSequenceAnnotations.clearAllCaching>, 'getSSBondPartner': <function ProteinSequenceAnnotations.getSSBondPartner>, 'inscode': <property object>, 'resnum': <property object>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(attr)

Returns a list of annotations, one for each residue in the sequence.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.annotation'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

destroyed(self, QObject = None) [signal]

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

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

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

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

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

objectNameChanged(self, str) [signal]

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

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
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: object

__class__

alias of enum_speedup.<locals>.meta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'resnum': <ANNOTATION_TYPES.resnum: 1>, 'rescode': <ANNOTATION_TYPES.rescode: 2>, 'disulfide_bonds': <ANNOTATION_TYPES.disulfide_bonds: 3>, 'helix_propensity': <ANNOTATION_TYPES.helix_propensity: 4>, 'beta_strand_propensity': <ANNOTATION_TYPES.beta_strand_propensity: 5>, 'turn_propensity': <ANNOTATION_TYPES.turn_propensity: 6>, 'helix_termination_tendency': <ANNOTATION_TYPES.helix_termination_tendency: 7>, 'exposure_tendency': <ANNOTATION_TYPES.exposure_tendency: 8>, 'steric_group': <ANNOTATION_TYPES.steric_group: 9>, 'side_chain_chem': <ANNOTATION_TYPES.side_chain_chem: 10>, 'hydrophobicity': <ANNOTATION_TYPES.hydrophobicity: 11>, 'isoelectric_point': <ANNOTATION_TYPES.isoelectric_point: 12>, 'b_factor': <ANNOTATION_TYPES.b_factor: 13>, 'window_hydrophobicity': <ANNOTATION_TYPES.window_hydrophobicity: 14>, 'window_isoelectric_point': <ANNOTATION_TYPES.window_isoelectric_point: 15>, 'secondary_structure': <ANNOTATION_TYPES.secondary_structure: 16>, 'binding_sites': <ANNOTATION_TYPES.binding_sites: 17>, 'antibody_cdr': <ANNOTATION_TYPES.antibody_cdr: 18>, 'sasa': <ANNOTATION_TYPES.sasa: 19>, '__module__': 'schrodinger.infra.util', '__dict__': <attribute '__dict__' of 'ANNOTATION_TYPES' objects>, '__weakref__': <attribute '__weakref__' of 'ANNOTATION_TYPES' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.infra.util'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

antibody_cdr = 18
b_factor = 13
beta_strand_propensity = 5
binding_sites = 17
disulfide_bonds = 3
exposure_tendency = 8
helix_propensity = 4
helix_termination_tendency = 7
hydrophobicity = 11
isoelectric_point = 12
rescode = 2
resnum = 1
sasa = 19
secondary_structure = 16
side_chain_chem = 10
steric_group = 9
turn_propensity = 6
window_hydrophobicity = 14
window_isoelectric_point = 15
RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.turn_propensity: 6>, <ANNOTATION_TYPES.steric_group: 9>, <ANNOTATION_TYPES.helix_propensity: 4>, <ANNOTATION_TYPES.side_chain_chem: 10>, <ANNOTATION_TYPES.helix_termination_tendency: 7>, <ANNOTATION_TYPES.exposure_tendency: 8>, <ANNOTATION_TYPES.beta_strand_propensity: 5>}
__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.annotation', '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(attr)

Returns a list of annotations, one for each residue in the sequence.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(seq)
Parameters:seq (sequence.Sequence) – The sequence to store annotations for.
__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.annotation'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

destroyed(self, QObject = None) [signal]

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

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

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

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

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)
inherits(self, str) → bool
inscode
installEventFilter(self, QObject)
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.

isAntibodyChain()
Returns:Whether the sequence described is an antibody chain
Return type:bool
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
ligands
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

onStructureChanged()
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)
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 schrodinger.protein.annotation.ProteinAlignmentAnnotations(aln)

Bases: object

Knows how to annotate an alignment (a collection of aligned sequences)

class ANNOTATION_TYPES

Bases: object

__class__

alias of enum_speedup.<locals>.meta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'indices': <ANNOTATION_TYPES.indices: 1>, 'mean_hydrophobicity': <ANNOTATION_TYPES.mean_hydrophobicity: 2>, 'mean_isoelectric_point': <ANNOTATION_TYPES.mean_isoelectric_point: 3>, 'consensus_symbols': <ANNOTATION_TYPES.consensus_symbols: 4>, 'consensus_seq': <ANNOTATION_TYPES.consensus_seq: 5>, 'consensus_freq': <ANNOTATION_TYPES.consensus_freq: 6>, 'sequence_logo': <ANNOTATION_TYPES.sequence_logo: 7>, '__module__': 'schrodinger.infra.util', '__dict__': <attribute '__dict__' of 'ANNOTATION_TYPES' objects>, '__weakref__': <attribute '__weakref__' of 'ANNOTATION_TYPES' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.infra.util'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

consensus_freq = 6
consensus_seq = 5
consensus_symbols = 4
indices = 1
mean_hydrophobicity = 2
mean_isoelectric_point = 3
__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

