Inheritance diagram for denoptim.graph.Template:

Collaboration diagram for denoptim.graph.Template:

Classes
enum	ContractLevel
	Enum specifying to what extent the template's inner graph can be changed. More...

Public Member Functions
	Template (Vertex.BBType bbType)

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

ContractLevel	getContractLevel ()
	Returns the contract level of this template, i.e., to what extent the content of this template can be changed. More...

void	setContractLevel (ContractLevel contract)
	Imposes the given contract to this template. More...

boolean	freezeTemplate ()
	Promotes the contract level of this template to the most constrained one (i.e., `ContractLevel#FIXED`), i.e. More...

Template	clone ()
	Returns a deep copy of this template. More...

DGraph	getInnerGraph ()

void	setInnerGraph (DGraph innerGraph) throws IllegalArgumentException

void	addInnerToOuterAPMapping (AttachmentPoint newInnerAP)
	Adds the projection of an AP in the template's inner graph (i.e., innerAP) to the list of APs visible from outside the template (i.e., the outerAPs). More...

void	updateInnerApID (AttachmentPoint oldInnerAP, AttachmentPoint newInnerAP)
	Replaces a given link between APs on the surface of this template (i.e., outerAP) and the corresponding APs in the embedded graph (i.e., innerAPs). More...

void	removeProjectionOfInnerAP (AttachmentPoint oldInnerAP) throws DENOPTIMException
	Removes the mapping of the given inner AP from this template's surface, if such mapping exists. More...

ArrayList< AttachmentPoint >	getAttachmentPoints ()
	Return the list of attachment points visible from outside the template, i.e., the so-called outer APs. More...

List< SymmetricAPs >	getSymmetricAPSets ()
	The `SymmetricSet` produced from this method contain indexes of the `AttachmentPoint`s in the list returned by `getAttachmentPoints()`. More...

int	getHeavyAtomsCount ()

boolean	containsAtoms ()

void	clearIAtomContainer ()
	Removes the molecular representation. More...

void	setIAtomContainer (IAtomContainer mol, boolean updateAPsAccordingToIAC) throws DENOPTIMException
	Attaches a molecular representation to this template. More...

IAtomContainer	getIAtomContainer ()
	The molecular representation, if any, is generated by this method and stored until further changes in the content of this template. More...

IAtomContainer	getIAtomContainer (Logger logger, Randomizer rng, boolean removeUsedRCAs, boolean rebuild)
	The molecular representation, if any, is generated by this method and stored until further changes in the content of this template. More...

AttachmentPoint	getInnerAPFromOuterAP (AttachmentPoint outerAP)

AttachmentPoint	getOuterAPFromInnerAP (AttachmentPoint innerAP)

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

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

void	addRequiredAP (Point3d pt, APClass apClass)
	Adds attachment point (AP) to the list of required APs on this template. More...

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

String	toJson ()
	Produces a string that represents this vertex and that adheres to the JSON format. 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 Template	getTestTemplate (ContractLevel contractLevel) throws DENOPTIMException
	Method meant for devel phase only. More...

static Template	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)
	This method exists by contract, but does not do anything because the concept of setting the symmetric set of APs in a template is not defined yet. More...

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 Member Functions
void	updateInnerToOuter (TreeMap< Integer, AttachmentPoint > map)

boolean	isValidInnerGraph (DGraph g)

void	updateMutTypeToFixedSTructure ()

List< AttachmentPoint >	getRequiredAPs ()

Private Attributes
DGraph	innerGraph
	Graph that is embedded in this vertex. More...

IAtomContainer	mol = null
	Molecular representation of the content of this template. More...

ContractLevel	contractLevel = ContractLevel.FIXED
	Denotes the constants in the template. More...

List< AttachmentPoint >	requiredAPs = new ArrayList<>()

APTreeMap	innerToOuterAPs

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

A template is a Vertex that contains a DGraph. The content of the template, i.e., the embedded DGraph, is subject to constraints that are defined by the ContractLevel of the template and may or may not allow changes on the embedded DGraph.

