An empty vertex has the behaviors of a vertex, but has no molecular structure. More...

Inheritance diagram for denoptim.graph.EmptyVertex:

Collaboration diagram for denoptim.graph.EmptyVertex:

Public Member Functions
	EmptyVertex ()
	Constructor for an empty vertex. More...

	EmptyVertex (BBType type)
	Constructor for an identified vertex without attachment points. More...

	EmptyVertex (long id)
	Constructor for an identified vertex without attachment points. More...

	EmptyVertex (long id, ArrayList< AttachmentPoint > lstAPs, ArrayList< SymmetricAPs > lstSymAPs, boolean isRCV)
	Constructor for an identified vertex. More...

List< AttachmentPoint >	getAttachmentPoints ()

void	setSymmetricAP (List< SymmetricAPs > sAPs)

List< SymmetricAPs >	getSymmetricAP ()

SymmetricAPs	getSymmetricAPs (AttachmentPoint ap)
	For the given attachment point index locate the symmetric partners i.e. More...

int	getNumberOfAPs ()

ArrayList< Integer >	getFreeAPList ()

int	getFreeAPCount ()

boolean	hasFreeAP ()

boolean	hasSymmetricAP ()

String	toString ()
	Produces a human readable, short string to represent the vertex by its vertex ID, building block ID (1-based), building block type, and level in the graph (if any). More...

void	cleanup ()

EmptyVertex	clone ()
	Returns a deep-copy of this vertex. More...

void	addAP ()
	Adds an attachment point with no `APClass` or other attribute. More...

void	addAP (APClass apClass)
	Adds an attachment point with the specified `APClass`. More...

boolean	sameAs (EmptyVertex other, StringBuilder reason)
	Compares this and another vertex ignoring vertex IDs. More...

int	getHeavyAtomsCount ()

boolean	containsAtoms ()

IAtomContainer	getIAtomContainer ()
	Although empty vertex do not contain atoms, by definitions, we allow the generation of an SDF representation that uses an empty atom list. More...

IAtomContainer	getIAtomContainer (Logger logger, Randomizer rng, boolean removeUsedRCAs, boolean rebuild)
	Although empty vertex do not contain atoms, by definitions, we allow the generation of an SDF representation that uses an empty atom list. More...

String	toJson ()
	Produces a string that represents this vertex and that adheres to the JSON format. More...

ArrayList< APClass >	getAllAPClasses ()
	Returns the list of all APClasses on present on this fragment. More...

List< SymmetricAPs >	getSymmetricAPSets ()

List< Vertex >	getMutationSites (List< MutationType > ignoredTypes)
	A list of mutation sites from within this vertex. More...

Public Member Functions inherited from denoptim.graph.Vertex
	Vertex (VertexType vertexType)
	Constructor for an empty vertex. More...

	Vertex (VertexType vertexType, long id)
	Constructor for an identified vertex without attachment points. More...

abstract List< AttachmentPoint >	getAttachmentPoints ()

void	setAsRCV (boolean isRCV)

void	setVertexId (long vertexId2)

long	getVertexId ()

int	getBuildingBlockId ()
	Returns the index of the building block that should correspond to the position of the building block in the library of building blocks of its kind. More...

void	setBuildingBlockId (int buildingBlockId)

Vertex.BBType	getBuildingBlockType ()

void	setBuildingBlockType (Vertex.BBType buildingBlockType)

abstract List< SymmetricAPs >	getSymmetricAPSets ()

SymmetricAPs	getSymmetricAPs (AttachmentPoint ap)
	For the given attachment point index locate the symmetric partners i.e. More...

int	getNumberOfAPs ()

int	getFreeAPCount ()

ArrayList< AttachmentPoint >	getFreeAPThroughout ()
	Gets attachment points that are availability throughout the graph level, i.e., checks also across the inner graph template boundary. More...

int	getFreeAPCountThroughout ()
	Counts the number of attachment points that are availability throughout the graph level, i.e., checks also across the inner graph template boundary. More...

ArrayList< AttachmentPoint >	getCappedAPs ()
	Gets attachment points that are used by capping groups. More...

