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 schrodinger.protein.annotation.AntibodyCDRLabel

Bases: enum.Enum

An enumeration.

H1 = 5
H2 = 6
H3 = 7
L1 = 2
L2 = 3
L3 = 4
NotCDR = 1
class schrodinger.protein.annotation.AntibodyCDR(label, start, end)

Bases: tuple

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

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 = '.'
tooltip
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.

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.AbstractProteinSequenceAnnotationsMixin(*args, **kwargs)

Bases: object

__init__(*args, **kwargs)
Parameters:seq (sequence.Sequence) – 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
binding_sites
ligands
setLigandDistance(distance)

Updates the ligand distance and invalidates the cache

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
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.

__init__(seq)
Parameters:seq (sequence.Sequence) – The sequence to store annotations for.
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.AbstractProteinSequenceAnnotationsMixin, schrodinger.protein.annotation.SequenceAnnotations

Knows how to annotate a ProteinSequence

invalidatedLigandContacts
class ANNOTATION_TYPES

Bases: schrodinger.models.json.JsonableClassMixin

__init__

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

alignment_set = 1
antibody_cdr = 19
b_factor = 14
beta_strand_propensity = 6
binding_sites = 18
disulfide_bonds = 4
exposure_tendency = 9
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 = 5
helix_termination_tendency = 8
hydrophobicity = 12
isoelectric_point = 13
pred_accessibility = 23
pred_disordered = 24
pred_disulfide_bonds = 21
pred_domain_arr = 25
pred_secondary_structure = 22
rescode = 3
resnum = 2
sasa = 20
secondary_structure = 17
side_chain_chem = 11
steric_group = 10
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 = 7
window_hydrophobicity = 15
window_isoelectric_point = 16
RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.beta_strand_propensity: 6>, <ANNOTATION_TYPES.turn_propensity: 7>, <ANNOTATION_TYPES.helix_termination_tendency: 8>, <ANNOTATION_TYPES.exposure_tendency: 9>, <ANNOTATION_TYPES.helix_propensity: 5>, <ANNOTATION_TYPES.steric_group: 10>, <ANNOTATION_TYPES.side_chain_chem: 11>}
PRED_ANNOTATION_TYPES = {<ANNOTATION_TYPES.pred_disulfide_bonds: 21>, <ANNOTATION_TYPES.pred_secondary_structure: 22>, <ANNOTATION_TYPES.pred_disordered: 24>, <ANNOTATION_TYPES.pred_domain_arr: 25>, <ANNOTATION_TYPES.pred_accessibility: 23>}
__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

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

resetAnnotation(ann)

Force a reset of an annotation’s cache.

clearAllCaching()
inscode
resnum
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)
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]

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)
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]

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 = 1
antibody_cdr = 19
b_factor = 14
beta_strand_propensity = 6
binding_sites = 18
disulfide_bonds = 4
exposure_tendency = 9
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 = 5
helix_termination_tendency = 8
hydrophobicity = 12
isoelectric_point = 13
pred_accessibility = 23
pred_disordered = 24
pred_disulfide_bonds = 21
pred_domain_arr = 25
pred_secondary_structure = 22
rescode = 3
resnum = 2
sasa = 20
secondary_structure = 17
side_chain_chem = 11
steric_group = 10
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 = 7
window_hydrophobicity = 15
window_isoelectric_point = 16
PRED_ANNOTATION_TYPES = {<ANNOTATION_TYPES.pred_disulfide_bonds: 21>, <ANNOTATION_TYPES.pred_secondary_structure: 22>, <ANNOTATION_TYPES.pred_disordered: 24>, <ANNOTATION_TYPES.pred_domain_arr: 25>, <ANNOTATION_TYPES.pred_accessibility: 23>}
RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.beta_strand_propensity: 6>, <ANNOTATION_TYPES.turn_propensity: 7>, <ANNOTATION_TYPES.helix_termination_tendency: 8>, <ANNOTATION_TYPES.exposure_tendency: 9>, <ANNOTATION_TYPES.helix_propensity: 5>, <ANNOTATION_TYPES.steric_group: 10>, <ANNOTATION_TYPES.side_chain_chem: 11>}
__init__(seq)
Parameters:seq (sequence.Sequence) – The sequence to store annotations for.
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)
hydrophobicity_window_padding
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.

invalidatedLigandContacts
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
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: 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
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:alnalignment.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 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 the ProteinSequenceAnnotations 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 = 1
antibody_cdr = 19
b_factor = 14
beta_strand_propensity = 6
binding_sites = 18
disulfide_bonds = 4
exposure_tendency = 9
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 = 5
helix_termination_tendency = 8
hydrophobicity = 12
isoelectric_point = 13
pred_accessibility = 23
pred_disordered = 24
pred_disulfide_bonds = 21
pred_domain_arr = 25
pred_secondary_structure = 22
rescode = 3
resnum = 2
sasa = 20
secondary_structure = 17
side_chain_chem = 11
steric_group = 10
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 = 7
window_hydrophobicity = 15
window_isoelectric_point = 16
PRED_ANNOTATION_TYPES = {<ANNOTATION_TYPES.pred_disulfide_bonds: 21>, <ANNOTATION_TYPES.pred_secondary_structure: 22>, <ANNOTATION_TYPES.pred_disordered: 24>, <ANNOTATION_TYPES.pred_domain_arr: 25>, <ANNOTATION_TYPES.pred_accessibility: 23>}
RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.beta_strand_propensity: 6>, <ANNOTATION_TYPES.turn_propensity: 7>, <ANNOTATION_TYPES.helix_termination_tendency: 8>, <ANNOTATION_TYPES.exposure_tendency: 9>, <ANNOTATION_TYPES.helix_propensity: 5>, <ANNOTATION_TYPES.steric_group: 10>, <ANNOTATION_TYPES.side_chain_chem: 11>}
alignment_set
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]

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

objectNameChanged(self, str) [signal]

parent(self) → QObject
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
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
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(ct, ligand)

Make a unique, human-readable name for a ligand. This name matches the ligand name in the structure hierarchy.

Parameters:
Returns:

The name for the ligand

Return type:

str