The embedded DGraph projects a reflection of any available AttachmentPoint to the surface of the template. The inner AttachmentPoints, i.e., those owned by the embedded DGraph, are not the same instances as the outer ones, i.e., those on the surface of the template. However, this class keeps a one-to-one mapping that is made available by the innerToOuterAPs method. The distinction of inner and outer AttachmentPoints determines the existence of a barrier between the inside and the outside of a template. Methods mark with the word "Throughout" are used for operations that go across such barrier.

For example, consider an AttachmentPoint in the embedded DGraph (i.e., the inner AttachmentPoint. The AttachmentPoint#isAvailable() method returns true even if its extra-template reflection (i.e., the outer AttachmentPoint) is used to make an edge to the template. Instead, the AttachmentPoint#isAvailableThroughout() returns false because it is capable of crossing the template barrier.

Definition at line 79 of file Template.java.

Constructor & Destructor Documentation

◆ Template()

denoptim.graph.Template.Template ( Vertex.BBType bbType )

Definition at line 134 of file Template.java.

References denoptim.graph.Vertex.setBuildingBlockType(), and denoptim.graph.Vertex.VertexType.Template.

Referenced by denoptim.graph.Template.clone(), denoptim.graph.Template.getTestTemplate(), and denoptim.graph.Template.updateMutTypeToFixedSTructure().

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Member Function Documentation

◆ addInnerToOuterAPMapping()

void denoptim.graph.Template.addInnerToOuterAPMapping ( AttachmentPoint newInnerAP )

Adds the projection of an AP in the template's inner graph (i.e., innerAP) to the list of APs visible from outside the template (i.e., the outerAPs).

The AP created on the template's surface is a clone of that given as argument. If the given AP already has a mapping, nothing happens.

Parameters

newInnerAP the inner AP to project on template's surface.

Definition at line 348 of file Template.java.

References denoptim.graph.Template.addInnerToOuterAPMapping(), denoptim.graph.AttachmentPoint.clone(), denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.Template.innerToOuterAPs, denoptim.graph.APTreeMap.put(), denoptim.graph.AttachmentPoint.setOwner(), and denoptim.graph.DGraph.templateJacket.

Referenced by denoptim.graph.Template.addInnerToOuterAPMapping(), denoptim.graph.DGraph.insertSingleVertex(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.DGraph.replaceSingleSubGraph(), and denoptim.graph.Template.setInnerGraph().

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◆ addRequiredAP()

void denoptim.graph.Template.addRequiredAP	(	Point3d	pt,
		APClass	apClass
	)

Adds attachment point (AP) to the list of required APs on this template.

Parameters

ap	attachment point to require from this template

Exceptions

DENOPTIMException

Definition at line 935 of file Template.java.

References denoptim.graph.Template.clearIAtomContainer(), denoptim.graph.Template.getInnerGraph(), and denoptim.graph.Template.requiredAPs.

Referenced by denoptim.graph.Template.clone(), and denoptim.graph.TemplateTest.testAddAP_after_setInnerGraph_throwsException().

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◆ addSymmetricAPSet()

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

protected

Reimplemented from denoptim.graph.Vertex.

Definition at line 482 of file Template.java.

◆ clearIAtomContainer()

void denoptim.graph.Template.clearIAtomContainer ( )

Removes the molecular representation.

Definition at line 600 of file Template.java.

Referenced by denoptim.graph.Template.addRequiredAP(), denoptim.ga.GraphOperations.performMutation(), denoptim.graph.DGraph.replaceSingleSubGraph(), denoptim.graph.Template.setInnerGraph(), and denoptim.graph.Template.updateInnerToOuter().

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◆ clone()

Template denoptim.graph.Template.clone ( )

Returns a deep copy of this template.

