Class defining a space of building blocks. More...

Collaboration diagram for denoptim.fragspace.FragmentSpace:

Public Member Functions
	FragmentSpace ()
	Creates an empty fragment space, which is marked as invalid. More...

	FragmentSpace (FragmentSpaceParameters settings, String scaffFile, String fragFile, String capFile, String cpmFile) throws DENOPTIMException
	Define all components of a fragment space that implements the attachment point class-approach. More...

	FragmentSpace (FragmentSpaceParameters settings, ArrayList< Vertex > scaffLib, ArrayList< Vertex > fragLib, ArrayList< Vertex > cappLib, HashMap< APClass, ArrayList< APClass > > cpMap, HashMap< APClass, APClass > capMap, HashSet< APClass > forbEnds, HashMap< APClass, ArrayList< APClass > > rcCpMap) throws DENOPTIMException
	Define all components of a fragment space that implements the attachment point class-approach. More...

	FragmentSpace (FragmentSpaceParameters settings, ArrayList< Vertex > scaffLib, ArrayList< Vertex > fragLib, ArrayList< Vertex > cappLib, HashMap< APClass, ArrayList< APClass > > cpMap, HashMap< APClass, APClass > capMap, HashSet< APClass > forbEnds, HashMap< APClass, ArrayList< APClass > > rcCpMap, HashMap< APClass, Double > symCntrMap) throws DENOPTIMException
	Define all components of a fragment space that implements the attachment point class-approach. More...

	FragmentSpace (FragmentSpaceParameters settings, String scaffFile, String fragFile, String capFile, String cpmFile, String rcpmFile, HashMap< APClass, Double > symCntrMap) throws DENOPTIMException
	Define all components of a fragment space that implements the attachment point class-approach. More...

boolean	isDefined ()
	Checks for valid definition of this fragment space. More...

Randomizer	getRandomizer ()
	Returns the program-specific randomizer that is associated with this program-specific fragment space. More...

void	setAPclassBasedApproach (boolean useAPC)
	Set the fragment space to behave according to APClass-based approach. More...

boolean	useAPclassBasedApproach ()
	Check usage of APClass-based approach, i.e., uses attachment points with annotated data (i.e., the APClass) to evaluate compatibilities between attachment points. More...

APClass	getAPClassForFragment (IdFragmentAndAP apId)
	Search for a specific AP on a specific fragment and finds out its class. More...

Vertex	getVertexFromLibrary (Vertex.BBType bbType, int bbIdx) throws DENOPTIMException
	Returns a clone of the requested building block. More...

int	getCappingFragment (APClass rcnCap)
	Select a compatible capping group for the given APClass. More...

ArrayList< Integer >	getCompatibleCappingFragments (APClass cmpReac)
	Retrieve a list of compatible capping groups. More...

Vertex	makeRandomScaffold ()
	Randomly select a scaffold and return a fully configured clone of it. More...

ArrayList< Vertex >	getScaffoldLibrary ()

ArrayList< Vertex >	getFragmentLibrary ()

ArrayList< Vertex >	getCappingLibrary ()

ArrayList< Integer >	getCappingGroupsWithAPClass (APClass capApCls)

Vertex	getCappingVertexWithAPClass (APClass capApCls)

void	importCompatibilityMatrixFromFile (String inFile) throws DENOPTIMException
	Load info from a compatibility matrix file. More...

void	importRCCompatibilityMatrixFromFile (String inFile) throws DENOPTIMException
	Load info for ring closures compatibilities from a compatibility matrix file. More...

HashMap< APClass, ArrayList< APClass > >	getCompatibilityMatrix ()

ArrayList< APClass >	getCompatibleAPClasses (APClass apc)
	Returns a list of APClasses compatible with the given APClass. More...

HashMap< APClass, ArrayList< APClass > >	getRCCompatibilityMatrix ()
	Returns the compatibility matrix for ring closing fragment-fragment connections or `null` if not provided in the parameters file. More...

HashMap< APClass, APClass >	getCappingMap ()

APClass	getAPClassOfCappingVertex (APClass srcApClass)

Set< APClass >	getForbiddenEndList ()

Set< APClass >	getAllAPClassesFromCPMap ()
	Return the set of APClasses that used in the compatibility matrix for the growing graph APs. More...

HashMap< Integer, ArrayList< Integer > >	getMapOfFragsPerNumAps ()

ArrayList< Integer >	getFragsWithNumAps (int nAps)
	Returns the list of fragments with given number of APs. More...

ArrayList< APClass >	getAPClassesPerFragment (int fragId)
	Returns the APclasses associated with a given fragment. More...

ArrayList< IdFragmentAndAP >	getFragsWithAPClass (APClass apc)
	Returns the list of attachment points with the given class. More...

ArrayList< Vertex >	getVerticesWithAPClass (APClass apc)
	Returns the list of attachment points with the given class. More...

ArrayList< Vertex >	getFragmentsCompatibleWithTheseAPs (ArrayList< IdFragmentAndAP > srcAPs)
	Searches for all building blocks that are compatible with the given list of APs. More...

List< Vertex >	getRCVsWithAPClass (APClass apc)
	Searches for all building blocks that are ring-closing vertexes and hold an AP with the given class. More...

List< Vertex >	getRCVsForAPClass (APClass apc)
	Searches for all building blocks that are ring-closing vertexes and are compatible with the given AP. More...

ArrayList< AttachmentPoint >	getAPsCompatibleWithThese (ArrayList< AttachmentPoint > srcAPs)
	Searches for all attachment points that are compatible with the given list of attachment points. More...

ArrayList< IdFragmentAndAP >	getFragAPsCompatibleWithTheseAPs (ArrayList< IdFragmentAndAP > srcAPs)
	Searches for all APs that are compatible with the given list of APs. More...

ArrayList< AttachmentPoint >	getAPsCompatibleWithClass (APClass aPC1)
	Returns the list of attachment points found in the fragment space and that are compatible with a given AP class. More...

ArrayList< IdFragmentAndAP >	getFragAPsCompatibleWithClass (APClass aPC1)
	Returns the list of attachment points found in the fragment space and that are compatible with a given AP class. More...

boolean	imposeSymmetryOnAPsOfClass (APClass apClass)
	Checks if the symmetry settings impose use of symmetry on attachment points of the given AP class. More...

boolean	hasSymmetryConstrain (APClass apClass)
	Checks if there is a constraint on the constitutional symmetry probability for the given AP class. More...

double	getSymmetryConstrain (APClass apClass)
	Return the constitutional symmetry constrain for the given APclass, or null. More...

void	setScaffoldLibrary (ArrayList< Vertex > lib)

void	setFragmentLibrary (ArrayList< Vertex > lib)

void	setCappingLibrary (ArrayList< Vertex > lib)

void	setCompatibilityMatrix (HashMap< APClass, ArrayList< APClass > > map)

void	setRCCompatibilityMatrix (HashMap< APClass, ArrayList< APClass > > map)

void	setCappingMap (HashMap< APClass, APClass > map)

void	setForbiddenEndList (Set< APClass > lst)

void	setFragPoolPerNumAP (HashMap< Integer, ArrayList< Integer > > map)

void	setSymmConstraints (HashMap< APClass, Double > map)

void	clearAll ()
	Clears all settings of this fragment space. More...

void	appendVerticesToLibrary (ArrayList< Vertex > list, Vertex.BBType bbt, ArrayList< Vertex > library)
	Takes a list of vertices and add them to a given library. More...

void	appendVertexToLibrary (Vertex v, Vertex.BBType bbt, ArrayList< Vertex > library)
	Takes a vertex and add it to a given library. More...

void	addFusedRingsToFragmentLibrary (DGraph graph)
	Extracts a system of one or more fused rings and adds them to the fragment space if not already present. More...

void	addFusedRingsToFragmentLibrary (DGraph graph, boolean addIfScaffold, boolean addIfFragment)
	Extracts a system of one or more fused rings and adds them to the fragment space if not already present. More...

void	addFusedRingsToFragmentLibrary (DGraph graph, boolean addIfScaffold, boolean addIfFragment, IAtomContainer wholeMol)
	Extracts a system of one or more fused rings and adds them to the fragment space if not already present. More...

boolean	hasIsomorph (DGraph graph, BBType type)
	Checks if a graph is isomorphic to another template's inner graph in its appropriate fragment space library (inferred from BBType). More...

void	registerRCV (Vertex v)
	Adds the reference to a ring-closing vertex (RCV) to the quick-access list of RCVs known in this building block space. More...

