Class representing a continuously connected portion of chemical object holding attachment points. More...

Inheritance diagram for denoptim.graph.Fragment:

Collaboration diagram for denoptim.graph.Fragment:

Public Member Functions
	Fragment ()
	Constructor of an empty fragment. More...

	Fragment (long vertexId)
	Constructor for a molecular fragment kind of vertex. More...

	Fragment (long l, IAtomContainer mol, BBType bbt) throws DENOPTIMException
	Constructor from an atom container, which has APs only as molecular properties. More...

	Fragment (long vertexId, IAtomContainer mol, BBType bbt, boolean isRCV) throws DENOPTIMException

	Fragment (IAtomContainer mol, BBType bbt) throws DENOPTIMException
	Constructor from another atom container, which has APs only as molecular properties. More...

boolean	is3D ()
	Checks if atoms and APs contained in this fragment have non-zero 3D coordinates. More...

void	addAP (int atomPositionNumber)
	Adds an attachment point with a dummy APClass. More...

void	addAP (int atomPositionNumber, APClass apClass)
	Adds an attachment point. More...

AttachmentPoint	addAP (int atomPositionNumber, Point3d dirVec, APClass apClass)
	Adds an attachment point. More...

void	addAP (int srcAtmId, APClass apc, Point3d vector)
	Add an attachment point to the specifies atom. More...

AttachmentPoint	addAPOnAtom (IAtom srcAtm, APClass apc, Point3d vector)
	Add an attachment point to the specifies atom. More...

void	removeAP (AttachmentPoint ap)

ArrayList< AttachmentPoint >	getAPsFromAtom (IAtom srcAtm)

int	getAPCountOnAtom (int srcAtmId)
	Returns the number of APs currently defined on a specific atom source. More...

int	getAPCountOnAtom (IAtom srcAtm)
	Returns the number of APs currently defined on a specific atom source. More...

void	updateAPs ()
	Changes the properties of each APs as to reflect the current atom list. More...

List< AttachmentPoint >	getCurrentAPs ()
	Collects APs currently defined as properties of the atoms. More...

void	projectPropertyToAP () throws DENOPTIMException
	Uses the molecular property defining attachment points to create the DENOPTIMAttachmentPoint objects in the Atom objects. More...

void	projectPropertyToAP (String allAtomsProp) throws DENOPTIMException
	Uses a string formatted like the molecular property used for defining attachment points to create the DENOPTIMAttachmentPoint objects in the Atom objects. More...

void	projectListAPToAtomProperties ()
	Takes the list of APs from the field of this class and projects the APs into properties of the `IAtom`s. More...

void	projectAPsToProperties ()
	Finds the DENOPTIMAttachmentPoint objects defined as properties of the atoms in this container, and defines the string-based molecular property used to print attachment points in SDF files. More...

Fragment	clone ()
	Returns a deep copy of this fragments. More...

IAtomContainer	getIAtomContainer ()

IAtomContainer	getIAtomContainer (Logger logger, Randomizer rng, boolean removeUsedRCAs, boolean rebuild)
	Although this type of vertex contains atoms, its content is fixed. More...

Iterable< IAtom >	atoms ()

Iterable< IBond >	bonds ()

void	addAtom (IAtom atom)

IAtom	getAtom (int number)

int	indexOf (IAtom atom)

int	getAtomCount ()

int	getBondCount ()

void	addBond (IBond bond)

IBond	removeBond (int position)

IBond	removeBond (IAtom atom1, IAtom atom2)

void	removeBond (IBond bond)

void	removeAtom (IAtom atom)

void	removeAtoms (Collection< IAtom > atoms)
	Removes a list of atoms and updates the list of attachment points. More...

List< IAtom >	getConnectedAtomsList (IAtom atom)

int	getConnectedAtomsCount (IAtom atom)

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

DefaultUndirectedGraph< FragIsomorphNode, FragIsomorphEdge >	getJGraphFragIsomorphism ()
	Creates a graph representation of this fragment where both atoms and `AttachmentPoint`s are represented as nodes, and edges are either bonds or atom-to-attachment point connections. More...

boolean	isIsomorphicTo (Vertex other)
	Checks for isomorphism of the graph representation of this and another fragment. More...

int	getHeavyAtomsCount ()

boolean	containsAtoms ()

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...

List< AttachmentPoint >	getAttachmentPoints ()

List< SymmetricAPs >	getSymmetricAPSets ()

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

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

IAtom	getAtomHoldingAP (AttachmentPoint ap)
	Returns the atom where the given attachment point is rooted, i.e., the atom that is involved in the bond resulting from using the attachment point to form an edge with a `BondType` that leads to bond creation. 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 Fragment	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 Member Functions
void	updateSymmetryRelations ()
	Depends on an healthy list of attachment points with properly set pointers to the source atoms. More...

Static Private Member Functions
static List< SymmetricAPs >	identifySymmetryRelatedAPSets (IAtomContainer mol, List< AttachmentPoint > daps)

static boolean	atomsAreCompatible (IAtomContainer mol, int a1, int a2)
	Checks if the atoms at the given positions have similar environments i.e. 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...