ArrayList< AttachmentPoint >	getCappedAPsThroughout ()
	Gets attachment points that are used by capping groups throughout the graph levels, i.e., checks also across the inner graph template boundary. More...

int	getCappedAPCountThroughout ()
	Counts the number of attachment points that are used by `BBType#CAP` vertex. More...

boolean	hasFreeAP ()

boolean	isRCV ()

boolean	hasSymmetricAP ()

String	toString ()
	Produces a human readable, short string to represent the vertex by its vertex ID, building block ID (1-based), building block type, and level in the graph (if any). More...

void	cleanup ()

abstract Vertex	clone ()
	Returns a deep-copy of this vertex. More...

boolean	sameAs (Vertex other)
	Compares this and another vertex ignoring vertex IDs. More...

boolean	sameAs (Vertex other, StringBuilder reason)
	Compares this and another vertex ignoring vertex IDs. More...

boolean	sameVertexFeatures (Vertex other, StringBuilder reason)
	Compares this and another vertex ignoring vertex IDs. More...

abstract int	getHeavyAtomsCount ()

abstract boolean	containsAtoms ()

abstract IAtomContainer	getIAtomContainer ()

abstract IAtomContainer	getIAtomContainer (Logger logger, Randomizer rng, boolean removeUsedRCAs, boolean rebuild)
	Method meant to trigger regeneration of the chemical representation, typically needed to drop a low quality structure that is good enough for most cheminformatic tasks, and replace it with a better quality structure that is suitable to be fed to molecular modeling tasks. More...

ArrayList< APClass >	getAllAPClasses ()
	Returns the list of all APClasses present on this vertex. More...

ArrayList< APClass >	getAllAvailableAPClasses ()
	Returns the list of all APClasses present on free attachment point on this vertex. More...

void	resetGraphOwner ()

void	setGraphOwner (DGraph owner)

DGraph	getGraphOwner ()
	Returns the graph this vertex belongs to or null. More...

List< Vertex >	getMutationSites ()
	A list of mutation sites from within this vertex. More...

abstract List< Vertex >	getMutationSites (List< MutationType > ignoredTypes)
	A list of mutation sites from within this vertex. More...

void	setMutationTypes (List< MutationType > lst)

boolean	removeMutationType (MutationType mt)
	Removes the specified mutation type. More...

List< MutationType >	getMutationTypes ()
	Returns the list of mutation types. More...

List< MutationType >	getMutationTypes (List< MutationType > excludedTypes)
	Returns the list of mutation types. More...

AttachmentPoint	getAP (int i)
	Get attachment point i on this vertex. More...

AttachmentPoint	getAPWithId (int i)
	Get attachment point that has the given identifier, or null. More...

int	getIndexOfAP (AttachmentPoint ap)
	Returns the position of the given AP in the list of APs of this vertex. More...

Edge	getEdgeToParent ()
	Looks into the edges that use any of the APs that belong to this vertex and returns the edge that has this vertex as the target, i.e., the edge to the parent vertex. More...

Vertex	getParent ()
	Looks into the edges that use any of the APs that belong to this vertex and returns the vertex which is the source of the edge in which this vertex is the target. More...

ArrayList< AttachmentPoint >	getAPsFromChildren ()
	Looks into the edges that use any of the APs that belong to this vertex and returns the list of attachment point on child vertices that form an edge with any of the APs of this vertex. More...

ArrayList< Vertex >	getChildrenThroughout ()
	Looks into the edges that use any of the APs that belong to this vertex and returns the list of vertices which are target of any edge departing from this vertex. More...

ArrayList< Vertex >	getChilddren ()
	Looks into the edges that use any of the APs that belong to this vertex and returns the list of vertices which are target of any edge departing from this vertex. More...

void	setUniquefyingProperty (String key)
	Add the given key among the properties that are checked for equality when comparing vertices with the `Vertex#sameAs(Vertex, StringBuilder)` method. More...

Map< Object, Object >	getProperties ()

boolean	hasProperty (Object property)

Object	getProperty (Object property)

void	setProperty (Object key, Object property)

void	removeProperty (Object key)

void	setProperties (Map< Object, Object > properties)

VertexType	getVertexType ()
	Returns the value of the vertex type. More...

String[]	getPathIDs (AttachmentPoint apA, AttachmentPoint apB)
	Produces a pair of strings that identify the "path" between two given attachment points. More...

boolean	connectedTo (Vertex other)
	Checks if this and another vertex are directly connected by an edge within the same graph recursion level, i.e., both vertices must belong to the same graph. More...

Edge	getEdgeWith (Vertex other)
	Finds the edge between this and the other vertex, if it exists. More...

Static Public Member Functions
static EmptyVertex	fromJson (String json)
	Reads a JSON string and returns an instance of this class. More...

