schrodinger.protein.annotation module

Annotations for biological sequences

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.annotation.BINDING_SITE

Bases: enum.Enum

An enumeration.

CloseContact = 1

FarContact = 2

NoContact = 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()

Return number of occurrences of value.

end

Alias for field number 2

index()

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.Domains

Bases: enum.Enum

An enumeration.

Domain = 1

NoDomain = 2

class schrodinger.protein.annotation.KinaseFeatureLabel(*args, **kwargs)

Bases: schrodinger.models.jsonable.JsonableEnum

An enumeration.

GLYCINE_RICH_LOOP = 'Glycine Rich Loop'

ALPHA_C = 'Alpha-C'

GATE_KEEPER = 'Gate Keeper'

HINGE = 'Hinge'

LINKER = 'Linker'

HRD = 'HRD'

CATALYTIC_LOOP = 'Catalytic Loop'

DFG = 'DFG'

ACTIVATION_LOOP = 'Activation Loop'

NO_FEATURE = 'No Feature'

class schrodinger.protein.annotation.Consensus

Bases: enum.Enum

An enumeration.

not_conserved = ' '

fully_conserved = '*'

strongly_conserved = ':'

weakly_conserved = '.'

tooltip

class schrodinger.protein.annotation.TupleWithRange

Bases: tuple

range

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

count()

Return number of occurrences of value.

index()

Return first index of value.

Raises ValueError if the value is not present.

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) → List[QObject]

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

deleteLater(self)

destroyed

destroyed(self, object: QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

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

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

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

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

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

domainsChanged

invalidatedDomains

__init__(*args, **kwargs)

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

max_b_factor

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

min_b_factor

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

invalidateMaxMinBFactor()

getKinaseFeatures()

Return the kinase features for the sequence.

Returns:Kinase features. Return type:list[KinaseFeature]

setKinaseFeatures(kinase_feature)

Set the kinase features for the sequence. Note that we also allow kinase_feature to be of NoneType to imply that kinase annotations have not been calculated because an empty list would imply the annotations were run no features were found.

Parameters:kinase_feature (list[KinaseFeature] or NoneType) – Kinase features.

getKinaseFeature(col)

Returns the KinaseFeature for the index in the sequence.

Parameters:col (int) – sequence index Returns:Kinase feature. Return type:KinaseFeature

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

isAntibodyHeavyChain()

Returns:Whether the sequence described is an antibody heavy chain Return type:bool

isAntibodyLightChain()

Returns:Whether the sequence described is an antibody light chain Return type:bool

binding_sites

ligands

setLigandDistance(distance)

Updates the ligand distance and invalidates the cache

domains

getSSBondPartner(index)

Return the residue’s intra-sequence disulfide bond partner, if any.

If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.

Parameters:index (int) – Index of the residue to check Returns:the other Residue in the disulfide bond or None Return type:schrodinger.protein.residue.Residue or None

clearAllCaching()

getNumAnnValues(ann)

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) → List[QObject]

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

deleteLater(self)

destroyed

destroyed(self, object: QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

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

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

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

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

inherits(self, str) → bool

installEventFilter(self, QObject)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

setParent(self, QObject)

setProperty(self, str, Any) → bool

signalsBlocked(self) → bool

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

thread(self) → QThread

timerEvent(self, QTimerEvent)

titleChanged

tr(self, str, disambiguation: str = None, n: int = -1) → str

class schrodinger.protein.annotation.ProteinSequenceAnnotations(seq)

Bases: schrodinger.protein.annotation.AbstractProteinSequenceAnnotationsMixin, schrodinger.protein.annotation.SequenceAnnotations

Knows how to annotate a ProteinSequence

annotationInvalidated

invalidatedLigandContacts

invalidatedMaxMinBFactor

class ANNOTATION_TYPES

Bases: schrodinger.models.json.JsonableClassMixin

__init__

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

alignment_set = 2

antibody_cdr = 21

b_factor = 15

beta_strand_propensity = 7

binding_sites = 19

disulfide_bonds = 5

domains = 20

exposure_tendency = 10

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file. Returns:An instance of the derived class.