Returns: the deep copy

Reimplemented from denoptim.graph.Vertex.

Definition at line 243 of file Template.java.

Referenced by denoptim.graph.Template.clone(), denoptim.graph.TemplateTest.testClone(), denoptim.graph.AttachmentPointTest.testHasConnectedSrcAtom(), and denoptim.graph.TemplateTest.testNestedTemplateCloning().

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◆ containsAtoms()

boolean denoptim.graph.Template.containsAtoms ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 585 of file Template.java.

References denoptim.graph.DGraph.containsAtoms(), denoptim.graph.Template.innerGraph, and denoptim.graph.Template.mol.

Referenced by denoptim.gui.VertexViewPanel.loadTemplateToViewer().

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◆ freezeTemplate()

boolean denoptim.graph.Template.freezeTemplate ( )

Promotes the contract level of this template to the most constrained one (i.e., ContractLevel#FIXED), i.e.

makes the template unable to change after calling this method.

Returns: true if already frozen. Else false.

Definition at line 231 of file Template.java.

References denoptim.graph.Template.contractLevel, and denoptim.graph.Template.ContractLevel.FIXED.

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

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◆ fromJson()

static Template denoptim.graph.Template.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 1028 of file Template.java.

References denoptim.graph.DGraph.fromJson(), denoptim.graph.Template.fromJson(), denoptim.graph.Template.getAttachmentPoints(), denoptim.json.DENOPTIMgson.getReader(), denoptim.graph.Template.innerGraph, denoptim.graph.Template.setInnerGraph(), and denoptim.graph.Template.updateInnerToOuter().

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

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◆ getAttachmentPoints()

ArrayList< AttachmentPoint > denoptim.graph.Template.getAttachmentPoints ( )

Return the list of attachment points visible from outside the template, i.e., the so-called outer APs.

Each outer AP is a projection of an AP present in the embedded graph, i.e., inner AP.

Returns: the list of outer AP

Reimplemented from denoptim.graph.Vertex.

Definition at line 458 of file Template.java.

References denoptim.graph.Template.innerToOuterAPs.

Referenced by denoptim.graph.Template.clone(), denoptim.graph.Template.fromJson(), denoptim.graph.Template.getIAtomContainer(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.gui.GraphViewerPanel.renumberAPs(), denoptim.graph.Template.setIAtomContainer(), denoptim.graph.TemplateTest.testGetIAtomContainer(), denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex(), and denoptim.json.DENOPTIMgsonTest.testTemplateSerialization().

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◆ getContractLevel()

ContractLevel denoptim.graph.Template.getContractLevel ( )

Returns the contract level of this template, i.e., to what extent the content of this template can be changed.

Returns: the contract level of this template.

Definition at line 203 of file Template.java.

References denoptim.graph.Template.contractLevel.

Referenced by denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), and denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol().

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◆ getHeavyAtomsCount()

int denoptim.graph.Template.getHeavyAtomsCount ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 577 of file Template.java.

References denoptim.graph.DGraph.getHeavyAtomsCount(), and denoptim.graph.Template.innerGraph.

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◆ getIAtomContainer() [1/2]

IAtomContainer denoptim.graph.Template.getIAtomContainer ( )

The molecular representation, if any, is generated by this method and stored until further changes in the content of this template.

Successive calls of this method (i.e., prior to any other modification in this template's content) return the result stored in the first run occurred after the last edit of this template's content.

Returns: the molecular representation of the content of this template.

Reimplemented from denoptim.graph.Vertex.

Definition at line 715 of file Template.java.

References denoptim.graph.Template.getIAtomContainer().

Referenced by denoptim.graph.Template.getIAtomContainer(), denoptim.gui.VertexViewPanel.loadTemplateToViewer(), denoptim.graph.TemplateTest.testGetIAtomContainer(), denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex(), denoptim.json.DENOPTIMgsonTest.testTemplateSerialization(), and denoptim.gui.GraphVertexMolViewerPanel.visualizeVertexInNestedViewer().