ArrayList< Vertex >	getRCVs ()
	Returns the list of registered ring-closing vertexes (RCVs). More...

List< APMapping >	mapAPClassCompatibilities (List< AttachmentPoint > listA, List< AttachmentPoint > listB, int maxCombinations)
	Given two lists of APs this method maps the APClass-compatibilities from between the two lists considering the APs in the first list the for the role of source AP in the hypothetical edge. More...

void	classifyFragment (Vertex frg, int fragId)
	Classify a fragment in terms of the number of APs and possibly their type (AP-Class). More...

void	groupAndClassifyFragments (boolean apClassBasedApproch) throws DENOPTIMException
	Performs grouping and classification operations on the library of building blocks of `BBType#FRAGMENT`. More...

Vertex	getPolarizedRCV (boolean polarity)
	Returns a newly-built vertex that can play the role of a ring-closing vertex even when working with 3D building blocks. More...

Private Member Functions
void	define (FragmentSpaceParameters settings, ArrayList< Vertex > scaffLib, ArrayList< Vertex > fragLib, ArrayList< Vertex > cappLib, HashMap< APClass, ArrayList< APClass > > cpMap, HashMap< APClass, APClass > capMap, HashSet< APClass > forbEnds, HashMap< APClass, ArrayList< APClass > > rcCpMap, HashMap< APClass, Double > symCntrMap) throws DENOPTIMException
	Define all components of this fragment space. More...

Private Attributes
ArrayList< Vertex >	scaffoldLib = null
	Data structure containing the molecular representation of building blocks: scaffolds section - fragments that can be used as seeds to grow a new molecule. More...

ArrayList< Vertex >	fragmentLib = null
	Data structure containing the molecular representation of building blocks: fragment section - fragments for general use. More...

ArrayList< Vertex >	cappingLib = null
	Data structure containing the molecular representation of building blocks: capping group section - fragments with only one attachment point used to saturate unused attachment points on a graph. More...

HashMap< APClass, ArrayList< APClass > >	apClassCompatibilityMatrix
	Data structure that stored the true entries of the attachment point classes compatibility matrix. More...

ArrayList< Vertex >	rcvs = new ArrayList<Vertex>()
	Store references to the Ring-Closing Vertexes found in the library of fragments. More...

HashMap< APClass, ArrayList< APClass > >	rcCompatMap
	Data structure that stores compatible APclasses for joining APs in ring-closing bonds. More...

HashMap< APClass, APClass >	cappingMap
	Data structure that stores the AP-classes to be used to cap unused APS on the growing molecule. More...

Set< APClass >	forbiddenEndList
	Data structure that stores AP classes that cannot be held unused. More...

HashMap< Integer, ArrayList< Integer > >	fragPoolPerNumAP
	Clusters of fragments based on the number of APs. More...

HashMap< Integer, ArrayList< APClass > >	apClassesPerFrag
	List of APClasses per each fragment. More...

HashMap< APClass, ArrayList< ArrayList< Integer > > >	fragsApsPerApClass
	Clusters of fragments'AP based on AP classes. More...

final Object	LOCK = new Object()
	Lock for synchronizing tasks. More...

HashMap< APClass, Double >	symmConstraints
	APclass-specific constraints to constitutional symmetry. More...

boolean	apClassBasedApproch = false
	Flag defining use of AP class-based approach. More...

boolean	isValid = false
	Flag signaling that this fragment space was built and validated. More...

FragmentSpaceParameters	settings = null
	Settings used to configure this fragment space. More...

Detailed Description

Class defining a space of building blocks.

The space comprises of the lists of building blocks and the rules governing the connection of building blocks to forms a DGraph.

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 66 of file FragmentSpace.java.

Constructor & Destructor Documentation

◆ FragmentSpace() [1/5]

denoptim.fragspace.FragmentSpace.FragmentSpace ( )

Creates an empty fragment space, which is marked as invalid.

Such fragment space has very limited functionality, but can be used to manipulate information related to fragment spaces, such as, handling compatibility rules even without having any defined vertex in it.

Definition at line 174 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.cappingLib, denoptim.fragspace.FragmentSpace.fragmentLib, denoptim.fragspace.FragmentSpace.scaffoldLib, and denoptim.fragspace.FragmentSpace.settings.

◆ FragmentSpace() [2/5]

denoptim.fragspace.FragmentSpace.FragmentSpace	(	FragmentSpaceParameters	settings,
		String	scaffFile,
		String	fragFile,
		String	capFile,
		String	cpmFile
	)		throws DENOPTIMException

Define all components of a fragment space that implements the attachment point class-approach.

Parameters

scaffFile	pathname to library of fragments used to start the construction of any new graph (i.e., seed or root fragments, a.k.a. scaffolds).
fragFile	pathname to the library of fragments for general purpose.
capFile	pathname to the library of single-AP fragments used to cap free attachment points (i.e., the capping groups).
cpmFile	pathname to the compatibility matrix, bond type mapping, capping, and forbidden ends rules.

Exceptions

DENOPTIMException

Definition at line 199 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.settings.

◆ FragmentSpace() [3/5]

denoptim.fragspace.FragmentSpace.FragmentSpace	(	FragmentSpaceParameters	settings,
		ArrayList< Vertex >	scaffLib,
		ArrayList< Vertex >	fragLib,
		ArrayList< Vertex >	cappLib,
		HashMap< APClass, ArrayList< APClass > >	cpMap,
		HashMap< APClass, APClass >	capMap,
		HashSet< APClass >	forbEnds,
		HashMap< APClass, ArrayList< APClass > >	rcCpMap
	)		throws DENOPTIMException

Define all components of a fragment space that implements the attachment point class-approach.

Parameters

scaffLib	library of fragments used to start the construction of any new graph (i.e., seed or root fragments, a.k.a. scaffolds).
fragLib	library of fragments for general purpose.
cappLib	library of single-AP fragments used to cap free attachment points (i.e., the capping groups).
cpMap	the APClass compatibility map. This data structure is a map of the APClass-on-growing-graph (key) to list of permitted APClasses on incoming fragment (values).
capMap	the capping rules. This data structure is a map of APClass-to-cap (keys) to APClass-of-capping-group (values).
forbEnds	the list of forbidden ends, i.e., APClasses that cannot be left unused neither capped.
rcCpMap	the APClass compatibility matrix for ring closures.

Exceptions

DENOPTIMException

Definition at line 230 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.define(), and denoptim.fragspace.FragmentSpace.settings.

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◆ FragmentSpace() [4/5]

denoptim.fragspace.FragmentSpace.FragmentSpace	(	FragmentSpaceParameters	settings,
		ArrayList< Vertex >	scaffLib,
		ArrayList< Vertex >	fragLib,
		ArrayList< Vertex >	cappLib,
		HashMap< APClass, ArrayList< APClass > >	cpMap,
		HashMap< APClass, APClass >	capMap,
		HashSet< APClass >	forbEnds,
		HashMap< APClass, ArrayList< APClass > >	rcCpMap,
		HashMap< APClass, Double >	symCntrMap
	)		throws DENOPTIMException

Define all components of a fragment space that implements the attachment point class-approach.

Parameters

scaffLib	library of fragments used to start the construction of any new graph (i.e., seed or root fragments, a.k.a. scaffolds).
fragLib	library of fragments for general purpose.
cappLib	library of single-AP fragments used to cap free attachment points (i.e., the capping groups).
cpMap	the APClass compatibility map. This data structure is a map of the APClass-on-growing-graph (key) to list of permitted APClasses on incoming fragment (values).
capMap	the capping rules. This data structure is a map of APClass-to-cap (keys) to APClass-of-capping-group (values).
forbEnds	the list of forbidden ends, i.e., APClasses that cannot be left unused neither capped.
rcCpMap	the APClass compatibility matrix for ring closures.
symCntrMap	map of symmetry probability constraints.

