Data structure to store and handle information about sub-structures (i.e., chains of fragments) and ring closure capability. More...

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Public Member Functions
	RingClosuresArchive ()
	Construct an empty archive. More...

	RingClosuresArchive (RingClosureParameters settings) throws DENOPTIMException
	Construct the library of ring closing substructures from an existing index file. More...

void	storeEntry (String chainId, boolean closable, RingClosingConformations rcc)
	Append a new closable chain entry to the archive. More...

ArrayList< ClosableChain >	getCCFromTurningPointId (int tpId)
	Returns the library of closable chains having the given turning point (i.e., the fragments involved in the ring that has lower level). More...

String	containsChain (PathSubGraph chain)

boolean	getClosabilityOfChain (String chainId)

RingClosingConformations	getRCCsOfChain (String chainId)

RingClosingConformations	getRCCsFromArchive (int rccId)
	Get serialized `RingClosingConformations` from archive. More...

Private Member Functions
void	readLibraryOfRCCs (String filename) throws DENOPTIMException

void	addRecord (String chainId, String rccIdNum, String closability) throws DENOPTIMException

Private Attributes
int	nextRccId = 0
	Index of the next entry to be added to the archive. More...

HashMap< String, ArrayList< String > >	rccsPerChainId
	Data structure containing the main information about the `RingClosingConformation`s (values) per each `ClosableChain` (keys). More...

HashMap< Integer, ArrayList< ClosableChain > >	libCCxTPIdx
	Data structure containing the library of `ClosableChain`s per each fragment that can act as a turning point fragment (TP; i.e., the fragments involved in the ring that has lower level in the `DENOPTIMGraph`). More...

RingClosureParameters	settings
	Parameters. More...

Detailed Description

Data structure to store and handle information about sub-structures (i.e., chains of fragments) and ring closure capability.

Author: Marco Foscato

Definition at line 48 of file RingClosuresArchive.java.

Constructor & Destructor Documentation

◆ RingClosuresArchive() [1/2]

denoptim.graph.rings.RingClosuresArchive.RingClosuresArchive ( )

Construct an empty archive.

Definition at line 88 of file RingClosuresArchive.java.

◆ RingClosuresArchive() [2/2]

denoptim.graph.rings.RingClosuresArchive.RingClosuresArchive ( RingClosureParameters settings ) throws DENOPTIMException

Construct the library of ring closing substructures from an existing index file.

Parameters

rccIndex the index file.

Definition at line 98 of file RingClosuresArchive.java.

References denoptim.files.FileUtils.checkExists(), denoptim.graph.rings.RingClosureParameters.getRCCLibraryIndexFile(), denoptim.graph.rings.RingClosuresArchive.readLibraryOfRCCs(), and denoptim.graph.rings.RingClosuresArchive.settings.

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Member Function Documentation

◆ addRecord()

void denoptim.graph.rings.RingClosuresArchive.addRecord	(	String	chainId,
		String	rccIdNum,
		String	closability
	)		throws DENOPTIMException

private

Definition at line 173 of file RingClosuresArchive.java.

References denoptim.graph.rings.ClosableChain.getTurningPointIdx(), denoptim.graph.rings.RingClosuresArchive.libCCxTPIdx, denoptim.graph.rings.RingClosuresArchive.nextRccId, and denoptim.graph.rings.RingClosuresArchive.rccsPerChainId.

Referenced by denoptim.graph.rings.RingClosuresArchive.readLibraryOfRCCs(), and denoptim.graph.rings.RingClosuresArchive.storeEntry().

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◆ containsChain()

String denoptim.graph.rings.RingClosuresArchive.containsChain ( PathSubGraph chain )

Parameters

chain the candidate chain

Returns: the already visited chainId that correspond to the same chain of fragments of chain, otherwise an empty string is returned.

Definition at line 360 of file RingClosuresArchive.java.

References denoptim.graph.rings.PathSubGraph.getAllAlternativeChainIDs(), and denoptim.graph.rings.RingClosuresArchive.rccsPerChainId.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ getCCFromTurningPointId()

ArrayList< ClosableChain > denoptim.graph.rings.RingClosuresArchive.getCCFromTurningPointId ( int tpId )

Returns the library of closable chains having the given turning point (i.e., the fragments involved in the ring that has lower level).

Parameters

tpId	the turning point molecule Id in the libraries.

Definition at line 342 of file RingClosuresArchive.java.

References denoptim.graph.rings.RingClosuresArchive.libCCxTPIdx.

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

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◆ getClosabilityOfChain()

boolean denoptim.graph.rings.RingClosuresArchive.getClosabilityOfChain ( String chainId )

Returns: the closability of a chain

Definition at line 380 of file RingClosuresArchive.java.

References denoptim.graph.rings.RingClosuresArchive.rccsPerChainId.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ getRCCsFromArchive()

RingClosingConformations denoptim.graph.rings.RingClosuresArchive.getRCCsFromArchive ( int rccId )

Get serialized RingClosingConformations from archive.

Parameters

rccId the index identifying the RingClosingConformations in the archive

Definition at line 429 of file RingClosuresArchive.java.

References denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.rings.RingClosureParameters.getRCCLibraryFolder(), and denoptim.graph.rings.RingClosuresArchive.settings.