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◆ getIAtomContainer() [2/2]

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

The molecular representation, if any, is generated by this method and stored until further changes in the content of this template.

Successive calls of this method (i.e., prior to any other modification in this template's content) return the result stored in the first run occurred after the last edit of this template's content.

Parameters

logger	tool dealing with log messages
rng	random number generator and decision tool.
removeUsedRCAs	use `true` to remove the ring closing attractors and replace them with a ring-closing bond according to the bond type defined by the ring.
rebuild	use `true` to ignore any previously stored chemical representation of this vertex and re-build from scratch.

Returns: the molecular representation of the content of this template.

Reimplemented from denoptim.graph.Vertex.

Definition at line 741 of file Template.java.

References denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.constants.DENOPTIMConstants.GCODETAG, denoptim.graph.AttachmentPoint.getAPDefinitionsForSDF(), denoptim.graph.AttachmentPoint.getAtomPositionNumberInMol(), denoptim.graph.Template.getAttachmentPoints(), denoptim.graph.AttachmentPoint.getDirectionVector(), denoptim.graph.Template.getInnerAPFromOuterAP(), denoptim.constants.DENOPTIMConstants.GRAPHJSONTAG, denoptim.constants.DENOPTIMConstants.GRAPHTAG, denoptim.graph.Template.innerGraph, denoptim.graph.Template.mol, denoptim.constants.DENOPTIMConstants.PROVENANCE, and denoptim.constants.DENOPTIMConstants.VERTEXJSONTAG.

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◆ getInnerAPFromOuterAP()

AttachmentPoint denoptim.graph.Template.getInnerAPFromOuterAP ( AttachmentPoint outerAP )

Definition at line 808 of file Template.java.

References denoptim.graph.Template.innerToOuterAPs.

Referenced by denoptim.graph.Template.getIAtomContainer(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.gui.GraphViewerPanel.renumberAPs(), and denoptim.graph.Template.setIAtomContainer().

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◆ getInnerGraph()

DGraph denoptim.graph.Template.getInnerGraph ( )

Definition at line 291 of file Template.java.

References denoptim.graph.Template.innerGraph.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.graph.Template.addRequiredAP(), denoptim.graph.Template.clone(), denoptim.graph.DGraph.containsOrEmbedsVertex(), denoptim.graph.DGraph.getEmbeddedGraphInClone(), denoptim.fragspace.FragmentSpace.hasIsomorph(), denoptim.graph.DGraph.hasOrEmbedsRings(), denoptim.gui.GraphViewerPanel.loadGraphToViewer(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), denoptim.graph.Template.sameAs(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure(), denoptim.graph.TemplateTest.testClone(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), denoptim.graph.DGraphTest.testGetEmbeddedGraphInClone(), denoptim.graph.DGraphTest.testGetEmbeddingPath(), denoptim.ga.GraphOperationsTest.testLocateCompatibleXOverPoints(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol(), denoptim.ga.XoverSiteTest.testProjectToClonedGraphs(), and denoptim.gui.GraphVertexMolViewerPanel.visualizeVertexInNestedViewer().

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◆ getMutationSites()

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

A list of mutation sites from within this vertex.

This method sets the mutation sites of the embedded vertices according to the Template#contractLevel of this template.

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 872 of file Template.java.

References denoptim.graph.Vertex.BBType.CAP, denoptim.graph.Template.contractLevel, denoptim.graph.Vertex.getBuildingBlockType(), denoptim.graph.Vertex.getMutationSites(), denoptim.graph.Vertex.getMutationTypes(), denoptim.graph.DGraph.gVertices, denoptim.graph.Template.innerGraph, and denoptim.graph.Template.updateMutTypeToFixedSTructure().

Referenced by denoptim.ga.EAUtilsTest.testBuildGraphFromTemplateScaffold().