IAtomContainer	mol
	Molecular representation of this fragment. More...

DefaultUndirectedGraph< FragIsomorphNode, FragIsomorphEdge >	jGraphFragIsomorphism
	jGraph representation used for detecting fragment isomorphism. 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

Class representing a continuously connected portion of chemical object holding attachment points.

Author: Marco Foscato

Definition at line 60 of file Fragment.java.

Constructor & Destructor Documentation

◆ Fragment() [1/5]

denoptim.graph.Fragment.Fragment ( )

Constructor of an empty fragment.

Definition at line 91 of file Fragment.java.

References denoptim.graph.Vertex.VertexType.MolecularFragment.

Referenced by denoptim.graph.Fragment.clone(), and denoptim.graph.Fragment.isIsomorphicTo().

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◆ Fragment() [2/5]

denoptim.graph.Fragment.Fragment ( long vertexId )

Constructor for a molecular fragment kind of vertex.

Parameters

vertexId unique identified of the vertex

Definition at line 107 of file Fragment.java.

References denoptim.graph.Vertex.VertexType.MolecularFragment, and denoptim.graph.Vertex.vertexId.

◆ Fragment() [3/5]

denoptim.graph.Fragment.Fragment	(	long	l,
		IAtomContainer	mol,
		BBType	bbt
	)		throws DENOPTIMException

Constructor from an atom container, which has APs only as molecular properties.

Property DENOPTIMConstants#ISOMORPHICFAMILYID is copied into the fragment, if present. WARNING: other properties of the atom container are not imported!

Parameters

l	the identifier of the vertex to construct
mol	the molecular representation

Exceptions

DENOPTIMException

Definition at line 130 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.graph.Fragment.getAttachmentPoints(), denoptim.graph.Vertex.getNumberOfAPs(), denoptim.graph.Fragment.identifySymmetryRelatedAPSets(), denoptim.constants.DENOPTIMConstants.ISOMORPHICFAMILYID, denoptim.utils.MoleculeUtils.makeSameAs(), denoptim.graph.Fragment.mol, denoptim.graph.Vertex.VertexType.MolecularFragment, denoptim.graph.Fragment.projectPropertyToAP(), denoptim.graph.rings.RingClosingAttractor.RCAAPCLASSSET, denoptim.graph.Vertex.setAsRCV(), denoptim.graph.Vertex.setBuildingBlockType(), denoptim.graph.Vertex.setProperty(), denoptim.graph.Fragment.setSymmetricAPSets(), and denoptim.utils.MoleculeUtils.setZeroImplicitHydrogensToAllAtoms().

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◆ Fragment() [4/5]

denoptim.graph.Fragment.Fragment	(	long	vertexId,
		IAtomContainer	mol,
		BBType	bbt,
		boolean	isRCV
	)		throws DENOPTIMException

Definition at line 167 of file Fragment.java.

References denoptim.graph.Vertex.isRCV, denoptim.graph.Fragment.mol, denoptim.graph.Vertex.setAsRCV(), and denoptim.graph.Vertex.vertexId.

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◆ Fragment() [5/5]

denoptim.graph.Fragment.Fragment	(	IAtomContainer	mol,
		BBType	bbt
	)		throws DENOPTIMException

Constructor from another atom container, which has APs only as molecular properties.

WARNING: properties of the atom container are not imported!

Parameters

mol	the molecular representation

Exceptions

DENOPTIMException

Definition at line 183 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Member Function Documentation

◆ addAP() [1/4]

void denoptim.graph.Fragment.addAP ( int atomPositionNumber )

Adds an attachment point with a dummy APClass.

Parameters

atomPositionNumber the index of the source atom (0-based)

Definition at line 343 of file Fragment.java.

References denoptim.graph.Fragment.addAP().

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◆ addAP() [2/4]

void denoptim.graph.Fragment.addAP	(	int	atomPositionNumber,
		APClass	apClass
	)

Adds an attachment point.

Parameters

atomPositionNumber	the index of the source atom (0-based)
apClass	the APClass

Definition at line 355 of file Fragment.java.

References denoptim.graph.Fragment.addAP().

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◆ addAP() [3/4]

AttachmentPoint denoptim.graph.Fragment.addAP	(	int	atomPositionNumber,
		Point3d	dirVec,
		APClass	apClass
	)

Adds an attachment point.

Parameters

atomPositionNumber	the index of the source atom (0-based)
dirVec	the AP direction vector end (the beginning at the coordinates of the source atom).
apClass	the APClass

Returns: the reference to the created AP.

Definition at line 369 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.graph.Fragment.getAPCountOnAtom(), denoptim.graph.Fragment.getAPsFromAtom(), denoptim.graph.Fragment.getAttachmentPoints(), denoptim.graph.Fragment.mol, and denoptim.graph.Fragment.updateSymmetryRelations().

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◆ addAP() [4/4]

void denoptim.graph.Fragment.addAP	(	int	srcAtmId,
		APClass	apc,
		Point3d	vector
	)

Add an attachment point to the specifies atom.