:rtype : cls

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

helix_propensity = 6

helix_termination_tendency = 9

hydrophobicity = 13

isoelectric_point = 14

kinase_features = 30

pairwise_constraints = 1

pfam = 23

pred_accessibility = 26

pred_disordered = 27

pred_disulfide_bonds = 24

pred_domain_arr = 28

pred_secondary_structure = 25

proximity_constraints = 29

rescode = 4

resnum = 3

sasa = 22

secondary_structure = 18

side_chain_chem = 12

steric_group = 11

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

turn_propensity = 8

window_hydrophobicity = 16

window_isoelectric_point = 17

RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.beta_strand_propensity: 7>, <ANNOTATION_TYPES.helix_termination_tendency: 9>, <ANNOTATION_TYPES.exposure_tendency: 10>, <ANNOTATION_TYPES.turn_propensity: 8>, <ANNOTATION_TYPES.helix_propensity: 6>, <ANNOTATION_TYPES.steric_group: 11>, <ANNOTATION_TYPES.side_chain_chem: 12>}

PRED_ANNOTATION_TYPES = {<ANNOTATION_TYPES.pred_accessibility: 26>, <ANNOTATION_TYPES.pred_secondary_structure: 25>, <ANNOTATION_TYPES.pred_domain_arr: 28>, <ANNOTATION_TYPES.pred_disordered: 27>, <ANNOTATION_TYPES.pred_disulfide_bonds: 24>}

__init__(seq)

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

invalidateMaxMinBFactor()

window_hydrophobicity

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

hydrophobicity_window_padding

isoelectric_point_window_padding

invalidateWindowHydrophobicity()

Invalidate the cached window hydrophobicity data. Note that this method is also called from the sequence when the window size changes.

window_isoelectric_point

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

invalidateWindowIsoelectricPoint()

Invalidate the cached window isoelectric point data. Note that this method is also called from the sequence when the window size changes.

sasa

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

getAntibodyCDR(col, scheme)

Returns the antibody CDR information of the col’th index in the sequence under a given antibody CDR numbering scheme.

Parameters:

• col (int) – index into the sequence
• scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use

Returns:

Antibody CDR label, start, and end positions

Return type:

AntibodyCDR, which is a named tuple of (AntibodyCDRLabel, int, int) if col is in a CDR, otherwise (AntibodyCDRLabel.NotCDR, None, None)

getAntibodyCDRs(scheme)

Returns a list of antibody CDR information for the entire sequence.

Parameters:scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use Returns:A list of Antibody CDR labels, starts, and end positions Return type:list(AntibodyCDR)

isAntibodyChain()

Returns:Whether the sequence described is an antibody chain Return type:bool

isAntibodyHeavyChain()

Returns:Whether the sequence described is an antibody heavy chain Return type:bool

isAntibodyLightChain()

Returns:Whether the sequence described is an antibody light chain Return type:bool

is_kinase_annotated

getKinaseFeatures()

Return the kinase features for the sequence.

Returns:Kinase features. Return type:list[KinaseFeature]

setKinaseFeatures(kinase_features)

Set the kinase features for the sequence. Note that we also allow kinase_feature to be of NoneType to imply that kinase annotations have not been calculated because an empty list would imply the annotations were run no features were found.

Parameters:kinase_feature (list[KinaseFeature] or NoneType) – Kinase features.

getKinaseFeature(col)

Returns the KinaseFeature for the index in the sequence.

Parameters:col (int) – sequence index Returns:Kinase feature. Return type:KinaseFeature

getSparseRescodes(modulo)

onStructureChanged()

setLigandDistance(distance)

Updates the ligand distance and invalidates the cache

parseDomains(filename)

Parse XML file from UniProt database to get domain information.