Exceptions

DENOPTIMException

Definition at line 268 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.define(), and denoptim.fragspace.FragmentSpace.settings.

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◆ FragmentSpace() [5/5]

denoptim.fragspace.FragmentSpace.FragmentSpace	(	FragmentSpaceParameters	settings,
		String	scaffFile,
		String	fragFile,
		String	capFile,
		String	cpmFile,
		String	rcpmFile,
		HashMap< APClass, Double >	symCntrMap
	)		throws DENOPTIMException

Define all components of a fragment space that implements the attachment point class-approach.

Parameters

scaffFile	pathname to library of fragments used to start the construction of any new graph (i.e., seed or root fragments, a.k.a. scaffolds). Can be null or empty in which case no scaffold is imported.
fragFile	pathname to the library of fragments for general purpose. Can be null or empty in which case no fragment is imported.
capFile	pathname to the library of single-AP fragments used to cap free attachment points (i.e., the capping groups).
cpmFile	pathname to the compatibility matrix, capping, and forbidden ends rules.
rcpmFile	the APClass compatibility matrix for ring closures.
symCntrMap	map of symmetry probability constraints.

Exceptions

DENOPTIMException

Definition at line 304 of file FragmentSpace.java.

References denoptim.graph.Vertex.BBType.CAP, denoptim.fragspace.FragmentSpace.define(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.io.DenoptimIO.readCompatibilityMatrix(), denoptim.io.DenoptimIO.readRCCompatibilityMatrix(), denoptim.io.DenoptimIO.readVertexes(), denoptim.graph.Vertex.BBType.SCAFFOLD, and denoptim.fragspace.FragmentSpace.settings.

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Member Function Documentation

◆ addFusedRingsToFragmentLibrary() [1/3]

void denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary ( DGraph graph )

Extracts a system of one or more fused rings and adds them to the fragment space if not already present.

This method does not create any molecular geometry in the building block that is stores in the library. See FragmentSpace#addFusedRingsToFragmentLibrary(DGraph, boolean, boolean, IAtomContainer) to include a molecular representation on the stored building block. WARNING Expanding the libraries of building blocks on-the-fly has the potential to overload the memory.

Definition at line 1526 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary().

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingOnlyAddedOnce(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ addFusedRingsToFragmentLibrary() [2/3]

void denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary	(	DGraph	graph,
		boolean	addIfScaffold,
		boolean	addIfFragment
	)

Extracts a system of one or more fused rings and adds them to the fragment space if not already present.

WARNING Expanding the libraries of building blocks on-the-fly has the potential to overload the memory.

Parameters

graph	the graph to analyze and possibly chop.
addIfScaffold	use `true` to enable saving of new ring systems that contain any scaffold vertexes as new scaffolds.
addIfFragment	use `true` to enable saving of new ring systems that do NOT contain any scaffold vertexes as new fragments.

Definition at line 1545 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary().

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◆ addFusedRingsToFragmentLibrary() [3/3]

void denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary	(	DGraph	graph,
		boolean	addIfScaffold,
		boolean	addIfFragment,
		IAtomContainer	wholeMol
	)

Extracts a system of one or more fused rings and adds them to the fragment space if not already present.

WARNING Expanding the libraries of building blocks on-the-fly has the potential to overload the memory.

Parameters

graph	the graph to analyze and possibly chop.
addIfScaffold	use `true` to enable saving of new ring systems that contain any scaffold vertexes as new scaffolds.
addIfFragment	use `true` to enable saving of new ring systems that do NOT contain any scaffold vertexes as new fragments.
wholeMol	the complete molecular representation of `graph`. If this parameter is not null, then we'll try to use the geometry found in this parameter to define the geometry of the fused-rings templates. The atoms in this container are expected to have property `DENOPTIMConstants#ATMPROPVERTEXID` that defines the ID of the vertex from which each atom comes from.

Definition at line 1578 of file FragmentSpace.java.

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◆ appendVertexToLibrary()

void denoptim.fragspace.FragmentSpace.appendVertexToLibrary	(	Vertex	v,
		Vertex.BBType	bbt,
		ArrayList< Vertex >	library
	)

Takes a vertex and add it to a given library.

Each vertex is assigned the building block type and ID.

Parameters

v	vertex to import.
bbt	the type of building block the vertex should be set to.
library	where to import the vertex to.

Definition at line 1498 of file FragmentSpace.java.

References denoptim.graph.Vertex.setBuildingBlockId(), and denoptim.graph.Vertex.setBuildingBlockType().

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpace.appendVerticesToLibrary(), denoptim.fragspace.GraphLinkFinderTest.prepare(), denoptim.ga.EAUtilsTest.prepare(), denoptim.graph.DGraphTest.prepare(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ appendVerticesToLibrary()

void denoptim.fragspace.FragmentSpace.appendVerticesToLibrary	(	ArrayList< Vertex >	list,
		Vertex.BBType	bbt,
		ArrayList< Vertex >	library
	)

Takes a list of vertices and add them to a given library.

Each vertex is assigned the building block type and ID.

Parameters

list	of vertices to import.
bbt	the type of building block the vertices should be set to.
library	where to import the vertices to.

Definition at line 1478 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.appendVertexToLibrary().

Referenced by denoptim.fragspace.FragmentSpace.setCappingLibrary(), denoptim.fragspace.FragmentSpace.setFragmentLibrary(), and denoptim.fragspace.FragmentSpace.setScaffoldLibrary().

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◆ classifyFragment()

void denoptim.fragspace.FragmentSpace.classifyFragment	(	Vertex	frg,
		int	fragId
	)

Classify a fragment in terms of the number of APs and possibly their type (AP-Class).

Parameters

frg	the building block to classify
id	the index of the fragment in the library

Exceptions

DENOPTIMException

Definition at line 1824 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassesPerFrag, denoptim.fragspace.FragmentSpace.fragsApsPerApClass, denoptim.graph.Vertex.getAllAPClasses(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.fragspace.FragmentSpace.getFragsWithNumAps(), denoptim.graph.Vertex.getFreeAPCount(), denoptim.fragspace.FragmentSpace.getMapOfFragsPerNumAps(), denoptim.graph.AttachmentPoint.isAvailable(), denoptim.graph.Vertex.isRCV, denoptim.fragspace.FragmentSpace.LOCK, denoptim.fragspace.FragmentSpace.registerRCV(), and denoptim.fragspace.FragmentSpace.useAPclassBasedApproach().

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), and denoptim.fragspace.FragmentSpace.groupAndClassifyFragments().

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◆ clearAll()

void denoptim.fragspace.FragmentSpace.clearAll ( )

Clears all settings of this fragment space.

All fields changed to null.

Definition at line 1451 of file FragmentSpace.java.

◆ define()

void denoptim.fragspace.FragmentSpace.define	(	FragmentSpaceParameters	settings,
		ArrayList< Vertex >	scaffLib,
		ArrayList< Vertex >	fragLib,
		ArrayList< Vertex >	cappLib,
		HashMap< APClass, ArrayList< APClass > >	cpMap,
		HashMap< APClass, APClass >	capMap,
		HashSet< APClass >	forbEnds,
		HashMap< APClass, ArrayList< APClass > >	rcCpMap,
		HashMap< APClass, Double >	symCntrMap
	)		throws DENOPTIMException

private

Define all components of this fragment space.

Parameters

scaffLib	library of fragments used to start the construction of any new graph (i.e., seed or root fragments, a.k.a. scaffolds).
fragLib	library of fragments for general purpose.
cappLib	library of single-AP fragments used to cap free attachment points (i.e., the capping groups).
cpMap	the APClass compatibility map. This data structure is a map of the APClass-on-growing-graph (key) to list of permitted APClasses on incoming fragment (values).
capMap	the capping rules. This data structure is a map of APClass-to-cap (keys) to APClass-of-capping-group (values).
forbEnds	the list of forbidden ends, i.e., APClasses that cannot be left unused neither capped.
rcCpMap	the APClass compatibility matrix for ring closures.
symCntrMap	map of symmetry probability constraints.