Parameters

srcAtmId	the index of the source atom in the atom list of this chemical representation. Index must be 0-based.
apc	the attachment point class, or null, if class should not be defines.
vector	the coordinates of the 3D point representing the end of the attachment point direction vector, or null. The coordinates must be consistent with the coordinates of the atoms.
valence	the valences used by this AP.

Definition at line 404 of file Fragment.java.

References denoptim.graph.Fragment.addAPOnAtom(), and denoptim.graph.Fragment.mol.

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◆ addAPOnAtom()

AttachmentPoint denoptim.graph.Fragment.addAPOnAtom	(	IAtom	srcAtm,
		APClass	apc,
		Point3d	vector
	)

Add an attachment point to the specifies atom.

Parameters

srcAtm	the source atom in the atom list of this chemical representation.
apc	the attachment point class, or null, if class should not be defines.
vector	the coordinates of the 3D point representing the end of the attachment point direction vector, or null. The coordinates must be consistent with the coordinates of the atoms.

Returns: the reference to the created AP.

Definition at line 424 of file Fragment.java.

References denoptim.graph.Fragment.addAP(), and denoptim.graph.Fragment.mol.

Referenced by denoptim.graph.Fragment.addAP(), denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.gui.GUIVertexInspector.convertAtomToAP(), denoptim.utils.MoleculeUtils.extractIACForSubgraph(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.graph.FragmentTest.makeFragment(), denoptim.graph.FragmentTest.makeFragmentA(), denoptim.graph.FragmentTest.makeFragmentB(), denoptim.graph.FragmentTest.makeFragmentC(), denoptim.graph.FragmentIsomorphismInspectorTest.makePathologicalFragment(), denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.graph.VertexTest.testClone(), denoptim.graph.FragmentTest.testConversionToIAC(), denoptim.graph.SymmetricAPsTest.testGetSameAsThis(), denoptim.graph.FragmentTest.testHandlingAPsAsObjOrProperty(), denoptim.graph.AttachmentPointTest.testHasConnectedSrcAtom(), denoptim.graph.AttachmentPointTest.testHasSameSrcAtom(), denoptim.io.DenoptimIOTest.testReadAllAPClasses(), denoptim.graph.SymmetricAPsTest.testSameAs(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ addAtom()

void denoptim.graph.Fragment.addAtom ( IAtom atom )

Definition at line 836 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.fragspace.FragmentSpace.getPolarizedRCV(), denoptim.graph.FragmentTest.makeFragment(), denoptim.graph.FragmentTest.makeFragmentA(), denoptim.graph.FragmentTest.makeFragmentB(), denoptim.graph.FragmentTest.makeFragmentC(), denoptim.graph.FragmentIsomorphismInspectorTest.makePathologicalFragment(), denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.graph.VertexTest.testClone(), denoptim.graph.AttachmentPointTest.testConstructorsAndSDFString(), denoptim.graph.AttachmentPointTest.testConstructorsAndSDFStringNoDirVec(), denoptim.molecularmodeling.ThreeDimTreeBuilderTest.testConversionTo3dTree(), denoptim.graph.FragmentTest.testConversionToIAC(), denoptim.ga.GraphOperationsTest.testExtendGraph(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass(), denoptim.graph.FragmentTest.testHandlingAPsAsObjOrProperty(), denoptim.graph.AttachmentPointTest.testHasConnectedSrcAtom(), denoptim.graph.AttachmentPointTest.testHasSameSrcAtom(), denoptim.io.DenoptimIOTest.testReadAllAPClasses(), denoptim.graph.DGraphTest.testRemoveUnusedRCVs(), denoptim.graph.AttachmentPointTest.testSortAPs(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ addBond()

void denoptim.graph.Fragment.addBond ( IBond bond )

Definition at line 871 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.FragmentTest.makeFragment(), denoptim.graph.FragmentTest.makeFragmentA(), denoptim.graph.FragmentTest.makeFragmentB(), denoptim.graph.FragmentTest.makeFragmentC(), denoptim.graph.FragmentIsomorphismInspectorTest.makePathologicalFragment(), denoptim.graph.VertexTest.testClone(), denoptim.molecularmodeling.ThreeDimTreeBuilderTest.testConversionTo3dTree(), denoptim.graph.FragmentTest.testConversionToIAC(), denoptim.ga.GraphOperationsTest.testExtendGraph(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass(), denoptim.graph.FragmentTest.testHandlingAPsAsObjOrProperty(), denoptim.graph.AttachmentPointTest.testHasConnectedSrcAtom(), denoptim.graph.AttachmentPointTest.testHasSameSrcAtom(), denoptim.graph.DGraphTest.testRemoveUnusedRCVs(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ addSymmetricAPSet()

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

protected

Reimplemented from denoptim.graph.Vertex.

Definition at line 1136 of file Fragment.java.

◆ atoms()

Iterable< IAtom > denoptim.graph.Fragment.atoms ( )

Definition at line 822 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.fragmenter.FragmentClustererTest.getMol(), denoptim.graph.Fragment.is3D(), denoptim.graph.Fragment.removeAtoms(), denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder(), denoptim.fragmenter.FragmentClustererTest.testCluster(), and denoptim.fragmenter.ConformerExtractorTaskTest.testExtractClusterableFragments().

