schrodinger.protein.annotation module

Annotations for biological sequences

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.annotation.BINDING_SITE(value)

Bases: enum.Enum

An enumeration.

CloseContact = 1

FarContact = 2

NoContact = 3

class schrodinger.protein.annotation.AntibodyCDRLabel(value)

Bases: enum.Enum

An enumeration.

NotCDR = 1

L1 = 2

L2 = 3

L3 = 4

H1 = 5

H2 = 6

H3 = 7

class schrodinger.protein.annotation.AntibodyCDR(label, start, end)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

end

Alias for field number 2

index(value, start=0, stop=9223372036854775807, /)

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(value)

Bases: enum.Enum

An enumeration.

Domain = 1

NoDomain = 2

class schrodinger.protein.annotation.KinaseConservation(value)

Bases: schrodinger.models.jsonable.JsonableEnum

An enumeration.

VeryLow = 'Very Low'

Low = 'Low'

Medium = 'Medium'

High = 'High'

VeryHigh = 'Very High'

class schrodinger.protein.annotation.KinaseFeatureLabel(value)

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(value)

Bases: enum.Enum

An enumeration.

not_conserved = ' '

fully_conserved = '*'

strongly_conserved = ':'

weakly_conserved = '.'

property tooltip

class schrodinger.protein.annotation.TupleWithRange(iterable=(), /)

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__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

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

isKinaseChain() → bool

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

property binding_sites

property ligands

property ligand_asls

setLigandDistance(distance)

Updates the ligand distance and invalidates the cache

property 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

kinaseFeaturesChanged

class ANNOTATION_TYPES(*args, **kwargs)

Bases: schrodinger.models.json.JsonableClassMixin

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.

Return type

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.

Return type

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_conservation = 31

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

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

__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

property hydrophobicity_window_padding

property 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

property is_kinase_annotated

isKinaseChain()

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()

property inscode

property resnum

getCDRResidueList(scheme)

Returns

List of CDR Residues.

Return type

List[str]

property 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)

property 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)

property ligand_asls

property 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

property is_kinase_annotated

isKinaseChain()

class ANNOTATION_TYPES(*args, **kwargs)

Bases: schrodinger.models.json.JsonableClassMixin

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.

Return type

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.

Return type

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_conservation = 31

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_domain_arr: 28>, <ANNOTATION_TYPES.pred_disulfide_bonds: 24>, <ANNOTATION_TYPES.pred_accessibility: 26>, <ANNOTATION_TYPES.pred_disordered: 27>, <ANNOTATION_TYPES.pred_secondary_structure: 25>}

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

__init__(seq)

Parameters

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

annotationInvalidated

property 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)

property 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)

getCDRResidueList(scheme)

Returns

List of CDR Residues.

Return type

List[str]

getKinaseFeature(col)

Returns the KinaseFeature for the index in the sequence.

Parameters

col (int) – sequence index

Returns

Kinase feature.

Return type

KinaseFeature

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

getSparseRescodes(modulo)

property hydrophobicity_window_padding

inherits(self, str) → bool

property 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

property isoelectric_point_window_padding

killTimer(self, int)

kinaseFeaturesChanged

property ligand_asls

property 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.

property 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(*args, **kwargs)

Bases: schrodinger.models.json.JsonableClassMixin

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.

Return type

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.

Return type

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.SeqTypeMixin(seq, *args, **kwargs)

Bases: object

Mixin to customize antibody.SeqType for MSV2. See _delayed_antibody_import for class declaration.

__init__(seq, *args, **kwargs)

isHeavyChain()

isLightChain()

class schrodinger.protein.annotation.CombinedChainSequenceAnnotationMeta(cls, bases, classdict, *, wraps=None, cached_annotations=(), wrapped_properties=())

Bases: schrodinger.application.msv.utils.QtDocstringWrapperMetaClass

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

__init__(*args, **kwargs)

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(*args, **kwargs)

Bases: schrodinger.models.json.JsonableClassMixin

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.

Return type

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.

Return type

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_conservation = 31

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_domain_arr: 28>, <ANNOTATION_TYPES.pred_disulfide_bonds: 24>, <ANNOTATION_TYPES.pred_accessibility: 26>, <ANNOTATION_TYPES.pred_disordered: 27>, <ANNOTATION_TYPES.pred_secondary_structure: 25>}

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

property alignment_set

property antibody_cdr

property b_factor

property beta_strand_propensity

property 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)

property disulfide_bonds

property domains

domainsChanged

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → List[QByteArray]

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

property 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

property helix_propensity

property helix_termination_tendency

property hydrophobicity

property 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

property isoelectric_point

property isoelectric_point_window_padding

killTimer(self, int)

property kinase_conservation

property kinase_features

property ligand_asls

property 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]

property pairwise_constraints

parent(self) → QObject

property pfam

property pred_accessibility

property pred_disordered

property pred_disulfide_bonds

property pred_domain_arr

property pred_secondary_structure

property(self, str) → Any

property 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)

property rescode

property 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

property 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

property side_chain_chem

signalsBlocked(self) → bool

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

property steric_group

thread(self) → QThread

timerEvent(self, QTimerEvent)

titleChanged

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

property 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

isKinaseChain()

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