Exceptions

DENOPTIMException

Definition at line 409 of file FragmentSpace.java.

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

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◆ getAllAPClassesFromCPMap()

Set< APClass > denoptim.fragspace.FragmentSpace.getAllAPClassesFromCPMap ( )

Return the set of APClasses that used in the compatibility matrix for the growing graph APs.

Note these APClasses do include subclasses. For example, for AP with class MyAPClass:0 the 0 is the subclass.

Returns: the lst of APClasses

Definition at line 908 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassCompatibilityMatrix.

Referenced by denoptim.gui.FSParametersForm.FSParametersForm().

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◆ getAPClassesPerFragment()

ArrayList< APClass > denoptim.fragspace.FragmentSpace.getAPClassesPerFragment ( int fragId )

Returns the APclasses associated with a given fragment.

Parameters

fragId the index of the fragment in the library

Returns: the list of APclasses found of the fragment

Definition at line 948 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassesPerFrag, and denoptim.fragspace.FragmentSpace.LOCK.

◆ getAPClassForFragment()

APClass denoptim.fragspace.FragmentSpace.getAPClassForFragment ( IdFragmentAndAP apId )

Search for a specific AP on a specific fragment and finds out its class.

Parameters

apId	the identified of a specific attachment point.

Returns: the AP class or null

Definition at line 495 of file FragmentSpace.java.

References denoptim.fragspace.IdFragmentAndAP.getApId(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.fragspace.FragmentSpace.getVertexFromLibrary(), denoptim.fragspace.IdFragmentAndAP.getVertexMolId(), and denoptim.fragspace.IdFragmentAndAP.getVertexMolType().

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

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◆ getAPClassOfCappingVertex()

APClass denoptim.fragspace.FragmentSpace.getAPClassOfCappingVertex ( APClass srcApClass )

Parameters

srcApClass the attachment point class of the attachment point to be capped

Returns: the APClass of the capping group or null

Definition at line 885 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.cappingMap.

Referenced by denoptim.fragspace.FragsCombinationIterator.FragsCombinationIterator(), and denoptim.graph.DGraph.graphNeedsCappingGroups().

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◆ getAPsCompatibleWithClass()

ArrayList< AttachmentPoint > denoptim.fragspace.FragmentSpace.getAPsCompatibleWithClass ( APClass aPC1 )

Returns the list of attachment points found in the fragment space and that are compatible with a given AP class.

Multiple APs can be found for each fragment.

Parameters

aPC1	the AP class for which we want compatible APs.

Definition at line 1244 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.getCompatibleAPClasses(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.fragspace.FragmentSpace.getVerticesWithAPClass(), and denoptim.fragspace.FragmentSpace.settings.

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

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◆ getAPsCompatibleWithThese()

ArrayList< AttachmentPoint > denoptim.fragspace.FragmentSpace.getAPsCompatibleWithThese ( ArrayList< AttachmentPoint > srcAPs )

Searches for all attachment points that are compatible with the given list of attachment points.

Parameters

srcAPs attachment points meant to results have to be compatible with.

Returns: a list of compatible attachment points found in the library of fragments.

Definition at line 1140 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.getAPsCompatibleWithClass().

Referenced by denoptim.gui.GUIGraphHandler.collectFragAndAPsCompatibleWithSelectedAPs().

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◆ getCappingFragment()

int denoptim.fragspace.FragmentSpace.getCappingFragment ( APClass rcnCap )

Select a compatible capping group for the given APClass.

Parameters

rcnCap the class of the attachment point to be capped.

Returns: the index of capping group

Definition at line 663 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.getCompatibleCappingFragments(), denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.utils.Randomizer.randomlyChooseOne(), and denoptim.fragspace.FragmentSpace.settings.

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◆ getCappingGroupsWithAPClass()

ArrayList< Integer > denoptim.fragspace.FragmentSpace.getCappingGroupsWithAPClass ( APClass capApCls )

Parameters

capApCls the APClass of the attachment point on the capping group

Returns: all the capping groups which have the given APClass.

Definition at line 752 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.cappingLib, and denoptim.graph.APClass.equals().

Referenced by denoptim.fragspace.FragsCombinationIterator.FragsCombinationIterator().

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◆ getCappingLibrary()

ArrayList< Vertex > denoptim.fragspace.FragmentSpace.getCappingLibrary ( )

Definition at line 740 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.cappingLib.

Referenced by denoptim.gui.GUIGraphHandler.extendGraphFromFragSpace(), denoptim.fragspace.FragmentSpace.getCompatibleCappingFragments(), and denoptim.graph.DGraphTest.prepare().

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◆ getCappingMap()

HashMap< APClass, APClass > denoptim.fragspace.FragmentSpace.getCappingMap ( )

Definition at line 872 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.cappingMap.

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), and denoptim.ga.EAUtils.buildCandidatesByXOver().

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◆ getCappingVertexWithAPClass()

Vertex denoptim.fragspace.FragmentSpace.getCappingVertexWithAPClass ( APClass capApCls )

Parameters

capApCls the APClass of the attachment point on the capping group.

Returns: a clone of the first 'capping group' having the given APClass, or null if none was found.

Definition at line 775 of file FragmentSpace.java.

References denoptim.graph.Vertex.BBType.CAP, denoptim.fragspace.FragmentSpace.cappingLib, denoptim.graph.APClass.equals(), and denoptim.fragspace.FragmentSpace.getVertexFromLibrary().

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◆ getCompatibilityMatrix()

HashMap< APClass, ArrayList< APClass > > denoptim.fragspace.FragmentSpace.getCompatibilityMatrix ( )

Definition at line 834 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassCompatibilityMatrix.

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

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◆ getCompatibleAPClasses()

ArrayList< APClass > denoptim.fragspace.FragmentSpace.getCompatibleAPClasses ( APClass apc )

Returns a list of APClasses compatible with the given APClass.

The compatibility among classes is defined by the compatibility matrix

Parameters

apc

Returns: the list of compatible APClasses. Can be empty but not null.

Definition at line 847 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassCompatibilityMatrix.

Referenced by denoptim.fragspace.FragmentSpace.getAPsCompatibleWithClass(), denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithClass(), and denoptim.graph.APClass.isCPMapCompatibleWith().

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◆ getCompatibleCappingFragments()

ArrayList< Integer > denoptim.fragspace.FragmentSpace.getCompatibleCappingFragments ( APClass cmpReac )

Retrieve a list of compatible capping groups.

Parameters

cmpReac

Returns: a list of compatible capping groups

Definition at line 687 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.cappingLib, denoptim.graph.Vertex.getAllAPClasses(), and denoptim.fragspace.FragmentSpace.getCappingLibrary().

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

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◆ getForbiddenEndList()

Set< APClass > denoptim.fragspace.FragmentSpace.getForbiddenEndList ( )

Definition at line 892 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.forbiddenEndList.

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EAUtils.foundForbiddenEnd(), denoptim.fragspace.FragsCombinationIterator.FragsCombinationIterator(), and denoptim.graph.DGraph.hasForbiddenEnd().

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◆ getFragAPsCompatibleWithClass()

ArrayList< IdFragmentAndAP > denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithClass ( APClass aPC1 )

Returns the list of attachment points found in the fragment space and that are compatible with a given AP class.

Multiple APs can be found for each fragment.

Parameters

aPC1	the AP class for which we want compatible APs.

Definition at line 1291 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.getCompatibleAPClasses(), and denoptim.fragspace.FragmentSpace.getFragsWithAPClass().

Referenced by denoptim.fragspace.FragsCombinationIterator.FragsCombinationIterator(), denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithTheseAPs(), and denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithClass().