Static Public Member Functions inherited from denoptim.graph.Vertex
static Vertex	newVertexFromLibrary (int bbId, Vertex.BBType bbt, FragmentSpace fragSpace) throws DENOPTIMException
	Builds a new molecular fragment kind of vertex. More...

static Vertex	newVertexFromLibrary (long vertexId, int bbId, Vertex.BBType bbt, FragmentSpace fragSpace) throws DENOPTIMException
	Make a new vertex that is a copy of a vertex in the fragment space. More...

static Vertex	fromJson (String json)

static Vertex	convertIACToVertex (IAtomContainer iac, Vertex.BBType bbt) throws DENOPTIMException
	Processes an `IAtomContainer` and builds a `Vertex` that is an instance of `Fragment`. More...

static Vertex	parseVertexFromSDFFormat (IAtomContainer mol, Gson reader, BBType bbt) throws DENOPTIMException
	Created a `Vertex` from the SDF representation, i.e., from an `IAtomContainer`. More...

Protected Member Functions
void	setSymmetricAPSets (List< SymmetricAPs > sAPs)

void	addSymmetricAPSet (SymmetricAPs symAPs)

Protected Member Functions inherited from denoptim.graph.Vertex
abstract void	setSymmetricAPSets (List< SymmetricAPs > sAPs)

abstract void	addSymmetricAPSet (SymmetricAPs symAPs)

int	getUniqueAPIndex ()

List< MutationType >	getUnfilteredMutationTypes ()
	Returns the mutation types that are constitutionally configures for this vertex irrespectively on the graph or the context in which this vertex is included. More...

Map< Object, Object >	copyStringBasedProperties ()
	Copies all the string-based properties and properties defined in the `Vertex#uniquefyingPropertyKeys` set. More...

Private Attributes
List< AttachmentPoint >	lstAPs
	Attachment points on this vertex. More...

List< SymmetricAPs >	lstSymAPs
	List of AP sets that are related to each other, so that we call them "symmetric" (though symmetry is a fuzzy concept here). More...

Additional Inherited Members
Protected Attributes inherited from denoptim.graph.Vertex
int	buildingBlockId = -99
	Index of this building block in the library of building blocks, or negative if this vertex is not part of a library. More...

BBType	buildingBlockType = Vertex.BBType.UNDEFINED

Map< Object, Object >	properties
	Map of customizable properties. More...

Set< String >	uniquefyingPropertyKeys = new HashSet<String>()
	List of properties required to make `Vertex#sameAs(Vertex, StringBuilder)` method return `false` when property values differ. More...

final VertexType	vertexType
	Field distinguishing implementations of `Vertex` when deserializing JSON representations. More...

Detailed Description

An empty vertex has the behaviors of a vertex, but has no molecular structure.

It has attachment points, as well as relations between those attachment points, but has no atoms.

Definition at line 44 of file EmptyVertex.java.

Constructor & Destructor Documentation

◆ EmptyVertex() [1/4]

denoptim.graph.EmptyVertex.EmptyVertex ( )

Constructor for an empty vertex.

Definition at line 62 of file EmptyVertex.java.

References denoptim.graph.Vertex.VertexType.EmptyVertex, denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.graph.EmptyVertex.lstAPs, and denoptim.graph.EmptyVertex.lstSymAPs.

Referenced by denoptim.graph.EmptyVertex.clone().

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◆ EmptyVertex() [2/4]

denoptim.graph.EmptyVertex.EmptyVertex ( BBType type )

Constructor for an identified vertex without attachment points.

Parameters

id	the VertedID of the vertex to construct. Note that this ID should be unique within a graph. To generate unique IDs either use `GraphUtils#getUniqueVertexIndex()` or use constructor `EmptyVertex()`.

Definition at line 78 of file EmptyVertex.java.

References denoptim.graph.Vertex.buildingBlockType, denoptim.graph.Vertex.VertexType.EmptyVertex, denoptim.graph.EmptyVertex.lstAPs, and denoptim.graph.EmptyVertex.lstSymAPs.

◆ EmptyVertex() [3/4]

denoptim.graph.EmptyVertex.EmptyVertex ( long id )

Constructor for an identified vertex without attachment points.

Parameters

id	the VertedID of the vertex to construct. Note that this ID should be unique within a graph. To generate unique IDs either use `GraphUtils#getUniqueVertexIndex()` or use constructor `EmptyVertex()`.

Definition at line 95 of file EmptyVertex.java.