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.annotation', '__doc__': '\n Knows how to annotate an alignment (a collection of aligned sequences)\n ', 'ANNOTATION_TYPES': <class 'schrodinger.infra.util.ANNOTATION_TYPES'>, 'alignment': <schrodinger.infra.util.WeakRefAttribute object>, '__init__': <function ProteinAlignmentAnnotations.__init__>, '_alnMeanAnnotation': <function ProteinAlignmentAnnotations._alnMeanAnnotation>, 'indices': <schrodinger.infra.util.cached_property object>, 'mean_hydrophobicity': <schrodinger.infra.util.cached_property object>, 'mean_isoelectric_point': <schrodinger.infra.util.cached_property object>, 'consensus_seq': <schrodinger.infra.util.cached_property object>, 'consensus_freq': <schrodinger.infra.util.cached_property object>, 'consensus_symbols': <schrodinger.infra.util.cached_property object>, 'sequence_logo': <schrodinger.infra.util.cached_property object>, 'clearAllCaching': <function ProteinAlignmentAnnotations.clearAllCaching>, '__dict__': <attribute '__dict__' of 'ProteinAlignmentAnnotations' objects>, '__weakref__': <attribute '__weakref__' of 'ProteinAlignmentAnnotations' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.annotation'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.protein.annotation.CombinedChainSequenceAnnotationMeta

Bases: schrodinger.application.msv.utils.QtDocstringWrapperMetaClass

The metaclass for CombinedChainSequenceAnnotations. This metaclass automatically wraps getters for all sequence annotations.

__base__

alias of schrodinger.application.msv.utils.QtDocstringWrapperMetaClass

__bases__ = (<class 'schrodinger.application.msv.utils.QtDocstringWrapperMetaClass'>,)
__basicsize__ = 904
__call__

Call self as a function.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.annotation', '__doc__': '\n The metaclass for `CombinedChainSequenceAnnotations`. This metaclass\n automatically wraps getters for all sequence annotations.\n ', '__new__': <staticmethod object>, '_createAnnotationWrapper': <staticmethod object>})
__dictoffset__ = 264
__dir__() → list

specialized __dir__ implementation for types

__eq__

Return self==value.

__flags__ = 2148292097
__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__instancecheck__() → bool

check if an object is an instance

__itemsize__ = 40
__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.annotation'
__mro__ = (<class 'schrodinger.protein.annotation.CombinedChainSequenceAnnotationMeta'>, <class 'schrodinger.application.msv.utils.QtDocstringWrapperMetaClass'>, <class 'schrodinger.application.msv.utils.DocstringWrapperMetaClass'>, <class 'sip.wrappertype'>, <class 'type'>, <class 'object'>)
__name__ = 'CombinedChainSequenceAnnotationMeta'
__ne__

Return self!=value.

static __new__(metacls, cls, bases, classdict, *, wraps=None)

See Python documentation for positional argument documentation.

Parameters:wraps (type or None) – The SequenceAnnotations subclass to wrap. If None, no wrapping will be done. (This allows for subclassing of the wrapper class.)
__prepare__() → dict

used to create the namespace for the class statement

__qualname__ = 'CombinedChainSequenceAnnotationMeta'
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

return memory consumption of the type object

__str__

Return str(self).

__subclasscheck__() → bool

check if a class is a subclass

__subclasses__() → list of immediate subclasses
__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__text_signature__ = None
__weakrefoffset__ = 368
mro() → list

return a type’s method resolution order

class schrodinger.protein.annotation.CombinedChainProteinSequenceAnnotations(seq)

Bases: schrodinger.protein.annotation.AbstractSequenceAnnotations

Sequence annotations for a sequence.CombinedChainProteinSequence. Annotations will be fetched from the ProteinSequenceAnnotations objects for each split-chain sequence.