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◆ getFragAPsCompatibleWithTheseAPs()

ArrayList< IdFragmentAndAP > denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithTheseAPs ( ArrayList< IdFragmentAndAP > srcAPs )

Searches for all APs that are compatible with the given list of APs.

Parameters

srcAPs the identifiers of APs meant to hold any of the desired fragments.

Returns: a list of identifiers for APs on fragments in the library.

Definition at line 1191 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.getAPClassForFragment(), and denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithClass().

Referenced by denoptim.fragspace.FragmentSpace.getFragmentsCompatibleWithTheseAPs(), and denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithTheseAPs().

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◆ getFragmentLibrary()

ArrayList< Vertex > denoptim.fragspace.FragmentSpace.getFragmentLibrary ( )

Definition at line 733 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.fragmentLib.

Referenced by denoptim.gui.GUIGraphHandler.extendGraphFromFragSpace(), denoptim.fragspace.GraphLinkFinder.getCandidateBBs(), denoptim.fragspace.FragmentSpace.groupAndClassifyFragments(), denoptim.fragspace.GraphLinkFinderTest.prepare(), denoptim.ga.EAUtilsTest.prepare(), denoptim.graph.DGraphTest.prepare(), denoptim.gui.GUIGraphHandler.startGraphFromFragSpaceOrCreationOfEmptyVertex(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingOnlyAddedOnce(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ getFragmentsCompatibleWithTheseAPs()

ArrayList< Vertex > denoptim.fragspace.FragmentSpace.getFragmentsCompatibleWithTheseAPs ( ArrayList< IdFragmentAndAP > srcAPs )

Searches for all building blocks that are compatible with the given list of APs.

Parameters

srcAPs the identifiers of APs meant to hold any of the desired fragments.

Returns: a list of fragments.

Definition at line 1026 of file FragmentSpace.java.

References denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithTheseAPs(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.fragspace.FragmentSpace.getVertexFromLibrary(), and denoptim.fragspace.FragmentSpace.settings.

Referenced by denoptim.fragspace.FragmentSpaceTest.testGetFragmentsCompatibleWithTheseAPs().

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◆ getFragsWithAPClass()

ArrayList< IdFragmentAndAP > denoptim.fragspace.FragmentSpace.getFragsWithAPClass ( APClass apc )

Returns the list of attachment points with the given class.

The returned identifiers have vertex_id=-1 because these APs are only on the individual fragments held in the library and do not belong to any graph.

Parameters

apc

Returns: the list of AP identifiers.

Definition at line 968 of file FragmentSpace.java.

References denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.fragspace.FragmentSpace.fragsApsPerApClass, and denoptim.fragspace.FragmentSpace.LOCK.

Referenced by denoptim.fragspace.FragmentSpace.getFragAPsCompatibleWithClass(), and denoptim.fragspace.FragmentSpaceTest.testGetFragsWithAPClass().

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◆ getFragsWithNumAps()

ArrayList< Integer > denoptim.fragspace.FragmentSpace.getFragsWithNumAps ( int nAps )

Returns the list of fragments with given number of APs.

Parameters

nAps	the number of attachment points

Returns: the list of fragments as indexes in the library of fragments.

Definition at line 929 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.fragPoolPerNumAP.

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

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◆ getMapOfFragsPerNumAps()

HashMap< Integer, ArrayList< Integer > > denoptim.fragspace.FragmentSpace.getMapOfFragsPerNumAps ( )

Definition at line 915 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.fragPoolPerNumAP.

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

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◆ getPolarizedRCV()

Vertex denoptim.fragspace.FragmentSpace.getPolarizedRCV ( boolean polarity )

Returns a newly-built vertex that can play the role of a ring-closing vertex even when working with 3D building blocks.

Parameters

polarity use true to get an RCV with attachment point class APClass#ATPLUSS and false to get APClass#ATMINUS.

Returns: the ring-closing vertex.

Definition at line 1927 of file FragmentSpace.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.Fragment.addAtom(), denoptim.graph.APClass.RCACLASSMINUS, denoptim.graph.APClass.RCACLASSPLUS, denoptim.graph.rings.RingClosingAttractor.RCALABELPERAPCLASS, and denoptim.graph.Vertex.setAsRCV().

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◆ getRandomizer()

Randomizer denoptim.fragspace.FragmentSpace.getRandomizer ( )

Returns the program-specific randomizer that is associated with this program-specific fragment space.

Returns: the program-specific randomizer.

Definition at line 456 of file FragmentSpace.java.

References denoptim.programs.RunTimeParameters.getRandomizer(), and denoptim.fragspace.FragmentSpace.settings.

Referenced by denoptim.fragspace.APMapFinder.findAllMappings().

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◆ getRCCompatibilityMatrix()

HashMap< APClass, ArrayList< APClass > > denoptim.fragspace.FragmentSpace.getRCCompatibilityMatrix ( )

Returns the compatibility matrix for ring closing fragment-fragment connections or null if not provided in the parameters file.

Returns

Definition at line 865 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.rcCompatMap.

Referenced by denoptim.graph.rings.RingSizeManager.evaluateRCVPair().

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◆ getRCVs()

ArrayList< Vertex > denoptim.fragspace.FragmentSpace.getRCVs ( )

Returns the list of registered ring-closing vertexes (RCVs).

Returns: the list of registered ring-closing vertexes (RCVs).

Definition at line 1741 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.rcvs.

Referenced by denoptim.fragspace.FragmentSpace.getRCVsForAPClass(), and denoptim.fragspace.FragmentSpace.getRCVsWithAPClass().

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◆ getRCVsForAPClass()

List< Vertex > denoptim.fragspace.FragmentSpace.getRCVsForAPClass ( APClass apc )

Searches for all building blocks that are ring-closing vertexes and are compatible with the given AP.

Parameters

apc	the class of the attachment point meant to hold the RCV.

Returns: a list of vertexes ready to be used (i.e., clones of the vertexes stored in the library). The list can be empty.

Definition at line 1100 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.getCompatibilityMatrix(), denoptim.fragspace.FragmentSpace.getRCVs(), and denoptim.fragspace.FragmentSpace.getVertexFromLibrary().

Referenced by denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass().

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◆ getRCVsWithAPClass()

List< Vertex > denoptim.fragspace.FragmentSpace.getRCVsWithAPClass ( APClass apc )

Searches for all building blocks that are ring-closing vertexes and hold an AP with the given class.

Parameters

apc	the desired class of the attachment point.

Returns: a list of vertexes ready to be used (i.e., clones of the vertexes stored in the library). The list can be empty.

Definition at line 1065 of file FragmentSpace.java.

References denoptim.graph.APClass.equals(), denoptim.fragspace.FragmentSpace.getRCVs(), and denoptim.fragspace.FragmentSpace.getVertexFromLibrary().

Referenced by denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass().

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◆ getScaffoldLibrary()

ArrayList< Vertex > denoptim.fragspace.FragmentSpace.getScaffoldLibrary ( )

Definition at line 726 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.scaffoldLib.

Referenced by denoptim.fragspace.GraphLinkFinder.getCandidateBBs(), denoptim.fragspace.GraphLinkFinderTest.prepare(), denoptim.ga.EAUtilsTest.prepare(), denoptim.graph.DGraphTest.prepare(), denoptim.gui.GUIGraphHandler.startGraphFromFragSpaceOrCreationOfEmptyVertex(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ getSymmetryConstrain()

double denoptim.fragspace.FragmentSpace.getSymmetryConstrain ( APClass apClass )

Return the constitutional symmetry constrain for the given APclass, or null.

The constrain is a fixed probability that is not dependent on the distance from the root of the DENOPTIMGraph (i.e. the level).

Parameters

apClass the attachment point class

Returns: the constrained value of the symmetric substitution probability (0.0 - 1.0).

Definition at line 1374 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.symmConstraints.

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

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◆ getVertexFromLibrary()

Vertex denoptim.fragspace.FragmentSpace.getVertexFromLibrary	(	Vertex.BBType	bbType,
		int	bbIdx
	)		throws DENOPTIMException

Returns a clone of the requested building block.