References denoptim.graph.Vertex.VertexType.EmptyVertex, denoptim.graph.EmptyVertex.lstAPs, and denoptim.graph.EmptyVertex.lstSymAPs.

◆ EmptyVertex() [4/4]

denoptim.graph.EmptyVertex.EmptyVertex	(	long	id,
		ArrayList< AttachmentPoint >	lstAPs,
		ArrayList< SymmetricAPs >	lstSymAPs,
		boolean	isRCV
	)

Constructor for an identified vertex.

Parameters

id	the VertedID of the vertex to construct. Note that this ID should be unique within a graph. To generate unique IDs either use
lstAPs	the list of attachment point on this vertex.
lstSymAPs	the list of symmetric sets of APs.
isRCV	set `true` to mark this vertex as a ring-closing vertex.

Definition at line 113 of file EmptyVertex.java.

References denoptim.graph.Vertex.VertexType.EmptyVertex, denoptim.graph.Vertex.isRCV, denoptim.graph.EmptyVertex.lstAPs, denoptim.graph.EmptyVertex.lstSymAPs, and denoptim.graph.Vertex.setAsRCV().

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Member Function Documentation

◆ addAP() [1/2]

void denoptim.graph.EmptyVertex.addAP ( )

Adds an attachment point with no APClass or other attribute.

This is used only for testing purposes.

Definition at line 298 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.getAttachmentPoints().

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◆ addAP() [2/2]

void denoptim.graph.EmptyVertex.addAP ( APClass apClass )

Adds an attachment point with the specified APClass.

Parameters

apClass the APClass

Definition at line 309 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.getAttachmentPoints().

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◆ addSymmetricAPSet()

void denoptim.graph.EmptyVertex.addSymmetricAPSet ( SymmetricAPs symAPs )

protected

Reimplemented from denoptim.graph.Vertex.

Definition at line 459 of file EmptyVertex.java.

Referenced by denoptim.graph.DGraphTest.makeTestGraphM(), denoptim.graph.DGraphTest.makeTestGraphN(), and denoptim.graph.VertexTest.testFromToJSON_withSymmetricAPs().

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◆ cleanup()

void denoptim.graph.EmptyVertex.cleanup ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 237 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstAPs, and denoptim.graph.EmptyVertex.lstSymAPs.

◆ clone()

EmptyVertex denoptim.graph.EmptyVertex.clone ( )

Returns a deep-copy of this vertex.

Returns: a deep-copy

Reimplemented from denoptim.graph.Vertex.

Definition at line 256 of file EmptyVertex.java.

Referenced by denoptim.graph.DGraphTest.makeTestGraphM(), denoptim.graph.DGraphTest.makeTestGraphN(), denoptim.graph.VertexTest.testClone(), denoptim.graph.AttachmentPointTest.testSameAs(), and denoptim.graph.AttachmentPointTest.testSameAs_DiffAPClass().

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◆ containsAtoms()

boolean denoptim.graph.EmptyVertex.containsAtoms ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 354 of file EmptyVertex.java.

◆ fromJson()

static EmptyVertex denoptim.graph.EmptyVertex.fromJson ( String json )

static

Reads a JSON string and returns an instance of this class.

Parameters

json	the string to parse.

Returns: a new instance of this class.

Reimplemented from denoptim.graph.Vertex.

Definition at line 416 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.fromJson(), denoptim.graph.EmptyVertex.getAttachmentPoints(), and denoptim.json.DENOPTIMgson.getReader().

Referenced by denoptim.graph.Vertex.DENOPTIMVertexDeserializer.deserialize(), and denoptim.graph.EmptyVertex.fromJson().

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◆ getAllAPClasses()

ArrayList< APClass > denoptim.graph.EmptyVertex.getAllAPClasses ( )

Returns the list of all APClasses on present on this fragment.

Returns: the list of APClassess

Reimplemented from denoptim.graph.Vertex.

Definition at line 434 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstAPs.

◆ getAttachmentPoints()

List< AttachmentPoint > denoptim.graph.EmptyVertex.getAttachmentPoints ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 124 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstAPs.

Referenced by denoptim.graph.EmptyVertex.addAP(), denoptim.graph.EmptyVertex.fromJson(), denoptim.fragspace.APMapFinderTest.testFindMappingCompatibileAPs(), and denoptim.graph.AttachmentPointTest.testGetEmbeddedAP().

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◆ getFreeAPCount()

int denoptim.graph.EmptyVertex.getFreeAPCount ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 194 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstAPs.