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◆ atomsAreCompatible()

static boolean denoptim.graph.Fragment.atomsAreCompatible	(	IAtomContainer	mol,
		int	a1,
		int	a2
	)

staticprivate

Checks if the atoms at the given positions have similar environments i.e.

are similar in atom types etc.

Parameters

mol
a1	atom position
a2	atom position

Returns: true if atoms have similar environments

Definition at line 298 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.graph.Fragment.identifySymmetryRelatedAPSets().

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◆ bonds()

Iterable< IBond > denoptim.graph.Fragment.bonds ( )

Definition at line 829 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.utils.MoleculeUtils.extractIACForSubgraph(), and denoptim.gui.GUIVertexInspector.removeAtoms().

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◆ clone()

Fragment denoptim.graph.Fragment.clone ( )

Returns a deep copy of this fragments.

Reimplemented from denoptim.graph.Vertex.

Definition at line 733 of file Fragment.java.

Referenced by denoptim.graph.Fragment.clone(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.fragmenter.ClusterableFragment.getTransformedCopy(), denoptim.graph.rings.RingSizeManagerTest.makeTestGraphA(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.graph.FragmentTest.testClone(), denoptim.graph.VertexTest.testClone(), denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), denoptim.ga.GraphOperationsTest.testExtendGraph(), denoptim.fragmenter.ConformerExtractorTaskTest.testExtractClusterableFragments(), denoptim.fragmenter.FragmentAlignementTest.testGetMinimumRMSD(), denoptim.graph.AttachmentPointTest.testHasConnectedSrcAtom(), and denoptim.graph.AttachmentPointTest.testHasSameSrcAtom().

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◆ containsAtoms()

boolean denoptim.graph.Fragment.containsAtoms ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 1100 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.graph.Fragment.sameAs().

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◆ fromJson()

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

static

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

Fields that depend on the context of this vertex, such as the graph 'owner' of this vertex and the 'user' of each attachment point, are recovered, if needed, upon deserialization of the graph that contains this vertex.

Parameters

json	the string to parse.

Returns: a new instance of this class.

Reimplemented from denoptim.graph.Vertex.

Definition at line 1207 of file Fragment.java.

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

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

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◆ getAPCountOnAtom() [1/2]

int denoptim.graph.Fragment.getAPCountOnAtom ( IAtom srcAtm )

Returns the number of APs currently defined on a specific atom source.

Parameters

srcAtm the source atom

Returns: the number of APs

Exceptions

DENOPTIMException

Definition at line 490 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, and denoptim.graph.Fragment.getAPsFromAtom().

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◆ getAPCountOnAtom() [2/2]

int denoptim.graph.Fragment.getAPCountOnAtom ( int srcAtmId )

Returns the number of APs currently defined on a specific atom source.

Parameters

srcAtmId the index of the atom

Returns: the number of APs

Exceptions

DENOPTIMException

Definition at line 475 of file Fragment.java.

References denoptim.graph.Fragment.getAPCountOnAtom(), and denoptim.graph.Fragment.mol.

Referenced by denoptim.graph.Fragment.addAP(), denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.graph.Fragment.getAPCountOnAtom(), denoptim.graph.Fragment.removeAP(), denoptim.graph.FragmentTest.testConversionToIAC(), denoptim.graph.FragmentTest.testHandlingAPsAsObjOrProperty(), and denoptim.json.DENOPTIMgsonTest.testMolecularFragmentSerialization().

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◆ getAPsFromAtom()

ArrayList< AttachmentPoint > denoptim.graph.Fragment.getAPsFromAtom ( IAtom srcAtm )

Definition at line 455 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS.

Referenced by denoptim.graph.Fragment.addAP(), denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.graph.Fragment.getAPCountOnAtom(), denoptim.graph.Fragment.getCurrentAPs(), denoptim.graph.Fragment.projectAPsToProperties(), denoptim.graph.Fragment.projectListAPToAtomProperties(), denoptim.graph.Fragment.removeAP(), denoptim.gui.GUIVertexInspector.removeAtoms(), denoptim.graph.Fragment.removeAtoms(), and denoptim.graph.Fragment.updateAPs().

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◆ getAtom()

IAtom denoptim.graph.Fragment.getAtom ( int number )

Definition at line 843 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.utils.MoleculeUtils.extractIACForSubgraph(), denoptim.gui.FragmentViewPanel.getAtomsSelectedFromJMol(), denoptim.gui.FragmentViewPanel.getLoadedStructure(), denoptim.fragmenter.ClusterableFragment.getTransformedCopy(), denoptim.graph.FragmentIsomorphismInspectorTest.makePathologicalFragment(), denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.fragmenter.FragmentClustererTest.testCluster(), denoptim.graph.SymmetricAPsTest.testGetSameAsThis(), denoptim.fragmenter.ClusterableFragmentTest.testGetTransformedCopy(), denoptim.graph.SymmetricAPsTest.testSameAs(), and denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer().

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◆ getAtomCount()

int denoptim.graph.Fragment.getAtomCount ( )

Definition at line 857 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.gui.FragmentViewPanel.getAtomsSelectedFromJMol(), denoptim.gui.FragmentViewPanel.getLoadedStructure(), and denoptim.fragmenter.ClusterableFragmentTest.testGetTransformedCopy().