The type of vertex returned depends on the type stored in the library.

Parameters

bbType the type of building block. This basically selects the sub library from which the building block is taken: 0 for scaffold (i.e., building blocks that can be used to start a new graph), 1 for standard building blocks (i.e., can be used freely to grow or modify an existing graph), or 2 for capping group (i.e., can be used only to saturate attachment points that cannot remain unused in a finished graph).

bbIdx the index (0-based) of the building block in the corresponding library defied by the type of building block 'bbType'

Returns: a clone of the chosen building block.

Exceptions

DENOPTIMException when the given indexes cannot be used, for example, any of the indexes is out of range.

Definition at line 532 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.cappingLib, denoptim.graph.Vertex.clone(), denoptim.fragspace.FragmentSpace.fragmentLib, denoptim.graph.Vertex.getBuildingBlockId(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.fragspace.FragmentSpace.scaffoldLib, denoptim.graph.Vertex.setBuildingBlockId(), denoptim.fragspace.FragmentSpace.settings, and denoptim.graph.Vertex.setVertexId().

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◆ getVerticesWithAPClass()

ArrayList< Vertex > denoptim.fragspace.FragmentSpace.getVerticesWithAPClass ( APClass apc )

Returns the list of attachment points with the given class.

Parameters

apc	the attachment point class to search.

Returns: the list of matching attachment points.

Definition at line 998 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.fragmentLib, denoptim.fragspace.FragmentSpace.fragsApsPerApClass, and denoptim.fragspace.FragmentSpace.LOCK.

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

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◆ groupAndClassifyFragments()

void denoptim.fragspace.FragmentSpace.groupAndClassifyFragments ( boolean apClassBasedApproch ) throws DENOPTIMException

Performs grouping and classification operations on the library of building blocks of BBType#FRAGMENT.

Parameters

apClassBasedApproch true if you are using class based approach

Definition at line 1894 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassBasedApproch, denoptim.fragspace.FragmentSpace.apClassesPerFrag, denoptim.fragspace.FragmentSpace.classifyFragment(), denoptim.fragspace.FragmentSpace.fragsApsPerApClass, denoptim.fragspace.FragmentSpace.getFragmentLibrary(), denoptim.fragspace.FragmentSpace.LOCK, and denoptim.fragspace.FragmentSpace.setFragPoolPerNumAP().

Referenced by denoptim.fragspace.FragmentSpace.define(), and denoptim.fragspace.GraphLinkFinderTest.prepare().

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◆ hasIsomorph()

boolean denoptim.fragspace.FragmentSpace.hasIsomorph	(	DGraph	graph,
		BBType	type
	)

Checks if a graph is isomorphic to another template's inner graph in its appropriate fragment space library (inferred from BBType).

Parameters

graph	to check if has an isomorph in the fragment space.
type	specifying which fragment library to check for isomorphs in.

Returns: true if there is an isomorph template in the library of the specified type.

Definition at line 1714 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.fragmentLib, denoptim.graph.Template.getInnerGraph(), denoptim.graph.Vertex.BBType.SCAFFOLD, and denoptim.fragspace.FragmentSpace.scaffoldLib.

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

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◆ hasSymmetryConstrain()

boolean denoptim.fragspace.FragmentSpace.hasSymmetryConstrain ( APClass apClass )

Checks if there is a constraint on the constitutional symmetry probability for the given AP class.

Parameters

apClass the attachment point class

Returns: true if there is a constraint on the constitutional symmetry probability for the given AP class.

Definition at line 1355 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.symmConstraints.

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

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◆ importCompatibilityMatrixFromFile()

void denoptim.fragspace.FragmentSpace.importCompatibilityMatrixFromFile ( String inFile ) throws DENOPTIMException

Load info from a compatibility matrix file.

This method imports information such as the compatibility matrix, bond order map, and forbidden ends from a compatibility matrix file (i.e., a formatted text file using DENOPTIM keyword. This overrides any previous setting of such information in this FragmentSpace.

Parameters

inFile the pathname of the compatibility matrix file

Definition at line 806 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassCompatibilityMatrix, denoptim.fragspace.FragmentSpace.cappingMap, denoptim.fragspace.FragmentSpace.forbiddenEndList, denoptim.io.DenoptimIO.readCompatibilityMatrix(), denoptim.fragspace.FragmentSpace.setCappingMap(), denoptim.fragspace.FragmentSpace.setCompatibilityMatrix(), and denoptim.fragspace.FragmentSpace.setForbiddenEndList().

Referenced by denoptim.gui.FSParametersForm.FSParametersForm().

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◆ importRCCompatibilityMatrixFromFile()

void denoptim.fragspace.FragmentSpace.importRCCompatibilityMatrixFromFile ( String inFile ) throws DENOPTIMException

Load info for ring closures compatibilities from a compatibility matrix file.

Parameters

inFile the pathname of the RC-compatibility matrix file

Definition at line 825 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.rcCompatMap, denoptim.io.DenoptimIO.readRCCompatibilityMatrix(), and denoptim.fragspace.FragmentSpace.setRCCompatibilityMatrix().

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◆ imposeSymmetryOnAPsOfClass()

boolean denoptim.fragspace.FragmentSpace.imposeSymmetryOnAPsOfClass ( APClass apClass )

Checks if the symmetry settings impose use of symmetry on attachment points of the given AP class.

The value returned is the result of the action of symmetry-related keyword affecting the definition of this FragmentSpace.

Parameters

apClass the attachment point class

Returns: true if symmetry has the applied on APs of the given class

Definition at line 1324 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpaceParameters.enforceSymmetry, denoptim.constants.DENOPTIMConstants.FLOATCOMPARISONTOLERANCE, denoptim.fragspace.FragmentSpace.getSymmetryConstrain(), denoptim.fragspace.FragmentSpace.hasSymmetryConstrain(), and denoptim.fragspace.FragmentSpace.settings.

Referenced by denoptim.ga.GraphOperations.attachFragmentInClosableChain(), denoptim.ga.GraphOperations.extendGraph(), denoptim.fragspace.FragsCombinationIterator.FragsCombinationIterator(), and denoptim.fragspace.FragsCombinationIterator.next().

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◆ isDefined()

boolean denoptim.fragspace.FragmentSpace.isDefined ( )

Checks for valid definition of this fragment space.

Returns: true if this fragment space has been defined

Definition at line 444 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.isValid.

Referenced by denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithClass(), denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithTheseAPs(), denoptim.fragspace.FragmentSpaceTest.testGetFragmentsCompatibleWithTheseAPs(), denoptim.fragspace.FragmentSpaceTest.testGetFragsWithAPClass(), and denoptim.fragspace.FragmentSpaceTest.testSymmetry().

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◆ makeRandomScaffold()

Vertex denoptim.fragspace.FragmentSpace.makeRandomScaffold ( )

Randomly select a scaffold and return a fully configured clone of it.

Returns: a scaffold-type building block ready to be used in a new graph.

Exceptions

DENOPTIMException

Definition at line 708 of file FragmentSpace.java.

References denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.graph.Vertex.newVertexFromLibrary(), denoptim.utils.Randomizer.nextInt(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.fragspace.FragmentSpace.scaffoldLib, and denoptim.fragspace.FragmentSpace.settings.

Referenced by denoptim.ga.EAUtils.buildGraph().

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◆ mapAPClassCompatibilities()

List< APMapping > denoptim.fragspace.FragmentSpace.mapAPClassCompatibilities	(	List< AttachmentPoint >	listA,
		List< AttachmentPoint >	listB,
		int	maxCombinations
	)

Given two lists of APs this method maps the APClass-compatibilities from between the two lists considering the APs in the first list the for the role of source AP in the hypothetical edge.

Parameters

listA	list of candidate source APs
listB	list of candidate target APs
maxCombinations	a maximum limit; if reached we are happy we give up finding more combination.

Returns

Definition at line 1758 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpaceUtils.recursiveCombiner(), and denoptim.fragspace.FragmentSpace.useAPclassBasedApproach().