◆ getFreeAPList()

ArrayList< Integer > denoptim.graph.EmptyVertex.getFreeAPList ( )

Returns: list of attachment points that have free valences

Definition at line 181 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstAPs.

◆ getHeavyAtomsCount()

int denoptim.graph.EmptyVertex.getHeavyAtomsCount ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 347 of file EmptyVertex.java.

◆ getIAtomContainer() [1/2]

IAtomContainer denoptim.graph.EmptyVertex.getIAtomContainer ( )

Although empty vertex do not contain atoms, by definitions, we allow the generation of an SDF representation that uses an empty atom list.

Returns: an empty atom container that contains the definition of the vertex in the JSON-formatted property.

Reimplemented from denoptim.graph.Vertex.

Definition at line 369 of file EmptyVertex.java.

References denoptim.constants.DENOPTIMConstants.APSTAG, and denoptim.constants.DENOPTIMConstants.VERTEXJSONTAG.

Referenced by denoptim.graph.EmptyVertex.getIAtomContainer().

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◆ getIAtomContainer() [2/2]

IAtomContainer denoptim.graph.EmptyVertex.getIAtomContainer	(	Logger	logger,
		Randomizer	rng,
		boolean	removeUsedRCAs,
		boolean	rebuild
	)

Although empty vertex do not contain atoms, by definitions, we allow the generation of an SDF representation that uses an empty atom list.

However, this method is ignoring all the parameters and calling getIAtomContainer()

Reimplemented from denoptim.graph.Vertex.

Definition at line 387 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.getIAtomContainer().

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◆ getMutationSites()

List< Vertex > denoptim.graph.EmptyVertex.getMutationSites ( List< MutationType > ignoredTypes )

A list of mutation sites from within this vertex.

Parameters

ignoredTypes a collection of mutation types to ignore. vertices that allow only ignored types of mutation will not be considered mutation sites.

Returns: the list of vertices that allow any non-ignored mutation type.

Reimplemented from denoptim.graph.Vertex.

Definition at line 487 of file EmptyVertex.java.

References denoptim.graph.Vertex.getBuildingBlockType(), and denoptim.graph.Vertex.getMutationTypes().

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◆ getNumberOfAPs()

int denoptim.graph.EmptyVertex.getNumberOfAPs ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 169 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstAPs.

Referenced by denoptim.graph.VertexTest.testClone().

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◆ getSymmetricAP()

List< SymmetricAPs > denoptim.graph.EmptyVertex.getSymmetricAP ( )

Definition at line 138 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstSymAPs.

◆ getSymmetricAPs()

SymmetricAPs denoptim.graph.EmptyVertex.getSymmetricAPs ( AttachmentPoint ap )

For the given attachment point index locate the symmetric partners i.e.

those with similar environments and class types.

Parameters

ap	index of the attachment point which we want to get the symmetrically related partners of.

Returns: the list of attachment point IDs, which include apIdx or null if no partners present

Reimplemented from denoptim.graph.Vertex.

Definition at line 155 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstSymAPs.

◆ getSymmetricAPSets()

List< SymmetricAPs > denoptim.graph.EmptyVertex.getSymmetricAPSets ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 471 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstSymAPs.

Referenced by denoptim.graph.VertexTest.testClone().

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◆ hasFreeAP()

boolean denoptim.graph.EmptyVertex.hasFreeAP ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 206 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstAPs.

◆ hasSymmetricAP()

boolean denoptim.graph.EmptyVertex.hasSymmetricAP ( )

Returns: true if vertex has symmetric APs

Reimplemented from denoptim.graph.Vertex.

Definition at line 222 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstSymAPs.

◆ sameAs()

boolean denoptim.graph.EmptyVertex.sameAs	(	EmptyVertex	other,
		StringBuilder	reason
	)

Compares this and another vertex ignoring vertex IDs.

A difference in any property that has been marked as an uniquefying property with the {} method makes this method return false.

Parameters

other
reason	string builder used to build the message clarifying the reason for returning `false`.

Returns: true if the two vertices represent the same graph node even if the vertex IDs are different.

Definition at line 328 of file EmptyVertex.java.

References denoptim.graph.Vertex.properties, denoptim.graph.Vertex.sameVertexFeatures(), and denoptim.graph.Vertex.uniquefyingPropertyKeys.

Referenced by denoptim.io.DenoptimIOTest.testIOEmptyVertex(), denoptim.graph.VertexTest.testSameAs_DiffAPNum(), and denoptim.graph.VertexTest.testSameAs_Equal().