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◆ getMutationTypes()

List< MutationType > denoptim.graph.Template.getMutationTypes ( List< MutationType > excludedTypes )

Returns the list of mutation types.

Parameters

excludedTypes list of mutation types to purge from before returning the list.

Returns: the purged list of mutation types.

Reimplemented from denoptim.graph.Vertex.

Definition at line 837 of file Template.java.

References denoptim.utils.MutationType.ADDLINK, denoptim.utils.MutationType.CHANGELINK, denoptim.utils.MutationType.EXTEND, denoptim.graph.Vertex.getBuildingBlockType(), denoptim.graph.Vertex.getChilddren(), denoptim.graph.Vertex.getNumberOfAPs(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

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◆ getOuterAPFromInnerAP()

AttachmentPoint denoptim.graph.Template.getOuterAPFromInnerAP ( AttachmentPoint innerAP )

Definition at line 828 of file Template.java.

References denoptim.graph.APTreeMap.get(), and denoptim.graph.Template.innerToOuterAPs.

Referenced by denoptim.graph.DGraph.embedPatternsInTemplates(), denoptim.graph.AttachmentPoint.getEdgeUserThroughout(), and denoptim.graph.AttachmentPoint.isAvailableThroughout().

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◆ getPathIDs()

String[] denoptim.graph.Template.getPathIDs	(	AttachmentPoint	apA,
		AttachmentPoint	apB
	)

Produces a pair of strings that identify the "path" between two given attachment points.

The two strings represent one the reverse path of the other. So they identify the path when starting from each of the two APs.

Parameters

apA
apB

Returns: a pair of strings that identify the "path" between two given attachment points.

Reimplemented from denoptim.graph.Vertex.

Definition at line 154 of file Template.java.

References denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Vertex.getBuildingBlockType(), and denoptim.graph.Vertex.getIndexOfAP().

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◆ getRequiredAPs()

List< AttachmentPoint > denoptim.graph.Template.getRequiredAPs ( )

private

Definition at line 996 of file Template.java.

References denoptim.graph.Template.requiredAPs.

Referenced by denoptim.graph.Template.isValidInnerGraph().

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◆ getSymmetricAPSets()

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

The SymmetricSet produced from this method contain indexes of the AttachmentPoints in the list returned by getAttachmentPoints().

Reimplemented from denoptim.graph.Vertex.

Definition at line 495 of file Template.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.APTreeMap.get(), denoptim.graph.Vertex.getSymmetricAPs(), denoptim.graph.DGraph.getSymVerticesForVertex(), denoptim.graph.Template.innerGraph, and denoptim.graph.Template.innerToOuterAPs.

Referenced by denoptim.json.DENOPTIMgsonTest.testTemplateSerialization().

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◆ getTestTemplate()

static Template denoptim.graph.Template.getTestTemplate ( ContractLevel contractLevel ) throws DENOPTIMException

static

Method meant for devel phase only.

Exceptions

DENOPTIMException

Definition at line 172 of file Template.java.

References denoptim.graph.EmptyVertex.addAP(), denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Template.contractLevel, denoptim.graph.Vertex.getAP(), denoptim.graph.Edge.BondType.SINGLE, denoptim.graph.Template.Template(), and denoptim.graph.Vertex.BBType.UNDEFINED.

Referenced by denoptim.graph.DGraphTest.testGetMutationSites().

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◆ isValidInnerGraph()

boolean denoptim.graph.Template.isValidInnerGraph ( DGraph g )

private

Definition at line 422 of file Template.java.

References denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.DGraph.getAvailableAPs(), denoptim.graph.Template.getRequiredAPs(), and denoptim.graph.Template.requiredAPs.

Referenced by denoptim.graph.Template.setInnerGraph().

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◆ removeProjectionOfInnerAP()

void denoptim.graph.Template.removeProjectionOfInnerAP ( AttachmentPoint oldInnerAP ) throws DENOPTIMException

Removes the mapping of the given inner AP from this template's surface, if such mapping exists.

