Static Public Member Functions
static void	checkElementalAnalysisAgainstFormula (File input, File output, Logger logger) throws DENOPTIMException, IOException
	Processes all molecules analyzing the composition of the structure in the chemical representation as compared to the molecular formula declared in the `DENOPTIMConstants#FORMULASTR` property, and extracts those molecules where the declared formula matches the composition of the chemical representation. More...

static boolean	prepareMolToFragmentation (IAtomContainer mol, FragmenterParameters settings, int index)
	Do any pre-processing on a `IAtomContainer` meant to be fragmented. More...

static void	filterStrucutresBySMARTS (File input, Set< String > smarts, File output, Logger logger) throws DENOPTIMException, IOException
	Removes from the structures anyone that matches any of the given SMARTS queries. More...

static boolean	fragmentationFromGraphs (File input, FragmenterParameters settings, File output, Logger logger) throws DENOPTIMException, Exception
	Performs fragmentation from graphs, i.e., extracts existing fragments from graphs (stored in a file). More...

static List< Vertex >	fragmentation (IAtomContainer mol, FragmenterParameters settings) throws DENOPTIMException
	Performs fragmentation according to the given settings. More...

static boolean	fragmentation (File input, FragmenterParameters settings, File output, Logger logger) throws CDKException, IOException, DENOPTIMException, IllegalArgumentException, UndetectedFileFormatException
	Performs fragmentation according to the given cutting rules. More...

static List< Vertex >	fragmentation (IAtomContainer mol, List< DGraph > templates, int maxBufferShellSize, Randomizer randomizer, Logger logger) throws DENOPTIMException
	Chops one chemical structure by applying the given fragmentation templates. More...

static List< Vertex >	fragmentation (IAtomContainer mol, List< CuttingRule > rules, Logger logger) throws DENOPTIMException
	Chops one chemical structure by applying the given cutting rules. More...

static void	manageFragmentCollection (File input, FragmenterParameters settings, File output, Logger logger) throws DENOPTIMException, IOException, IllegalArgumentException, UndetectedFileFormatException
	Management of fragments: includes application of fragment filters, rejection rules, and collection rules (also of isomorphic fragments, thus management of duplicates) to manipulate collection of fragments. More...

static void	manageFragmentCollection (Vertex frag, int fragCounter, FragmenterParameters settings, List< Vertex > collector, Logger logger) throws DENOPTIMException, IllegalArgumentException, UndetectedFileFormatException, IOException
	Management of fragments: includes application of fragment filters, rejection rules, and collection rules (also of isomorphic fragments, thus management of duplicates) to manipulate collection of fragments. More...

static boolean	filterFragment (Fragment frag, FragmenterParameters settings)
	Filter fragments according to the criteria defined in the settings. More...

static boolean	filterFragment (Fragment frag, FragmenterParameters settings, Logger logger)
	Filter fragments according to the criteria defined in the settings. More...

static String	getMWSlotIdentifier (Vertex frag, int slotSize)
	Determines the name of the MW slot to use when comparing the given fragment with previously stored fragments. More...

static Vertex	getRCVForAP (AttachmentPoint ap, APClass rcvApClass) throws DENOPTIMException

Static Package Functions
static Set< IAtom >	exploreHapticity (IAtom seed, IAtom centralAtom, ArrayList< IAtom > candidates, IAtomContainer mol)
	Identifies non-central atoms involved in the same n-hapto ligand as the seed atom. More...

static Set< IAtom >	exploreConnectivity (IAtom seed, IAtomContainer mol)
	Explores the connectivity annotating which atoms have been visited. More...

static Map< String, List< MatchedBond > >	getMatchingBondsAllInOne (IAtomContainer mol, List< CuttingRule > rules, Logger logger)
	Identification of the bonds matching a list of SMARTS queries. More...

Static Private Member Functions
static void	exploreDGraphForMappings (DGraph graph, IAtomContainer graphIAC, Fragment masterFrag, IAtomContainer masterFragIAC, IAtomContainer mol, Map< IAtom, IAtom > graphToMolMapping) throws DENOPTIMException
	Recursive function to process edges at any level of embedding to remove the corresponding bonds and create the corresponding attachment points. More...

static Point3d	findPointAlignedWithTmpl (AttachmentPoint ap, IAtom graphAtmSrc, IAtomContainer graphIAC, IAtomContainer masterFragIAC, IAtomContainer mol, Map< IAtom, IAtom > graphToMolMapping) throws DENOPTIMException
	Finds the point on the master fragment that is aligned with the template geometry. More...

Detailed Description

Definition at line 63 of file FragmenterTools.java.

Member Function Documentation

◆ checkElementalAnalysisAgainstFormula()

static void denoptim.fragmenter.FragmenterTools.checkElementalAnalysisAgainstFormula	(	File	input,
		File	output,
		Logger	logger
	)		throws DENOPTIMException, IOException

static

Processes all molecules analyzing the composition of the structure in the chemical representation as compared to the molecular formula declared in the DENOPTIMConstants#FORMULASTR property, and extracts those molecules where the declared formula matches the composition of the chemical representation.