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◆ registerRCV()

void denoptim.fragspace.FragmentSpace.registerRCV ( Vertex v )

Adds the reference to a ring-closing vertex (RCV) to the quick-access list of RCVs known in this building block space.

Parameters

v	the RCV to add to the list.

Definition at line 1730 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.rcvs.

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

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◆ setAPclassBasedApproach()

void denoptim.fragspace.FragmentSpace.setAPclassBasedApproach ( boolean useAPC )

Set the fragment space to behave according to APClass-based approach.

Definition at line 466 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassBasedApproch.

Referenced by denoptim.fragspace.APMapFinderTest.prepare(), denoptim.fragspace.GraphLinkFinderTest.prepare(), denoptim.ga.EAUtilsTest.prepare(), denoptim.ga.GraphOperationsTest.prepare(), denoptim.ga.PopulationTest.prepare(), denoptim.graph.DGraphTest.prepare(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.molecularmodeling.ThreeDimTreeBuilderTest.testConversionTo3dTree(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), denoptim.ga.GraphOperationsTest.testExtendGraph(), denoptim.fragspace.APMapFinderTest.testFindMappingCompatibileAPs(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass(), and denoptim.graph.DGraphTest.testRemoveUnusedRCVs().

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◆ setCappingLibrary()

void denoptim.fragspace.FragmentSpace.setCappingLibrary ( ArrayList< Vertex > lib )

Definition at line 1395 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.appendVerticesToLibrary(), denoptim.graph.Vertex.BBType.CAP, and denoptim.fragspace.FragmentSpace.cappingLib.

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

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◆ setCappingMap()

void denoptim.fragspace.FragmentSpace.setCappingMap ( HashMap< APClass, APClass > map )

Definition at line 1418 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.cappingMap.

Referenced by denoptim.fragspace.FragmentSpace.define(), and denoptim.fragspace.FragmentSpace.importCompatibilityMatrixFromFile().

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◆ setCompatibilityMatrix()

void denoptim.fragspace.FragmentSpace.setCompatibilityMatrix ( HashMap< APClass, ArrayList< APClass > > map )

Definition at line 1403 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassCompatibilityMatrix.

Referenced by denoptim.fragspace.FragmentSpace.define(), and denoptim.fragspace.FragmentSpace.importCompatibilityMatrixFromFile().

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◆ setForbiddenEndList()

void denoptim.fragspace.FragmentSpace.setForbiddenEndList ( Set< APClass > lst )

Definition at line 1425 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.forbiddenEndList.

Referenced by denoptim.fragspace.FragmentSpace.define(), and denoptim.fragspace.FragmentSpace.importCompatibilityMatrixFromFile().

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◆ setFragmentLibrary()

void denoptim.fragspace.FragmentSpace.setFragmentLibrary ( ArrayList< Vertex > lib )

Definition at line 1387 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.appendVerticesToLibrary(), denoptim.graph.Vertex.BBType.FRAGMENT, and denoptim.fragspace.FragmentSpace.fragmentLib.

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

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◆ setFragPoolPerNumAP()

void denoptim.fragspace.FragmentSpace.setFragPoolPerNumAP ( HashMap< Integer, ArrayList< Integer > > map )

Definition at line 1432 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.fragPoolPerNumAP.

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

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◆ setRCCompatibilityMatrix()

void denoptim.fragspace.FragmentSpace.setRCCompatibilityMatrix ( HashMap< APClass, ArrayList< APClass > > map )

Definition at line 1410 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.rcCompatMap.

Referenced by denoptim.fragspace.FragmentSpace.define(), and denoptim.fragspace.FragmentSpace.importRCCompatibilityMatrixFromFile().

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◆ setScaffoldLibrary()

void denoptim.fragspace.FragmentSpace.setScaffoldLibrary ( ArrayList< Vertex > lib )

Definition at line 1381 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.appendVerticesToLibrary(), denoptim.graph.Vertex.BBType.SCAFFOLD, and denoptim.fragspace.FragmentSpace.scaffoldLib.

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

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◆ setSymmConstraints()

void denoptim.fragspace.FragmentSpace.setSymmConstraints ( HashMap< APClass, Double > map )

Definition at line 1440 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.symmConstraints.

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

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◆ useAPclassBasedApproach()

boolean denoptim.fragspace.FragmentSpace.useAPclassBasedApproach ( )

Check usage of APClass-based approach, i.e., uses attachment points with annotated data (i.e., the APClass) to evaluate compatibilities between attachment points.

Returns: true if this fragment space makes use of APClass-based approach

Definition at line 481 of file FragmentSpace.java.

References denoptim.fragspace.FragmentSpace.apClassBasedApproch.

Referenced by denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.combinatorial.GraphBuildingTask.call(), denoptim.graph.DGraph.checkConsistency(), denoptim.fragspace.FragmentSpace.classifyFragment(), denoptim.fragspace.APMapFinder.findMappingCompatibileAPs(), denoptim.fragspace.GraphLinkFinder.GraphLinkFinder(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), denoptim.fragspace.FragmentSpace.mapAPClassCompatibilities(), denoptim.ga.Population.Population(), and denoptim.ga.EAUtils.setupRings().

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Member Data Documentation

◆ apClassBasedApproch

boolean denoptim.fragspace.FragmentSpace.apClassBasedApproch = false

private

Flag defining use of AP class-based approach.

Definition at line 153 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.define(), denoptim.fragspace.FragmentSpace.groupAndClassifyFragments(), denoptim.fragspace.FragmentSpace.setAPclassBasedApproach(), and denoptim.fragspace.FragmentSpace.useAPclassBasedApproach().

◆ apClassCompatibilityMatrix

HashMap<APClass, ArrayList<APClass> > denoptim.fragspace.FragmentSpace.apClassCompatibilityMatrix

private

Data structure that stored the true entries of the attachment point classes compatibility matrix.

Definition at line 100 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.getAllAPClassesFromCPMap(), denoptim.fragspace.FragmentSpace.getCompatibilityMatrix(), denoptim.fragspace.FragmentSpace.getCompatibleAPClasses(), denoptim.fragspace.FragmentSpace.importCompatibilityMatrixFromFile(), and denoptim.fragspace.FragmentSpace.setCompatibilityMatrix().

◆ apClassesPerFrag

HashMap<Integer, ArrayList<APClass> > denoptim.fragspace.FragmentSpace.apClassesPerFrag

private

List of APClasses per each fragment.

Definition at line 133 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.classifyFragment(), denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.getAPClassesPerFragment(), and denoptim.fragspace.FragmentSpace.groupAndClassifyFragments().

◆ cappingLib

ArrayList<Vertex> denoptim.fragspace.FragmentSpace.cappingLib = null

private

Data structure containing the molecular representation of building blocks: capping group section - fragments with only one attachment point used to saturate unused attachment points on a graph.

WARNING! The objects stores in the library do not have a meaningful value for the two indexes representing the type of building block and the position of the list of all building blocks of that type.

Definition at line 94 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.FragmentSpace(), denoptim.fragspace.FragmentSpace.getCappingGroupsWithAPClass(), denoptim.fragspace.FragmentSpace.getCappingLibrary(), denoptim.fragspace.FragmentSpace.getCappingVertexWithAPClass(), denoptim.fragspace.FragmentSpace.getCompatibleCappingFragments(), denoptim.fragspace.FragmentSpace.getVertexFromLibrary(), and denoptim.fragspace.FragmentSpace.setCappingLibrary().

◆ cappingMap

HashMap<APClass, APClass> denoptim.fragspace.FragmentSpace.cappingMap

private

Data structure that stores the AP-classes to be used to cap unused APS on the growing molecule.

Definition at line 118 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.getAPClassOfCappingVertex(), denoptim.fragspace.FragmentSpace.getCappingMap(), denoptim.fragspace.FragmentSpace.importCompatibilityMatrixFromFile(), and denoptim.fragspace.FragmentSpace.setCappingMap().