If the old innerAP maps to an outer AP that is used, then the edge user and any vertex reachable from it are removed.

Parameters

oldInnerAP the inner AP of the mapping to remove.

Definition at line 399 of file Template.java.

References denoptim.graph.APTreeMap.get(), denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.AttachmentPoint.getLinkedAP(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Template.innerToOuterAPs, denoptim.graph.AttachmentPoint.isAvailable(), denoptim.graph.APTreeMap.remove(), denoptim.graph.DGraph.removeBranchStartingAt(), denoptim.graph.Template.removeProjectionOfInnerAP(), and denoptim.graph.DGraph.templateJacket.

Referenced by denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.Template.removeProjectionOfInnerAP(), denoptim.graph.DGraph.removeSingleVertexAndWeld(), and denoptim.graph.DGraph.replaceSingleSubGraph().

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◆ sameAs()

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

Compares this and another template ignoring vertex IDs.

Parameters

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

Returns: true if the two templates have the same content even if the vertex IDs are different.

Definition at line 956 of file Template.java.

References denoptim.graph.Template.contractLevel, denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Template.getInnerGraph(), denoptim.graph.Template.requiredAPs, denoptim.graph.Template.sameAs(), and denoptim.graph.Vertex.sameVertexFeatures().

Referenced by denoptim.graph.Template.sameAs(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), denoptim.io.DenoptimIOTest.testIOTemplate(), and denoptim.graph.TemplateTest.testNestedTemplateCloning().

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◆ setContractLevel()

void denoptim.graph.Template.setContractLevel ( ContractLevel contract )

Imposes the given contract to this template.

Parameters

contract the contract to impose on this template.

Definition at line 214 of file Template.java.

References denoptim.graph.Template.ContractLevel.FIXED_STRUCT, and denoptim.graph.Template.updateMutTypeToFixedSTructure().

Referenced by denoptim.graph.DGraph.embedPatternsInTemplates(), denoptim.ga.GraphOperationsTest.getPairOfTestGraphs(), denoptim.ga.PopulationTest.getPairOfTestGraphsB(), denoptim.ga.PopulationTest.getPairOfTestGraphsBxo(), denoptim.ga.PopulationTest.getPairOfTestGraphsBxoxo(), denoptim.gui.GUIGraphHandler.initialize(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure(), and denoptim.ga.GraphOperationsTest.testLocateCompatibleXOverPoints().

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◆ setIAtomContainer()

void denoptim.graph.Template.setIAtomContainer	(	IAtomContainer	mol,
		boolean	updateAPsAccordingToIAC
	)		throws DENOPTIMException

Attaches a molecular representation to this template.

Note that changes to this Template have the power to trigger the request to update the molecular representation that we set here, thus removing the representation we define in this method.

Parameters

mol	the atom container to be used as molecular representation of this template.
updateAPsAccordingToIAC	flag that prevents actions when the IAC does not have the details needed to update the APs on the template. For instance, when cloning a template or reading in a template with IAC from file. In these cases we only want to add a molecular representation and we set this flag to `false`.

Exceptions

DENOPTIMException

Definition at line 621 of file Template.java.

References denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.constants.DENOPTIMConstants.ATMPROPORIGINALATMID, denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.constants.DENOPTIMConstants.GCODETAG, denoptim.graph.AttachmentPoint.getAPDefinitionsForSDF(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Template.getAttachmentPoints(), denoptim.graph.AttachmentPoint.getDirectionVector(), denoptim.graph.Template.getInnerAPFromOuterAP(), denoptim.graph.Vertex.getVertexId(), denoptim.constants.DENOPTIMConstants.GRAPHJSONTAG, denoptim.constants.DENOPTIMConstants.GRAPHTAG, denoptim.constants.DENOPTIMConstants.LINKAPS, denoptim.graph.Template.mol, denoptim.constants.DENOPTIMConstants.PROVENANCE, denoptim.graph.AttachmentPoint.setDirectionVector(), and denoptim.constants.DENOPTIMConstants.VERTEXJSONTAG.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary().