Parameters:filename (str) – the XML file to parse for domain information Returns:a list of the domains (names) for the sequence in order Return type:list(str)

resetAnnotation(ann)

Force a reset of an annotation’s cache.

clearAllCaching()

inscode

resnum

binding_sites

blockSignals(self, bool) → bool

childEvent(self, QChildEvent)

children(self) → List[QObject]

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

deleteLater(self)

destroyed

destroyed(self, object: QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

domains

domainsChanged

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

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

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

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

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

getNumAnnValues(ann)

getSSBondPartner(index)

Return the residue’s intra-sequence disulfide bond partner, if any.

If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.

Parameters:index (int) – Index of the residue to check Returns:the other Residue in the disulfide bond or None Return type:schrodinger.protein.residue.Residue or None

inherits(self, str) → bool

installEventFilter(self, QObject)

invalidatedDomains

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

ligands

max_b_factor

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

metaObject(self) → QMetaObject

min_b_factor

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

sender(self) → QObject

senderSignalIndex(self) → int

setObjectName(self, str)

setParent(self, QObject)

setProperty(self, str, Any) → bool

signalsBlocked(self) → bool

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

thread(self) → QThread

timerEvent(self, QTimerEvent)

titleChanged

tr(self, str, disambiguation: str = None, n: int = -1) → str

class schrodinger.protein.annotation.NucleicAcidSequenceAnnotations(seq)

Bases: schrodinger.protein.annotation.ProteinSequenceAnnotations

isAntibodyChain()

Returns:Whether the sequence described is an antibody chain Return type:bool

getKinaseFeatures()

Return the kinase features for the sequence.

Returns:Kinase features. Return type:list[KinaseFeature]

class ANNOTATION_TYPES

Bases: schrodinger.models.json.JsonableClassMixin

__init__

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

alignment_set = 2

antibody_cdr = 21

b_factor = 15

beta_strand_propensity = 7

binding_sites = 19

disulfide_bonds = 5

domains = 20

exposure_tendency = 10

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file. Returns:An instance of the derived class.

:rtype : cls

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

helix_propensity = 6

helix_termination_tendency = 9

hydrophobicity = 13

isoelectric_point = 14

kinase_features = 30

pairwise_constraints = 1

pfam = 23

pred_accessibility = 26

pred_disordered = 27

pred_disulfide_bonds = 24

pred_domain_arr = 28

pred_secondary_structure = 25

proximity_constraints = 29

rescode = 4

resnum = 3

sasa = 22

secondary_structure = 18

side_chain_chem = 12

steric_group = 11

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

turn_propensity = 8

window_hydrophobicity = 16

window_isoelectric_point = 17

PRED_ANNOTATION_TYPES = {<ANNOTATION_TYPES.pred_accessibility: 26>, <ANNOTATION_TYPES.pred_secondary_structure: 25>, <ANNOTATION_TYPES.pred_domain_arr: 28>, <ANNOTATION_TYPES.pred_disordered: 27>, <ANNOTATION_TYPES.pred_disulfide_bonds: 24>}

RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.beta_strand_propensity: 7>, <ANNOTATION_TYPES.helix_termination_tendency: 9>, <ANNOTATION_TYPES.exposure_tendency: 10>, <ANNOTATION_TYPES.turn_propensity: 8>, <ANNOTATION_TYPES.helix_propensity: 6>, <ANNOTATION_TYPES.steric_group: 11>, <ANNOTATION_TYPES.side_chain_chem: 12>}

__init__(seq)

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

annotationInvalidated

binding_sites

blockSignals(self, bool) → bool

childEvent(self, QChildEvent)

children(self) → List[QObject]

clearAllCaching()

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

deleteLater(self)

destroyed

destroyed(self, object: QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

domains

domainsChanged

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

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

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

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

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

getAntibodyCDR(col, scheme)

Returns the antibody CDR information of the col’th index in the sequence under a given antibody CDR numbering scheme.