◆ forbiddenEndList

Set<APClass> denoptim.fragspace.FragmentSpace.forbiddenEndList

private

Data structure that stores AP classes that cannot be held unused.

Definition at line 123 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.getForbiddenEndList(), denoptim.fragspace.FragmentSpace.importCompatibilityMatrixFromFile(), and denoptim.fragspace.FragmentSpace.setForbiddenEndList().

◆ fragmentLib

ArrayList<Vertex> denoptim.fragspace.FragmentSpace.fragmentLib = null

private

Data structure containing the molecular representation of building blocks: fragment section - fragments for general use.

WARNING! The objects stores in the library do not have a meaningful value for the two indexes representing the type of building block and the position of the list of all building blocks of that type.

Definition at line 84 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.FragmentSpace(), denoptim.fragspace.FragmentSpace.getFragmentLibrary(), denoptim.fragspace.FragmentSpace.getVertexFromLibrary(), denoptim.fragspace.FragmentSpace.getVerticesWithAPClass(), denoptim.fragspace.FragmentSpace.hasIsomorph(), and denoptim.fragspace.FragmentSpace.setFragmentLibrary().

◆ fragPoolPerNumAP

HashMap<Integer, ArrayList<Integer> > denoptim.fragspace.FragmentSpace.fragPoolPerNumAP

private

Clusters of fragments based on the number of APs.

Definition at line 128 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.getFragsWithNumAps(), denoptim.fragspace.FragmentSpace.getMapOfFragsPerNumAps(), and denoptim.fragspace.FragmentSpace.setFragPoolPerNumAP().

◆ fragsApsPerApClass

HashMap<APClass, ArrayList<ArrayList<Integer> > > denoptim.fragspace.FragmentSpace.fragsApsPerApClass

private

Clusters of fragments'AP based on AP classes.

Definition at line 138 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.classifyFragment(), denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.getFragsWithAPClass(), denoptim.fragspace.FragmentSpace.getVerticesWithAPClass(), and denoptim.fragspace.FragmentSpace.groupAndClassifyFragments().

◆ isValid

boolean denoptim.fragspace.FragmentSpace.isValid = false

private

Flag signaling that this fragment space was built and validated.

Definition at line 158 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.define(), and denoptim.fragspace.FragmentSpace.isDefined().

◆ LOCK

final Object denoptim.fragspace.FragmentSpace.LOCK = new Object()

private

Lock for synchronizing tasks.

Definition at line 143 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpace.classifyFragment(), denoptim.fragspace.FragmentSpace.getAPClassesPerFragment(), denoptim.fragspace.FragmentSpace.getFragsWithAPClass(), denoptim.fragspace.FragmentSpace.getVerticesWithAPClass(), and denoptim.fragspace.FragmentSpace.groupAndClassifyFragments().

◆ rcCompatMap

HashMap<APClass, ArrayList<APClass> > denoptim.fragspace.FragmentSpace.rcCompatMap

private

Data structure that stores compatible APclasses for joining APs in ring-closing bonds.

Symmetric, purpose specific compatibility matrix.

Definition at line 112 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.getRCCompatibilityMatrix(), denoptim.fragspace.FragmentSpace.importRCCompatibilityMatrixFromFile(), and denoptim.fragspace.FragmentSpace.setRCCompatibilityMatrix().

◆ rcvs

ArrayList<Vertex> denoptim.fragspace.FragmentSpace.rcvs = new ArrayList<Vertex>()

private

Store references to the Ring-Closing Vertexes found in the library of fragments.

Definition at line 106 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.getRCVs(), and denoptim.fragspace.FragmentSpace.registerRCV().

◆ scaffoldLib

ArrayList<Vertex> denoptim.fragspace.FragmentSpace.scaffoldLib = null

private

Data structure containing the molecular representation of building blocks: scaffolds section - fragments that can be used as seeds to grow a new molecule.

WARNING! The objects stores in the library do not have a meaningful value for the two indexes representing the type of building block and the position of the list of all building blocks of that type.

Definition at line 75 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.FragmentSpace(), denoptim.fragspace.FragmentSpace.getScaffoldLibrary(), denoptim.fragspace.FragmentSpace.getVertexFromLibrary(), denoptim.fragspace.FragmentSpace.hasIsomorph(), denoptim.fragspace.FragmentSpace.makeRandomScaffold(), and denoptim.fragspace.FragmentSpace.setScaffoldLibrary().

◆ settings

FragmentSpaceParameters denoptim.fragspace.FragmentSpace.settings = null

private

Settings used to configure this fragment space.

Contains the default values unless its value is reassigned.

Definition at line 164 of file FragmentSpace.java.

◆ symmConstraints

HashMap<APClass, Double> denoptim.fragspace.FragmentSpace.symmConstraints

private

APclass-specific constraints to constitutional symmetry.

Definition at line 148 of file FragmentSpace.java.

Referenced by denoptim.fragspace.FragmentSpace.clearAll(), denoptim.fragspace.FragmentSpace.getSymmetryConstrain(), denoptim.fragspace.FragmentSpace.hasSymmetryConstrain(), and denoptim.fragspace.FragmentSpace.setSymmConstraints().

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

/github/workspace/src/main/java/denoptim/fragspace/FragmentSpace.java

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FragmentSpace() [1/5]

◆ FragmentSpace() [2/5]

◆ FragmentSpace() [3/5]

◆ FragmentSpace() [4/5]

◆ FragmentSpace() [5/5]

Member Function Documentation

◆ addFusedRingsToFragmentLibrary() [1/3]

◆ addFusedRingsToFragmentLibrary() [2/3]

◆ addFusedRingsToFragmentLibrary() [3/3]

◆ appendVertexToLibrary()

◆ appendVerticesToLibrary()

◆ classifyFragment()

◆ clearAll()

◆ define()

◆ getAllAPClassesFromCPMap()

◆ getAPClassesPerFragment()

◆ getAPClassForFragment()

◆ getAPClassOfCappingVertex()

◆ getAPsCompatibleWithClass()

◆ getAPsCompatibleWithThese()

◆ getCappingFragment()

◆ getCappingGroupsWithAPClass()

◆ getCappingLibrary()

◆ getCappingMap()

◆ getCappingVertexWithAPClass()

◆ getCompatibilityMatrix()

◆ getCompatibleAPClasses()

◆ getCompatibleCappingFragments()

◆ getForbiddenEndList()

◆ getFragAPsCompatibleWithClass()

◆ getFragAPsCompatibleWithTheseAPs()

◆ getFragmentLibrary()

◆ getFragmentsCompatibleWithTheseAPs()

◆ getFragsWithAPClass()

◆ getFragsWithNumAps()

◆ getMapOfFragsPerNumAps()

◆ getPolarizedRCV()

◆ getRandomizer()

◆ getRCCompatibilityMatrix()

◆ getRCVs()

◆ getRCVsForAPClass()

◆ getRCVsWithAPClass()

◆ getScaffoldLibrary()

◆ getSymmetryConstrain()

◆ getVertexFromLibrary()

◆ getVerticesWithAPClass()

◆ groupAndClassifyFragments()

◆ hasIsomorph()

◆ hasSymmetryConstrain()

◆ importCompatibilityMatrixFromFile()

◆ importRCCompatibilityMatrixFromFile()

◆ imposeSymmetryOnAPsOfClass()

◆ isDefined()

◆ makeRandomScaffold()

◆ mapAPClassCompatibilities()

◆ registerRCV()

◆ setAPclassBasedApproach()

◆ setCappingLibrary()

◆ setCappingMap()

◆ setCompatibilityMatrix()

◆ setForbiddenEndList()

◆ setFragmentLibrary()

◆ setFragPoolPerNumAP()

◆ setRCCompatibilityMatrix()

◆ setScaffoldLibrary()

◆ setSymmConstraints()

◆ useAPclassBasedApproach()

Member Data Documentation

◆ apClassBasedApproch

◆ apClassCompatibilityMatrix

◆ apClassesPerFrag

◆ cappingLib

◆ cappingMap

◆ forbiddenEndList

◆ fragmentLib