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◆ getAtomHoldingAP()

IAtom denoptim.graph.Fragment.getAtomHoldingAP ( AttachmentPoint ap )

Returns the atom where the given attachment point is rooted, i.e., the atom that is involved in the bond resulting from using the attachment point to form an edge with a BondType that leads to bond creation.

Parameters

ap	the attachment point to find the source of.

Returns: the source atom of the attachment point, or null is the attachment point does not belong to this vertex.

Definition at line 1234 of file Fragment.java.

References denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.AttachmentPoint.getOwner(), and denoptim.graph.Fragment.mol.

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◆ getAttachmentPoints()

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

Reimplemented from denoptim.graph.Vertex.

Definition at line 1120 of file Fragment.java.

References denoptim.graph.Fragment.lstAPs.

Referenced by denoptim.graph.Fragment.addAP(), denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.graph.Fragment.Fragment(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.graph.Fragment.fromJson(), denoptim.graph.Fragment.getJGraphFragIsomorphism(), denoptim.fragmenter.FragmentClustererTest.getMol(), denoptim.graph.Fragment.is3D(), denoptim.graph.Fragment.isIsomorphicTo(), denoptim.graph.Fragment.removeAP(), denoptim.gui.GUIVertexInspector.removeAtoms(), denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder(), denoptim.fragmenter.FragmentClustererTest.testCluster(), denoptim.fragmenter.ConformerExtractorTaskTest.testExtractClusterableFragments(), denoptim.json.DENOPTIMgsonTest.testMolecularFragmentSerialization(), denoptim.graph.AttachmentPointTest.testSortAPs(), and denoptim.graph.Fragment.updateSymmetryRelations().

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◆ getBondCount()

int denoptim.graph.Fragment.getBondCount ( )

Definition at line 864 of file Fragment.java.

References denoptim.graph.Fragment.mol.

◆ getConnectedAtomsCount()

int denoptim.graph.Fragment.getConnectedAtomsCount ( IAtom atom )

Definition at line 950 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), and denoptim.gui.GUIVertexInspector.convertAtomToAP().

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◆ getConnectedAtomsList()

List< IAtom > denoptim.graph.Fragment.getConnectedAtomsList ( IAtom atom )

Definition at line 943 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), and denoptim.gui.GUIVertexInspector.convertAtomToAP().

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◆ getCurrentAPs()

List< AttachmentPoint > denoptim.graph.Fragment.getCurrentAPs ( )

Collects APs currently defined as properties of the atoms.

Converts the internal notation defining APs (i.e., APs are stored in as atom-specific properties) to the standard DENOPTIM formalism (i.e., APs are collected in a molecular property). WARNING: cannot be used after altering the atom list!

Returns: the list of APs. Note that these APs cannot respond to changes in the atom list!

Definition at line 541 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.graph.Fragment.getAPsFromAtom(), denoptim.graph.Fragment.lstAPs, denoptim.graph.Fragment.mol, and denoptim.graph.Fragment.updateAPs().

Referenced by denoptim.gui.FragmentViewPanel.updateAPsMapAndTable().

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◆ getHeavyAtomsCount()

int denoptim.graph.Fragment.getHeavyAtomsCount ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 1093 of file Fragment.java.

References denoptim.utils.MoleculeUtils.getHeavyAtomCount(), and denoptim.graph.Fragment.mol.

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◆ getIAtomContainer() [1/2]

IAtomContainer denoptim.graph.Fragment.getIAtomContainer ( )

Reimplemented from denoptim.graph.Vertex.

Definition at line 788 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.constants.DENOPTIMConstants.ATMPROPORIGINALATMID, denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.graph.Vertex.getProperty(), denoptim.graph.Vertex.getVertexId(), denoptim.constants.DENOPTIMConstants.ISOMORPHICFAMILYID, denoptim.graph.Fragment.mol, denoptim.graph.Fragment.projectAPsToProperties(), and denoptim.constants.DENOPTIMConstants.VERTEXJSONTAG.

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.utils.MoleculeUtils.extractIACForSubgraph(), denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.graph.Fragment.getIAtomContainer(), denoptim.gui.FragmentViewPanel.getLoadedStructure(), denoptim.gui.FragmentViewPanel.loadStructure(), denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), denoptim.graph.FragmentTest.testConversionToIAC(), denoptim.fragmenter.ConformerExtractorTaskTest.testExtractClusterableFragments(), and denoptim.json.DENOPTIMgsonTest.testMolecularFragmentSerialization().

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◆ getIAtomContainer() [2/2]

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

Although this type of vertex contains atoms, its content is fixed.

So, there is no need to regenerate its chemical representation. Accordingly, this method is ignoring all the parameters and calling getIAtomContainer()

Reimplemented from denoptim.graph.Vertex.

Definition at line 814 of file Fragment.java.

References denoptim.graph.Fragment.getIAtomContainer().