Parameters:

• col (int) – index into the sequence
• scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use

Returns:

Antibody CDR label, start, and end positions

Return type:

AntibodyCDR, which is a named tuple of (AntibodyCDRLabel, int, int) if col is in a CDR, otherwise (AntibodyCDRLabel.NotCDR, None, None)

getAntibodyCDRs(scheme)

Returns a list of antibody CDR information for the entire sequence.

Parameters:scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use Returns:A list of Antibody CDR labels, starts, and end positions Return type:list(AntibodyCDR)

getKinaseFeature(col)

Returns the KinaseFeature for the index in the sequence.

Parameters:col (int) – sequence index Returns:Kinase feature. Return type:KinaseFeature

getNumAnnValues(ann)

getSSBondPartner(index)

Return the residue’s intra-sequence disulfide bond partner, if any.

If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.

Parameters:index (int) – Index of the residue to check Returns:the other Residue in the disulfide bond or None Return type:schrodinger.protein.residue.Residue or None

getSparseRescodes(modulo)

hydrophobicity_window_padding

inherits(self, str) → bool

inscode

installEventFilter(self, QObject)

invalidateMaxMinBFactor()

invalidateWindowHydrophobicity()

Invalidate the cached window hydrophobicity data. Note that this method is also called from the sequence when the window size changes.

invalidateWindowIsoelectricPoint()

Invalidate the cached window isoelectric point data. Note that this method is also called from the sequence when the window size changes.

invalidatedDomains

invalidatedLigandContacts

invalidatedMaxMinBFactor

isAntibodyHeavyChain()

Returns:Whether the sequence described is an antibody heavy chain Return type:bool

isAntibodyLightChain()

Returns:Whether the sequence described is an antibody light chain Return type:bool

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

is_kinase_annotated

isoelectric_point_window_padding

killTimer(self, int)

ligands

max_b_factor

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

metaObject(self) → QMetaObject

min_b_factor

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

onStructureChanged()

parent(self) → QObject

parseDomains(filename)

Parse XML file from UniProt database to get domain information.

Parameters:filename (str) – the XML file to parse for domain information Returns:a list of the domains (names) for the sequence in order Return type:list(str)

property(self, str) → Any

pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

resetAnnotation(ann)

Force a reset of an annotation’s cache.

resnum

sasa

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

sender(self) → QObject

senderSignalIndex(self) → int

setKinaseFeatures(kinase_features)

Set the kinase features for the sequence. Note that we also allow kinase_feature to be of NoneType to imply that kinase annotations have not been calculated because an empty list would imply the annotations were run no features were found.

Parameters:kinase_feature (list[KinaseFeature] or NoneType) – Kinase features.

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

sequence_logo = 7

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

__init__(aln)

Parameters:aln – alignment.Alignment

alignment

A descriptor for an instance attribute that should be stored as a weakref. Unlike weakref.proxy, this descriptor allows the attribute to be hashed.

Note that the weakref is stored on the instance using the same name as the descriptor (which is stored on the class). Since this descriptor implements __set__, it will always take precedence over the value stored on the instance.

indices

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

mean_hydrophobicity

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

mean_isoelectric_point

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

consensus_seq

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

consensus_freq

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

consensus_symbols

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

sequence_logo

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

clearAllCaching()

class schrodinger.protein.annotation.KinaseFeatureFinder(seq)

Bases: object

Class to find kinase features in the sequence.