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◆ setSymmetricAP()

void denoptim.graph.EmptyVertex.setSymmetricAP ( List< SymmetricAPs > sAPs )

Definition at line 131 of file EmptyVertex.java.

References denoptim.graph.EmptyVertex.lstSymAPs.

◆ setSymmetricAPSets()

void denoptim.graph.EmptyVertex.setSymmetricAPSets ( List< SymmetricAPs > sAPs )

protected

Reimplemented from denoptim.graph.Vertex.

Definition at line 451 of file EmptyVertex.java.

Referenced by denoptim.graph.EmptyVertex.clone().

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◆ toJson()

String denoptim.graph.EmptyVertex.toJson ( )

Produces a string that represents this vertex and that adheres to the JSON format.

Returns: the JSON format as a single string

Definition at line 401 of file EmptyVertex.java.

References denoptim.json.DENOPTIMgson.getWriter().

Referenced by denoptim.graph.VertexTest.testFromToJSON_minimal(), and denoptim.graph.VertexTest.testFromToJSON_withSymmetricAPs().

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◆ toString()

String denoptim.graph.EmptyVertex.toString ( )

Produces a human readable, short string to represent the vertex by its vertex ID, building block ID (1-based), building block type, and level in the graph (if any).

This is the old syntax used up to version 2 for reporting a vertex in the string representation of a graph. Such notation cannot hold all the information needed to define a template, and is, therefore, obsolete. Use JSON format to serialize a graph that may contain templates.

Reimplemented from denoptim.graph.Vertex.

Definition at line 230 of file EmptyVertex.java.

References denoptim.graph.Vertex.getVertexId().

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Member Data Documentation

◆ lstAPs

List<AttachmentPoint> denoptim.graph.EmptyVertex.lstAPs

private

Attachment points on this vertex.

Definition at line 49 of file EmptyVertex.java.

Referenced by denoptim.graph.EmptyVertex.cleanup(), denoptim.graph.EmptyVertex.clone(), denoptim.graph.EmptyVertex.EmptyVertex(), denoptim.graph.EmptyVertex.getAllAPClasses(), denoptim.graph.EmptyVertex.getAttachmentPoints(), denoptim.graph.EmptyVertex.getFreeAPCount(), denoptim.graph.EmptyVertex.getFreeAPList(), denoptim.graph.EmptyVertex.getNumberOfAPs(), and denoptim.graph.EmptyVertex.hasFreeAP().

◆ lstSymAPs

List<SymmetricAPs> denoptim.graph.EmptyVertex.lstSymAPs

private

List of AP sets that are related to each other, so that we call them "symmetric" (though symmetry is a fuzzy concept here).

Definition at line 55 of file EmptyVertex.java.

Referenced by denoptim.graph.EmptyVertex.cleanup(), denoptim.graph.EmptyVertex.clone(), denoptim.graph.EmptyVertex.EmptyVertex(), denoptim.graph.EmptyVertex.getSymmetricAP(), denoptim.graph.EmptyVertex.getSymmetricAPs(), denoptim.graph.EmptyVertex.getSymmetricAPSets(), denoptim.graph.EmptyVertex.hasSymmetricAP(), and denoptim.graph.EmptyVertex.setSymmetricAP().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/graph/EmptyVertex.java

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ EmptyVertex() [1/4]

◆ EmptyVertex() [2/4]

◆ EmptyVertex() [3/4]

◆ EmptyVertex() [4/4]

Member Function Documentation

◆ addAP() [1/2]

◆ addAP() [2/2]

◆ addSymmetricAPSet()

◆ cleanup()

◆ clone()

◆ containsAtoms()

◆ fromJson()

◆ getAllAPClasses()

◆ getAttachmentPoints()

◆ getFreeAPCount()

◆ getFreeAPList()

◆ getHeavyAtomsCount()

◆ getIAtomContainer() [1/2]

◆ getIAtomContainer() [2/2]

◆ getMutationSites()

◆ getNumberOfAPs()

◆ getSymmetricAP()

◆ getSymmetricAPs()

◆ getSymmetricAPSets()

◆ hasFreeAP()

◆ hasSymmetricAP()

◆ sameAs()

◆ setSymmetricAP()

◆ setSymmetricAPSets()

◆ toJson()

◆ toString()

Member Data Documentation

◆ lstAPs

◆ lstSymAPs