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◆ getJGraphFragIsomorphism()

DefaultUndirectedGraph< FragIsomorphNode, FragIsomorphEdge > denoptim.graph.Fragment.getJGraphFragIsomorphism ( )

Creates a graph representation of this fragment where both atoms and AttachmentPoints are represented as nodes, and edges are either bonds or atom-to-attachment point connections.

Note that dummy atoms meant to heal linearities ({@value DENOPTIMConstants::DUMMYATMSYMBOL} with only one connected neighbor) are ignored.

Returns: the graph.

Definition at line 996 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.graph.Fragment.getAttachmentPoints(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.graph.Fragment.jGraphFragIsomorphism, and denoptim.graph.Fragment.mol.

Referenced by denoptim.graph.FragmentIsomorphismInspector.FragmentIsomorphismInspector(), denoptim.fragmenter.ClusterableFragment.getJGraphFragIsomorphism(), and denoptim.fragmenter.ClusterableFragment.setNaturalNodeOrder().

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◆ getMutationSites()

List< Vertex > denoptim.graph.Fragment.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 1164 of file Fragment.java.

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

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◆ getSymmetricAPSets()

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

Reimplemented from denoptim.graph.Vertex.

Definition at line 1148 of file Fragment.java.

References denoptim.graph.Fragment.lstSymAPs.

Referenced by denoptim.graph.Fragment.clone(), denoptim.graph.FragmentTest.testClone(), denoptim.graph.VertexTest.testClone(), denoptim.graph.FragmentTest.testConversionToIAC(), denoptim.graph.SymmetricAPsTest.testGetSameAsThis(), denoptim.json.DENOPTIMgsonTest.testMolecularFragmentSerialization(), and denoptim.graph.SymmetricAPsTest.testSameAs().

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◆ identifySymmetryRelatedAPSets()

static List< SymmetricAPs > denoptim.graph.Fragment.identifySymmetryRelatedAPSets	(	IAtomContainer	mol,
		List< AttachmentPoint >	daps
	)

staticprivate

Definition at line 239 of file Fragment.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.Fragment.atomsAreCompatible(), denoptim.graph.APClass.compareTo(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), and denoptim.graph.Fragment.mol.

Referenced by denoptim.graph.Fragment.Fragment(), and denoptim.graph.Fragment.updateSymmetryRelations().

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◆ indexOf()

int denoptim.graph.Fragment.indexOf ( IAtom atom )

Definition at line 850 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.gui.GUIVertexInspector.convertAtomToAP(), and denoptim.fragmenter.ClusterableFragment.getTransformedCopy().

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◆ is3D()

boolean denoptim.graph.Fragment.is3D ( )

Checks if atoms and APs contained in this fragment have non-zero 3D coordinates.

Definition at line 195 of file Fragment.java.

References denoptim.graph.Fragment.atoms(), denoptim.utils.MathUtils.distance(), and denoptim.graph.Fragment.getAttachmentPoints().

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

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◆ isIsomorphicTo()

boolean denoptim.graph.Fragment.isIsomorphicTo ( Vertex other )

Checks for isomorphism of the graph representation of this and another fragment.

The graph representation results from the combination of the molecular structure (atoms as nodes, bonds as edges of the graph) and the presence of attachment points (attachment points as nodes of the graph). See getJGraphFragIsomorphism() for details. Does not consider three-dimensional features. Does not consider dummy atoms on linearities so, de facto, fragments can be isomorphic and have a different number of atoms and bonds.

Parameters

other the other building block to consider.

Returns: true if at least one isomorphism exists.

Definition at line 1066 of file Fragment.java.

References denoptim.graph.Fragment.Fragment(), denoptim.graph.Fragment.getAttachmentPoints(), and denoptim.graph.FragmentIsomorphismInspector.isomorphismExists().

Referenced by denoptim.graph.DGraph.areApsUsedBySymmetricUsers(), denoptim.graph.FragmentTest.testIsomorphicInLinear(), and denoptim.graph.FragmentTest.testIsomorphicTo().

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◆ projectAPsToProperties()

void denoptim.graph.Fragment.projectAPsToProperties ( )

Finds the DENOPTIMAttachmentPoint objects defined as properties of the atoms in this container, and defines the string-based molecular property used to print attachment points in SDF files.

Definition at line 693 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.graph.AttachmentPoint.getAPDefinitionsForSDF(), denoptim.graph.Fragment.getAPsFromAtom(), denoptim.graph.Fragment.mol, and denoptim.graph.Vertex.setProperty().

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.Fragment.getIAtomContainer(), denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.molecularmodeling.ThreeDimTreeBuilderTest.testConversionTo3dTree(), denoptim.graph.FragmentTest.testConversionToIAC(), denoptim.graph.FragmentTest.testHandlingAPsAsObjOrProperty(), denoptim.io.DenoptimIOTest.testReadAllAPClasses(), denoptim.graph.DGraphTest.testRemoveUnusedRCVs(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ projectListAPToAtomProperties()

void denoptim.graph.Fragment.projectListAPToAtomProperties ( )

Takes the list of APs from the field of this class and projects the APs into properties of the IAtoms.

This method does not update the symmetry relation between APs because it might have been read from file, which takes priority over recalculating it.