BACKEND_SINGLE_LETTER_CODE_TO_KINASE_FEATURE = {'A': <KinaseFeatureLabel.ALPHA_C: 'Alpha-C'>, 'C': <KinaseFeatureLabel.CATALYTIC_LOOP: 'Catalytic Loop'>, 'D': <KinaseFeatureLabel.DFG: 'DFG'>, 'G': <KinaseFeatureLabel.GLYCINE_RICH_LOOP: 'Glycine Rich Loop'>, 'H': <KinaseFeatureLabel.HINGE: 'Hinge'>, 'K': <KinaseFeatureLabel.GATE_KEEPER: 'Gate Keeper'>, 'L': <KinaseFeatureLabel.LINKER: 'Linker'>, 'R': <KinaseFeatureLabel.HRD: 'HRD'>, 'T': <KinaseFeatureLabel.ACTIVATION_LOOP: 'Activation Loop'>, '~': <KinaseFeatureLabel.NO_FEATURE: 'No Feature'>}

__init__(seq)

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

seq

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.

is_annotated

getKinaseFeatures()

Return the kinase features for the sequence. If the sequence is not annotated, generate and return the found features.

Raises:ModuleNotFoundError – If kinase_annotation backend is not found and kinase features are to be generated. Returns:Kinase features for the sequence. Return type:list[KinaseFeature]

setKinaseFeatures(kinase_features)

Set the kinase features for the sequence.

Parameters:kinase_features (list[KinaseFeature] or NoneType) – Kinase features for the sequence

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()

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 = 2

antibody_cdr = 21

b_factor = 15

beta_strand_propensity = 7

binding_sites = 19

disulfide_bonds = 5

domains = 20

exposure_tendency = 10

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file. Returns:An instance of the derived class.

:rtype : cls

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

helix_propensity = 6

helix_termination_tendency = 9

hydrophobicity = 13

isoelectric_point = 14

kinase_features = 30

pairwise_constraints = 1

pfam = 23

pred_accessibility = 26

pred_disordered = 27

pred_disulfide_bonds = 24

pred_domain_arr = 28

pred_secondary_structure = 25

proximity_constraints = 29

rescode = 4

resnum = 3

sasa = 22

secondary_structure = 18

side_chain_chem = 12

steric_group = 11

toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

turn_propensity = 8

window_hydrophobicity = 16

window_isoelectric_point = 17

PRED_ANNOTATION_TYPES = {<ANNOTATION_TYPES.pred_accessibility: 26>, <ANNOTATION_TYPES.pred_secondary_structure: 25>, <ANNOTATION_TYPES.pred_domain_arr: 28>, <ANNOTATION_TYPES.pred_disordered: 27>, <ANNOTATION_TYPES.pred_disulfide_bonds: 24>}

RES_PROPENSITY_ANNOTATIONS = {<ANNOTATION_TYPES.beta_strand_propensity: 7>, <ANNOTATION_TYPES.helix_termination_tendency: 9>, <ANNOTATION_TYPES.exposure_tendency: 10>, <ANNOTATION_TYPES.turn_propensity: 8>, <ANNOTATION_TYPES.helix_propensity: 6>, <ANNOTATION_TYPES.steric_group: 11>, <ANNOTATION_TYPES.side_chain_chem: 12>}

alignment_set

antibody_cdr

b_factor

beta_strand_propensity

binding_sites

blockSignals(self, bool) → bool

childEvent(self, QChildEvent)

children(self) → List[QObject]

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

deleteLater(self)

destroyed

destroyed(self, object: QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

disulfide_bonds

domains

domainsChanged

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

exposure_tendency

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

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

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

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

getKinaseFeatures()

Return the kinase features for the sequence.

Returns:Kinase features. Return type:list[KinaseFeature]

getNumAnnValues(ann)

getSSBondPartner(index)

Return the residue’s intra-sequence disulfide bond partner, if any.

If the residue is not involved in a disulfide bond, its partner has been deleted, or its partner is in another sequence, it will return None.