Parameters

input	the source of chemical structures.
output	the file where to write extracted structures.
logger	a task-dedicated logger where we print messages for the user.

Exceptions

DENOPTIMException
IOException

Definition at line 82 of file FragmenterTools.java.

References denoptim.utils.FormulaUtils.compareFormulaAndElementalAnalysis(), denoptim.constants.DENOPTIMConstants.FORMULASTR, and denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.fragmenter.FragmenterTask.call().

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◆ exploreConnectivity()

static Set< IAtom > denoptim.fragmenter.FragmenterTools.exploreConnectivity	(	IAtom	seed,
		IAtomContainer	mol
	)

staticpackage

Explores the connectivity annotating which atoms have been visited.

Parameters

seed	atom acting as starting point.
mol	the atom container that own all the atoms we work with.

Returns: list of atoms that is confirmed to belong the continuously connected system of the seed atom.

Definition at line 1212 of file FragmenterTools.java.

Referenced by denoptim.fragmenter.FragmenterTools.fragmentation(), and denoptim.fragmenter.FragmenterToolsTest.testExploreConnectivity().

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◆ exploreDGraphForMappings()

static void denoptim.fragmenter.FragmenterTools.exploreDGraphForMappings	(	DGraph	graph,
		IAtomContainer	graphIAC,
		Fragment	masterFrag,
		IAtomContainer	masterFragIAC,
		IAtomContainer	mol,
		Map< IAtom, IAtom >	graphToMolMapping
	)		throws DENOPTIMException

staticprivate

Recursive function to process edges at any level of embedding to remove the corresponding bonds and create the corresponding attachment points.

TODO: 1) deal with RCVs in the graph. 2) deal with multihapticity.

Definition at line 701 of file FragmenterTools.java.

References denoptim.fragmenter.FragmenterTools.exploreDGraphForMappings(), denoptim.fragmenter.FragmenterTools.findPointAlignedWithTmpl(), denoptim.utils.MoleculeUtils.getPoint3d(), and denoptim.graph.AttachmentPoint.setCutId().

Referenced by denoptim.fragmenter.FragmenterTools.exploreDGraphForMappings(), and denoptim.fragmenter.FragmenterTools.fragmentation().

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◆ exploreHapticity()

static Set< IAtom > denoptim.fragmenter.FragmenterTools.exploreHapticity	(	IAtom	seed,
		IAtom	centralAtom,
		ArrayList< IAtom >	candidates,
		IAtomContainer	mol
	)

staticpackage

Identifies non-central atoms involved in the same n-hapto ligand as the seed atom.

Parameters

seed	atom acting as starting point.
centralAtom	the central atom (typically the metal) to which the seed is bonded as part of the multihapto system.
candidates	atoms that may belong to the multihapto ligand (i.e., atoms that have matches the cutting rule).
mol	the atom container that own all the atoms we work with.

Returns: list of atoms that is confirmed to belong the multihapto system.

Definition at line 1172 of file FragmenterTools.java.

Referenced by denoptim.fragmenter.FragmenterTools.fragmentation(), and denoptim.fragmenter.FragmenterToolsTest.testExploreHapticity().

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◆ filterFragment() [1/2]

static boolean denoptim.fragmenter.FragmenterTools.filterFragment	(	Fragment	frag,
		FragmenterParameters	settings
	)

static

Filter fragments according to the criteria defined in the settings.

Log is sent to logger in the FragmenterParameters argument.

Parameters

frag	the fragment to analyze.
settings	collection of settings including filtering criteria.

Returns: true if the fragment should be kept, or false if any of the filtering criteria is offended and, therefore, the fragment should be rejected.

Definition at line 1531 of file FragmenterTools.java.

References denoptim.fragmenter.FragmenterTools.filterFragment(), and denoptim.programs.RunTimeParameters.getLogger().

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), and denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ filterFragment() [2/2]

static boolean denoptim.fragmenter.FragmenterTools.filterFragment	(	Fragment	frag,
		FragmenterParameters	settings,
		Logger	logger
	)

static

Filter fragments according to the criteria defined in the settings.

Parameters

frag	the fragment to analyze.
settings	collection of settings including filtering criteria.
logger	where to direct log messages. This is typically different from the logger registered in the `FragmenterParameters`, which is the master logger, as we want thread-specific logging.

Returns: true if the fragment should be kept, or false if any of the filtering criteria is offended and, therefore, the fragment should be rejected.

Definition at line 1550 of file FragmenterTools.java.

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◆ filterStrucutresBySMARTS()

static void denoptim.fragmenter.FragmenterTools.filterStrucutresBySMARTS	(	File	input,
		Set< String >	smarts,
		File	output,
		Logger	logger
	)		throws DENOPTIMException, IOException

static

Removes from the structures anyone that matches any of the given SMARTS queries.