class ANNOTATION_TYPES

Bases: object

__class__

alias of enum_speedup.<locals>.meta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'resnum': <ANNOTATION_TYPES.resnum: 1>, 'rescode': <ANNOTATION_TYPES.rescode: 2>, 'disulfide_bonds': <ANNOTATION_TYPES.disulfide_bonds: 3>, 'helix_propensity': <ANNOTATION_TYPES.helix_propensity: 4>, 'beta_strand_propensity': <ANNOTATION_TYPES.beta_strand_propensity: 5>, 'turn_propensity': <ANNOTATION_TYPES.turn_propensity: 6>, 'helix_termination_tendency': <ANNOTATION_TYPES.helix_termination_tendency: 7>, 'exposure_tendency': <ANNOTATION_TYPES.exposure_tendency: 8>, 'steric_group': <ANNOTATION_TYPES.steric_group: 9>, 'side_chain_chem': <ANNOTATION_TYPES.side_chain_chem: 10>, 'hydrophobicity': <ANNOTATION_TYPES.hydrophobicity: 11>, 'isoelectric_point': <ANNOTATION_TYPES.isoelectric_point: 12>, 'b_factor': <ANNOTATION_TYPES.b_factor: 13>, 'window_hydrophobicity': <ANNOTATION_TYPES.window_hydrophobicity: 14>, 'window_isoelectric_point': <ANNOTATION_TYPES.window_isoelectric_point: 15>, 'secondary_structure': <ANNOTATION_TYPES.secondary_structure: 16>, 'binding_sites': <ANNOTATION_TYPES.binding_sites: 17>, 'antibody_cdr': <ANNOTATION_TYPES.antibody_cdr: 18>, 'sasa': <ANNOTATION_TYPES.sasa: 19>, '__module__': 'schrodinger.infra.util', '__dict__': <attribute '__dict__' of 'ANNOTATION_TYPES' objects>, '__weakref__': <attribute '__weakref__' of 'ANNOTATION_TYPES' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.infra.util'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

antibody_cdr = 18
b_factor = 13
beta_strand_propensity = 5
binding_sites = 17
disulfide_bonds = 3
exposure_tendency = 8
helix_propensity = 4
helix_termination_tendency = 7
hydrophobicity = 11
isoelectric_point = 12
rescode = 2
resnum = 1
sasa = 19
secondary_structure = 16
side_chain_chem = 10
steric_group = 9
turn_propensity = 6
window_hydrophobicity = 14
window_isoelectric_point = 15
RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.turn_propensity: 6>, <ANNOTATION_TYPES.steric_group: 9>, <ANNOTATION_TYPES.helix_propensity: 4>, <ANNOTATION_TYPES.side_chain_chem: 10>, <ANNOTATION_TYPES.helix_termination_tendency: 7>, <ANNOTATION_TYPES.exposure_tendency: 8>, <ANNOTATION_TYPES.beta_strand_propensity: 5>}
__class__

alias of CombinedChainSequenceAnnotationMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.annotation', '__doc__': '\n Sequence annotations for a `sequence.CombinedChainProteinSequence`.\n Annotations will be fetched from the `ProteinSequenceAnnotations` objects\n for each split-chain sequence.\n ', 'sequence': <schrodinger.infra.util.WeakRefAttribute object>, '__init__': <function CombinedChainProteinSequenceAnnotations.__init__>, '_adjustCDR': <function CombinedChainProteinSequenceAnnotations._adjustCDR>, 'getAntibodyCDR': <function CombinedChainProteinSequenceAnnotations.getAntibodyCDR>, 'getAntibodyCDRs': <function CombinedChainProteinSequenceAnnotations.getAntibodyCDRs>, 'isAntibodyChain': <function CombinedChainProteinSequenceAnnotations.isAntibodyChain>, 'resnum': <property object>, 'rescode': <property object>, 'disulfide_bonds': <property object>, 'helix_propensity': <property object>, 'beta_strand_propensity': <property object>, 'turn_propensity': <property object>, 'helix_termination_tendency': <property object>, 'exposure_tendency': <property object>, 'steric_group': <property object>, 'side_chain_chem': <property object>, 'hydrophobicity': <property object>, 'isoelectric_point': <property object>, 'b_factor': <property object>, 'window_hydrophobicity': <property object>, 'window_isoelectric_point': <property object>, 'secondary_structure': <property object>, 'binding_sites': <property object>, 'antibody_cdr': <property object>, 'sasa': <property object>, 'ANNOTATION_TYPES': <class 'schrodinger.infra.util.ANNOTATION_TYPES'>, 'RES_PROPENSITY_ANNOTATIONS': {<ANNOTATION_TYPES.turn_propensity: 6>, <ANNOTATION_TYPES.steric_group: 9>, <ANNOTATION_TYPES.helix_propensity: 4>, <ANNOTATION_TYPES.side_chain_chem: 10>, <ANNOTATION_TYPES.helix_termination_tendency: 7>, <ANNOTATION_TYPES.exposure_tendency: 8>, <ANNOTATION_TYPES.beta_strand_propensity: 5>}})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.annotation'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
disulfide_bonds
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
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]

helix_propensity
helix_termination_tendency
hydrophobicity
inherits(self, str) → bool
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
isoelectric_point
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)
rescode
resnum
sasa
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
window_isoelectric_point
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.
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