Parameters:index (int) – Index of the residue to check Returns:the other Residue in the disulfide bond or None Return type:schrodinger.protein.residue.Residue or None

helix_propensity

helix_termination_tendency

hydrophobicity

hydrophobicity_window_padding

inherits(self, str) → bool

installEventFilter(self, QObject)

invalidateMaxMinBFactor()

invalidatedDomains

isAntibodyHeavyChain()

Returns:Whether the sequence described is an antibody heavy chain Return type:bool

isAntibodyLightChain()

Returns:Whether the sequence described is an antibody light chain Return type:bool

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

isoelectric_point

isoelectric_point_window_padding

killTimer(self, int)

kinase_features

ligands

max_b_factor

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

metaObject(self) → QMetaObject

min_b_factor

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

pairwise_constraints

parent(self) → QObject

pfam

pred_accessibility

pred_disordered

pred_disulfide_bonds

pred_domain_arr

pred_secondary_structure

property(self, str) → Any

proximity_constraints

pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

rescode

resnum

sasa

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

secondary_structure

sender(self) → QObject

senderSignalIndex(self) → int

setKinaseFeatures(kinase_feature)

Set the kinase features for the sequence. Note that we also allow kinase_feature to be of NoneType to imply that kinase annotations have not been calculated because an empty list would imply the annotations were run no features were found.

Parameters:kinase_feature (list[KinaseFeature] or NoneType) – Kinase features.

setObjectName(self, str)

setParent(self, QObject)

setProperty(self, str, Any) → bool

side_chain_chem

signalsBlocked(self) → bool

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

steric_group

thread(self) → QThread

timerEvent(self, QTimerEvent)

titleChanged

tr(self, str, disambiguation: str = None, n: int = -1) → str

turn_propensity

window_hydrophobicity

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

window_isoelectric_point

Decorator that converts a method with a single self argument into a property cached on the instance.

Use del to delete the currently cached value and force a recalculation on the next access. See the tests for examples.

This class is based on code that is Copyright (c) Django Software Foundation

chainAdded(chain)

Respond to a new chain being added to the sequence. The sequence is responsible for calling this method whenever a chain is added.

Parameters:chain (sequence.ProteinSequence) – The newly added chain.

chainRemoved(chain)

Respond to a chain being removed from the sequence. The sequence is responsible for calling this method whenever a chain is removed.

Parameters:chain (sequence.ProteinSequence) – The removed chain.

getAntibodyCDR(col, scheme)

Returns the antibody CDR information of the col’th index in the sequence under a given antibody CDR numbering scheme.

Parameters:

• col (int) – index into the sequence
• scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use

Returns:

Antibody CDR label, start, and end positions

Return type:

AntibodyCDR, which is a named tuple of (AntibodyCDRLabel, int, int) if col is in a CDR, otherwise (AntibodyCDRLabel.NotCDR, None, None)

getAntibodyCDRs(scheme)

Returns a list of antibody CDR information for the entire sequence.

Parameters:scheme (AntibodyCDRScheme) – The antibody CDR numbering scheme to use Returns:A list of Antibody CDR labels, starts, and end positions Return type:list(AntibodyCDR)

isAntibodyChain()

Returns:Whether the sequence described is an antibody chain Return type:bool

setLigandDistance(distance)

Updates the ligand distance and invalidates the cache

getKinaseFeature(col)

Returns the KinaseFeature for the index in the sequence.

Parameters:col (int) – sequence index Returns:Kinase feature. Return type:KinaseFeature

clearAllCaching()

schrodinger.protein.annotation.make_ligand_name_atom(ct, atom_index)

Make a unique, human-readable name for a ligand identified by atom index.

Parameters:

• ct (schrodinger.structure.Structure) – Structure the ligand belongs to
• atom_index (int) – the atom index of the ligand to make a name for

Returns:

The name for the ligand

Return type:

str

schrodinger.protein.annotation.make_ligand_name(ct, ligand)

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

Parameters:

• ct (schrodinger.structure.Structure) – Structure the ligand belongs to
• ligand (schrodinger.structutils.analyze.Ligand) – the ligand to make a name for

Returns:

The name for the ligand

Return type:

str