Exceptions

DENOPTIMException

Definition at line 659 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.graph.Fragment.getAPsFromAtom(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Fragment.lstAPs, and denoptim.graph.Fragment.mol.

Referenced by denoptim.graph.Fragment.clone(), denoptim.graph.Fragment.fromJson(), and denoptim.graph.Fragment.projectPropertyToAP().

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◆ projectPropertyToAP() [1/2]

void denoptim.graph.Fragment.projectPropertyToAP ( ) throws DENOPTIMException

Uses the molecular property defining attachment points to create the DENOPTIMAttachmentPoint objects in the Atom objects.

Does not overwrite existing APs in the atoms.

Exceptions

DENOPTIMException

Definition at line 572 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.APSTAG, denoptim.graph.Vertex.getProperty(), and denoptim.graph.Fragment.projectPropertyToAP().

Referenced by denoptim.graph.Fragment.Fragment(), denoptim.graph.Fragment.projectPropertyToAP(), and denoptim.graph.FragmentTest.testHandlingAPsAsObjOrProperty().

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◆ projectPropertyToAP() [2/2]

void denoptim.graph.Fragment.projectPropertyToAP ( String allAtomsProp ) throws DENOPTIMException

Uses a string formatted like the molecular property used for defining attachment points to create the DENOPTIMAttachmentPoint objects in the Atom objects.

Does not overwrite existing APs in the atoms.

Parameters

allAtomsProp the content of the molecular property.

Exceptions

DENOPTIMException

Definition at line 594 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Fragment.lstAPs, denoptim.graph.Fragment.mol, denoptim.graph.Fragment.projectListAPToAtomProperties(), denoptim.constants.DENOPTIMConstants.SEPARATORAPPROPAAP, denoptim.constants.DENOPTIMConstants.SEPARATORAPPROPAPS, denoptim.constants.DENOPTIMConstants.SEPARATORAPPROPATMS, and denoptim.graph.Fragment.updateSymmetryRelations().

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◆ removeAP()

void denoptim.graph.Fragment.removeAP ( AttachmentPoint ap )

Definition at line 433 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.graph.Fragment.getAPCountOnAtom(), denoptim.graph.Fragment.getAPsFromAtom(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Fragment.getAttachmentPoints(), denoptim.graph.Fragment.mol, and denoptim.graph.Fragment.updateSymmetryRelations().

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◆ removeAtom()

void denoptim.graph.Fragment.removeAtom ( IAtom atom )

Definition at line 899 of file Fragment.java.

References denoptim.graph.Fragment.removeAtoms().

Referenced by denoptim.utils.MoleculeUtils.extractIACForSubgraph(), and denoptim.gui.GUIVertexInspector.removeAtoms().

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◆ removeAtoms()

void denoptim.graph.Fragment.removeAtoms ( Collection< IAtom > atoms )

Removes a list of atoms and updates the list of attachment points.

Use this method instead of removeAtom(IAtom) to run the regeneration of the list of APs only once instead of for every atom deletion.

Parameters

atoms the atoms to remove.

Definition at line 913 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.graph.Fragment.atoms(), denoptim.graph.Fragment.getAPsFromAtom(), denoptim.graph.Fragment.lstAPs, denoptim.graph.Fragment.mol, denoptim.graph.AttachmentPoint.setAtomPositionNumber(), and denoptim.graph.Fragment.updateSymmetryRelations().

Referenced by denoptim.fragmenter.FragmenterTools.fragmentation(), and denoptim.graph.Fragment.removeAtom().

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◆ removeBond() [1/3]

IBond denoptim.graph.Fragment.removeBond	(	IAtom	atom1,
		IAtom	atom2
	)

Definition at line 885 of file Fragment.java.

References denoptim.graph.Fragment.mol.

◆ removeBond() [2/3]

void denoptim.graph.Fragment.removeBond ( IBond bond )

Definition at line 892 of file Fragment.java.

References denoptim.graph.Fragment.mol.

◆ removeBond() [3/3]

IBond denoptim.graph.Fragment.removeBond ( int position )

Definition at line 878 of file Fragment.java.

References denoptim.graph.Fragment.mol.

Referenced by denoptim.utils.MoleculeUtils.extractIACForSubgraph(), and denoptim.gui.GUIVertexInspector.removeAtoms().

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◆ sameAs()

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

Compares this and another fragment ignoring vertex IDs.

Ignores isomerism and geometric differences as it only considers the number of atoms and bonds.

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 967 of file Fragment.java.

References denoptim.graph.Fragment.containsAtoms(), denoptim.graph.Fragment.mol, and denoptim.graph.Vertex.sameVertexFeatures().

Referenced by denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass(), and denoptim.io.DenoptimIOTest.testIOMolFragment().

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◆ setSymmetricAPSets()

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

protected

Reimplemented from denoptim.graph.Vertex.

Definition at line 1128 of file Fragment.java.

Referenced by denoptim.graph.Fragment.clone(), denoptim.graph.Fragment.Fragment(), denoptim.graph.FragmentTest.makeFragment(), and denoptim.graph.Fragment.updateSymmetryRelations().

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◆ toJson()

String denoptim.graph.Fragment.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 1188 of file Fragment.java.