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◆ setInnerGraph()

void denoptim.graph.Template.setInnerGraph ( DGraph innerGraph ) throws IllegalArgumentException

Definition at line 298 of file Template.java.

References denoptim.graph.Template.addInnerToOuterAPMapping(), denoptim.graph.Template.clearIAtomContainer(), denoptim.graph.DGraph.getAvailableAPs(), denoptim.graph.Template.innerGraph, denoptim.graph.Template.isValidInnerGraph(), and denoptim.graph.DGraph.setTemplateJacket().

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◆ setSymmetricAPSets()

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

protected

This method exists by contract, but does not do anything because the concept of setting the symmetric set of APs in a template is not defined yet.

Reimplemented from denoptim.graph.Vertex.

Definition at line 474 of file Template.java.

◆ toJson()

String denoptim.graph.Template.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 1008 of file Template.java.

References denoptim.graph.DGraph.ensureUniqueApIDs(), denoptim.json.DENOPTIMgson.getWriter(), and denoptim.graph.Template.innerGraph.

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

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◆ updateInnerApID()

void denoptim.graph.Template.updateInnerApID	(	AttachmentPoint	oldInnerAP,
		AttachmentPoint	newInnerAP
	)

Replaces a given link between APs on the surface of this template (i.e., outerAP) and the corresponding APs in the embedded graph (i.e., innerAPs).

This method does change the attributes of the outerAP to reflect the change on innerAP, i.e., the APClass of innerAP is assigned to the outerAP. If there is now mapping for the oldInnerAP, then nothing happens.

Parameters

oldInnerAP	the inner AP to be changed
newInnerAP	the inner AP to change the old one with.

Definition at line 377 of file Template.java.

References denoptim.graph.APTreeMap.get(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.Template.innerToOuterAPs, denoptim.graph.APTreeMap.put(), denoptim.graph.APTreeMap.remove(), and denoptim.graph.AttachmentPoint.setAPClass().

Referenced by denoptim.graph.DGraph.removeSingleVertexAndWeld(), and denoptim.graph.DGraph.replaceSingleSubGraph().

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◆ updateInnerToOuter()

void denoptim.graph.Template.updateInnerToOuter ( TreeMap< Integer, AttachmentPoint > map )

private

Definition at line 325 of file Template.java.

References denoptim.graph.Template.clearIAtomContainer(), denoptim.graph.DGraph.getAPWithId(), denoptim.graph.Template.innerGraph, denoptim.graph.APTreeMap.put(), and denoptim.graph.AttachmentPoint.setOwner().

Referenced by denoptim.graph.Template.fromJson().

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◆ updateMutTypeToFixedSTructure()

void denoptim.graph.Template.updateMutTypeToFixedSTructure ( )

private

Definition at line 908 of file Template.java.

References denoptim.utils.MutationType.ADDLINK, denoptim.utils.MutationType.CHANGEBRANCH, denoptim.utils.MutationType.DELETE, denoptim.utils.MutationType.DELETECHAIN, denoptim.utils.MutationType.DELETELINK, denoptim.utils.MutationType.EXTEND, denoptim.graph.Template.ContractLevel.FIXED_STRUCT, denoptim.graph.DGraph.gVertices, denoptim.graph.Template.innerGraph, denoptim.graph.Vertex.removeMutationType(), and denoptim.graph.Template.Template().

Referenced by denoptim.graph.Template.getMutationSites(), and denoptim.graph.Template.setContractLevel().

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Member Data Documentation

◆ contractLevel

ContractLevel denoptim.graph.Template.contractLevel = ContractLevel.FIXED

private

Denotes the constants in the template.

Definition at line 99 of file Template.java.