Referenced by denoptim.graph.rings.RingClosuresArchive.getRCCsOfChain().

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◆ getRCCsOfChain()

RingClosingConformations denoptim.graph.rings.RingClosuresArchive.getRCCsOfChain ( String chainId )

Returns: the RingClosingConformations of a chain as stored in the archive

Definition at line 394 of file RingClosuresArchive.java.

References denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.rings.RingClosuresArchive.getRCCsFromArchive(), denoptim.graph.rings.RingClosureParameters.getVerbosity(), denoptim.graph.rings.RingClosuresArchive.rccsPerChainId, and denoptim.graph.rings.RingClosuresArchive.settings.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ readLibraryOfRCCs()

void denoptim.graph.rings.RingClosuresArchive.readLibraryOfRCCs ( String filename ) throws DENOPTIMException

private

Definition at line 108 of file RingClosuresArchive.java.

References denoptim.graph.rings.RingClosuresArchive.addRecord(), denoptim.graph.rings.RingClosuresArchive.nextRccId, and denoptim.graph.rings.RingClosuresArchive.rccsPerChainId.

Referenced by denoptim.graph.rings.RingClosuresArchive.RingClosuresArchive().

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◆ storeEntry()

void denoptim.graph.rings.RingClosuresArchive.storeEntry	(	String	chainId,
		boolean	closable,
		RingClosingConformations	rcc
	)

Append a new closable chain entry to the archive.

Parameters

chainId	the string representing the chain of fragments
closable	`true` for verified closable chains
rcc	the ensemble of `RingClosingConformations` of the chain

Definition at line 218 of file RingClosuresArchive.java.

References denoptim.graph.rings.RingClosuresArchive.addRecord(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.rings.RingClosureParameters.getRCCLibraryFolder(), denoptim.graph.rings.RingClosureParameters.getRCCLibraryIndexFile(), denoptim.graph.rings.RingClosuresArchive.nextRccId, denoptim.graph.rings.RingClosuresArchive.rccsPerChainId, denoptim.graph.rings.RingClosureParameters.serializeRCCs, and denoptim.graph.rings.RingClosuresArchive.settings.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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Member Data Documentation

◆ libCCxTPIdx

HashMap<Integer,ArrayList<ClosableChain> > denoptim.graph.rings.RingClosuresArchive.libCCxTPIdx

private

Initial value:

=

new HashMap<>()

Data structure containing the library of ClosableChains per each fragment that can act as a turning point fragment (TP; i.e., the fragments involved in the ring that has lower level in the DENOPTIMGraph).

The possible TPs are
identified by the molecular fragment Id in the proper library of fragments.

Definition at line 75 of file RingClosuresArchive.java.

Referenced by denoptim.graph.rings.RingClosuresArchive.addRecord(), and denoptim.graph.rings.RingClosuresArchive.getCCFromTurningPointId().

◆ nextRccId

int denoptim.graph.rings.RingClosuresArchive.nextRccId = 0

private

Index of the next entry to be added to the archive.

Definition at line 53 of file RingClosuresArchive.java.

Referenced by denoptim.graph.rings.RingClosuresArchive.addRecord(), denoptim.graph.rings.RingClosuresArchive.readLibraryOfRCCs(), and denoptim.graph.rings.RingClosuresArchive.storeEntry().

◆ rccsPerChainId

HashMap<String,ArrayList<String> > denoptim.graph.rings.RingClosuresArchive.rccsPerChainId

private

Initial value:

=

new HashMap<>()

Data structure containing the main information about the RingClosingConformations (values) per each ClosableChain (keys).

Each value identifies (i) a unique Id that permits to retrieve the list ring-closing conformations from the archive of serialized objects, and (ii) the closability of the chain.

Definition at line 63 of file RingClosuresArchive.java.

Referenced by denoptim.graph.rings.RingClosuresArchive.addRecord(), denoptim.graph.rings.RingClosuresArchive.containsChain(), denoptim.graph.rings.RingClosuresArchive.getClosabilityOfChain(), denoptim.graph.rings.RingClosuresArchive.getRCCsOfChain(), denoptim.graph.rings.RingClosuresArchive.readLibraryOfRCCs(), and denoptim.graph.rings.RingClosuresArchive.storeEntry().

◆ settings

RingClosureParameters denoptim.graph.rings.RingClosuresArchive.settings

private

Parameters.

Definition at line 81 of file RingClosuresArchive.java.

Referenced by denoptim.graph.rings.RingClosuresArchive.getRCCsFromArchive(), denoptim.graph.rings.RingClosuresArchive.getRCCsOfChain(), denoptim.graph.rings.RingClosuresArchive.RingClosuresArchive(), and denoptim.graph.rings.RingClosuresArchive.storeEntry().

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

/github/workspace/src/main/java/denoptim/graph/rings/RingClosuresArchive.java

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RingClosuresArchive() [1/2]

◆ RingClosuresArchive() [2/2]

Member Function Documentation

◆ addRecord()

◆ containsChain()

◆ getCCFromTurningPointId()

◆ getClosabilityOfChain()

◆ getRCCsFromArchive()

◆ getRCCsOfChain()

◆ readLibraryOfRCCs()

◆ storeEntry()

Member Data Documentation

◆ libCCxTPIdx

◆ nextRccId

◆ rccsPerChainId

◆ settings