References denoptim.json.DENOPTIMgson.getWriter().

Referenced by denoptim.graph.FragmentIsomorphismInspector.getMappings(), denoptim.graph.FragmentIsomorphismInspector.isomorphismExists(), and denoptim.graph.VertexTest.testFromToJSON_minimal().

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◆ toString()

String denoptim.graph.Fragment.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 1111 of file Fragment.java.

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

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◆ updateAPs()

void denoptim.graph.Fragment.updateAPs ( )

Changes the properties of each APs as to reflect the current atom list.

AttachmentPoint include the index of their source atom, and this method updates such indexes to reflect the current atom list. This method is needed upon reordering of the atom list.

Definition at line 511 of file Fragment.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPAPS, denoptim.graph.Fragment.getAPsFromAtom(), denoptim.graph.Fragment.mol, denoptim.graph.AttachmentPoint.setAtomPositionNumber(), and denoptim.graph.Fragment.updateSymmetryRelations().

Referenced by denoptim.utils.MoleculeUtils.extractIACForSubgraph(), denoptim.graph.Fragment.getCurrentAPs(), denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), and denoptim.gui.GUIVertexInspector.removeAtoms().

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◆ updateSymmetryRelations()

void denoptim.graph.Fragment.updateSymmetryRelations ( )

private

Depends on an healthy list of attachment points with properly set pointers to the source atoms.

Definition at line 231 of file Fragment.java.

References denoptim.graph.Fragment.getAttachmentPoints(), denoptim.graph.Fragment.identifySymmetryRelatedAPSets(), denoptim.graph.Fragment.mol, and denoptim.graph.Fragment.setSymmetricAPSets().

Referenced by denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.projectPropertyToAP(), denoptim.graph.Fragment.removeAP(), denoptim.graph.Fragment.removeAtoms(), and denoptim.graph.Fragment.updateAPs().

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Member Data Documentation

◆ jGraphFragIsomorphism

DefaultUndirectedGraph<FragIsomorphNode,FragIsomorphEdge> denoptim.graph.Fragment.jGraphFragIsomorphism

private

jGraph representation used for detecting fragment isomorphism.

Definition at line 82 of file Fragment.java.

Referenced by denoptim.graph.Fragment.getJGraphFragIsomorphism().

◆ lstAPs

List<AttachmentPoint> denoptim.graph.Fragment.lstAPs

private

attachment points on this vertex

Definition at line 65 of file Fragment.java.

Referenced by denoptim.graph.Fragment.clone(), denoptim.graph.Fragment.getAttachmentPoints(), denoptim.graph.Fragment.getCurrentAPs(), denoptim.graph.Fragment.projectListAPToAtomProperties(), denoptim.graph.Fragment.projectPropertyToAP(), and denoptim.graph.Fragment.removeAtoms().

◆ lstSymAPs

List<SymmetricAPs> denoptim.graph.Fragment.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 71 of file Fragment.java.

Referenced by denoptim.graph.Fragment.getSymmetricAPSets().

◆ mol

IAtomContainer denoptim.graph.Fragment.mol

private

Molecular representation of this fragment.

Definition at line 76 of file Fragment.java.

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

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Fragment() [1/5]

◆ Fragment() [2/5]

◆ Fragment() [3/5]

◆ Fragment() [4/5]

◆ Fragment() [5/5]

Member Function Documentation

◆ addAP() [1/4]

◆ addAP() [2/4]

◆ addAP() [3/4]

◆ addAP() [4/4]

◆ addAPOnAtom()

◆ addAtom()

◆ addBond()

◆ addSymmetricAPSet()

◆ atoms()

◆ atomsAreCompatible()

◆ bonds()

◆ clone()

◆ containsAtoms()

◆ fromJson()

◆ getAPCountOnAtom() [1/2]

◆ getAPCountOnAtom() [2/2]

◆ getAPsFromAtom()

◆ getAtom()

◆ getAtomCount()

◆ getAtomHoldingAP()

◆ getAttachmentPoints()

◆ getBondCount()

◆ getConnectedAtomsCount()

◆ getConnectedAtomsList()

◆ getCurrentAPs()

◆ getHeavyAtomsCount()

◆ getIAtomContainer() [1/2]

◆ getIAtomContainer() [2/2]

◆ getJGraphFragIsomorphism()

◆ getMutationSites()

◆ getSymmetricAPSets()

◆ identifySymmetryRelatedAPSets()

◆ indexOf()

◆ is3D()

◆ isIsomorphicTo()

◆ projectAPsToProperties()

◆ projectListAPToAtomProperties()

◆ projectPropertyToAP() [1/2]

◆ projectPropertyToAP() [2/2]

◆ removeAP()

◆ removeAtom()

◆ removeAtoms()

◆ removeBond() [1/3]

◆ removeBond() [2/3]

◆ removeBond() [3/3]

◆ sameAs()

◆ setSymmetricAPSets()

◆ toJson()

◆ toString()

◆ updateAPs()

◆ updateSymmetryRelations()

Member Data Documentation

◆ jGraphFragIsomorphism

◆ lstAPs

◆ lstSymAPs

◆ mol