Referenced by denoptim.graph.Template.clone(), denoptim.graph.Template.freezeTemplate(), denoptim.graph.Template.getContractLevel(), denoptim.graph.Template.getMutationSites(), denoptim.graph.Template.getTestTemplate(), and denoptim.graph.Template.sameAs().

◆ innerGraph

DGraph denoptim.graph.Template.innerGraph

private

Graph that is embedded in this vertex.

Definition at line 84 of file Template.java.

Referenced by denoptim.graph.Template.containsAtoms(), denoptim.graph.Template.fromJson(), denoptim.graph.Template.getHeavyAtomsCount(), denoptim.graph.Template.getIAtomContainer(), denoptim.graph.Template.getInnerGraph(), denoptim.graph.Template.getMutationSites(), denoptim.graph.Template.getSymmetricAPSets(), denoptim.graph.Template.setInnerGraph(), denoptim.graph.Template.toJson(), denoptim.graph.Template.updateInnerToOuter(), and denoptim.graph.Template.updateMutTypeToFixedSTructure().

◆ innerToOuterAPs

APTreeMap denoptim.graph.Template.innerToOuterAPs

private

Definition at line 129 of file Template.java.

Referenced by denoptim.graph.Template.addInnerToOuterAPMapping(), denoptim.graph.Template.getAttachmentPoints(), denoptim.graph.Template.getInnerAPFromOuterAP(), denoptim.graph.Template.getOuterAPFromInnerAP(), denoptim.graph.Template.getSymmetricAPSets(), denoptim.graph.Template.removeProjectionOfInnerAP(), and denoptim.graph.Template.updateInnerApID().

◆ mol

IAtomContainer denoptim.graph.Template.mol = null

private

Molecular representation of the content of this template.

This filed is meant to speed up handling of template's molecular analog. In particular, rather than recalculating the molecular representation multiple times, we make it once (upon calling getIAtomContainer()) and we store the result until further changes in the content of the template.

Definition at line 94 of file Template.java.

Referenced by denoptim.graph.Template.clone(), denoptim.graph.Template.containsAtoms(), denoptim.graph.Template.getIAtomContainer(), and denoptim.graph.Template.setIAtomContainer().

◆ requiredAPs

List<AttachmentPoint> denoptim.graph.Template.requiredAPs = new ArrayList<>()

private

Definition at line 127 of file Template.java.

Referenced by denoptim.graph.Template.addRequiredAP(), denoptim.graph.Template.getRequiredAPs(), denoptim.graph.Template.isValidInnerGraph(), and denoptim.graph.Template.sameAs().

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

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

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Template()

Member Function Documentation

◆ addInnerToOuterAPMapping()

◆ addRequiredAP()

◆ addSymmetricAPSet()

◆ clearIAtomContainer()

◆ clone()

◆ containsAtoms()

◆ freezeTemplate()

◆ fromJson()

◆ getAttachmentPoints()

◆ getContractLevel()

◆ getHeavyAtomsCount()

◆ getIAtomContainer() [1/2]

◆ getIAtomContainer() [2/2]

◆ getInnerAPFromOuterAP()

◆ getInnerGraph()

◆ getMutationSites()

◆ getMutationTypes()

◆ getOuterAPFromInnerAP()

◆ getPathIDs()

◆ getRequiredAPs()

◆ getSymmetricAPSets()

◆ getTestTemplate()

◆ isValidInnerGraph()

◆ removeProjectionOfInnerAP()

◆ sameAs()

◆ setContractLevel()

◆ setIAtomContainer()

◆ setInnerGraph()

◆ setSymmetricAPSets()

◆ toJson()

◆ updateInnerApID()

◆ updateInnerToOuter()

◆ updateMutTypeToFixedSTructure()

Member Data Documentation

◆ contractLevel

◆ innerGraph

◆ innerToOuterAPs

◆ mol

◆ requiredAPs