Parameters

input	the source of chemical structures.
smarts	the queries leading to rejection.
output	the file where to write extracted structures.
logger	a task-dedicated logger where we print messages for the user.

Exceptions

DENOPTIMException
IOException

Definition at line 233 of file FragmenterTools.java.

References denoptim.utils.ManySMARTSQuery.getAllMatches(), denoptim.utils.ManySMARTSQuery.getMessage(), denoptim.utils.ManySMARTSQuery.getProblem(), denoptim.utils.ManySMARTSQuery.hasProblems(), and denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.fragmenter.FragmenterTask.call().

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◆ findPointAlignedWithTmpl()

static Point3d denoptim.fragmenter.FragmenterTools.findPointAlignedWithTmpl	(	AttachmentPoint	ap,
		IAtom	graphAtmSrc,
		IAtomContainer	graphIAC,
		IAtomContainer	masterFragIAC,
		IAtomContainer	mol,
		Map< IAtom, IAtom >	graphToMolMapping
	)		throws DENOPTIMException

staticprivate

Finds the point on the master fragment that is aligned with the template geometry.

Parameters

ap	the AP for which we do the alignement
graphAtmSrc	the atom in the template graph that is the source of the AP. It belongs to graphIAC.
graphIAC	the atom container corresonding to the template graph
masterFragIAC	the fragment being created by fragmentation (may be discontinuous). Must be consistent with mol.
mol	the molecule being fragmented
graphToMolMapping	the mapping between the atoms in the template graph (graphIAC) and the atoms in the molecule being fragmented (mol).

Returns: the point on the master fragment that is aligned with the template geometry

Exceptions

DENOPTIMException

Definition at line 781 of file FragmenterTools.java.

References denoptim.utils.MathUtils.angle(), denoptim.constants.DENOPTIMConstants.FLOATCOMPARISONTOLERANCE, denoptim.utils.CartesianSpaceUtils.getNormalDirection(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.utils.CartesianSpaceUtils.getVectorFromTo(), denoptim.utils.MoleculeUtils.makeSameAs(), and denoptim.utils.CartesianSpaceUtils.rotatedVectorWAxisAngle().

Referenced by denoptim.fragmenter.FragmenterTools.exploreDGraphForMappings().

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◆ fragmentation() [1/4]

static boolean denoptim.fragmenter.FragmenterTools.fragmentation	(	File	input,
		FragmenterParameters	settings,
		File	output,
		Logger	logger
	)		throws CDKException, IOException, DENOPTIMException, IllegalArgumentException, UndetectedFileFormatException

static

Performs fragmentation according to the given cutting rules.

Parameters

input	the source of chemical structures.
settings	configurations including cutting rules and filtration criteria.
output	the file where to write extracted structures.
logger	where to direct log messages. This is typically different from the logger registered in the `FragmenterParameters`, which is the master logger, as we want thread-specific logging.

Exceptions

DENOPTIMException
IOException
UndetectedFileFormatException
IllegalArgumentException
CDKException

Returns: true if the fragmentation produced at least one fragment that survived post filtering, i.e., the output file does contain something.

Definition at line 404 of file FragmenterTools.java.

References denoptim.io.IteratingAtomContainerReader.close(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.io.IteratingAtomContainerReader.hasNext(), denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), denoptim.io.IteratingAtomContainerReader.next(), denoptim.files.FileFormat.VRTXSDF, and denoptim.io.DenoptimIO.writeVertexesToFile().

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◆ fragmentation() [2/4]

static List< Vertex > denoptim.fragmenter.FragmenterTools.fragmentation	(	IAtomContainer	mol,
		FragmenterParameters	settings
	)		throws DENOPTIMException

static

Performs fragmentation according to the given settings.

Parameters

mol	the molecule to fragment
settings	the parameters controlling the fragmentation

Returns: the list of fragments

Exceptions

DENOPTIMException

Definition at line 366 of file FragmenterTools.java.

References denoptim.fragmenter.FragmenterTools.fragmentation().

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.gui.GUIVertexInspector.initialize(), and denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol().

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◆ fragmentation() [3/4]

static List< Vertex > denoptim.fragmenter.FragmenterTools.fragmentation	(	IAtomContainer	mol,
		List< CuttingRule >	rules,
		Logger	logger
	)		throws DENOPTIMException

static

Chops one chemical structure by applying the given cutting rules.

Parameters

mol
rules
logger

Returns: the list of fragments

Exceptions

DENOPTIMException

Definition at line 958 of file FragmenterTools.java.

References denoptim.graph.Fragment.addAPOnAtom(), denoptim.graph.Fragment.atoms(), denoptim.graph.Fragment.clone(), denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.fragmenter.FragmenterTools.exploreConnectivity(), denoptim.fragmenter.FragmenterTools.exploreHapticity(), denoptim.graph.Fragment.getAtomCount(), denoptim.graph.Fragment.getAttachmentPoints(), denoptim.graph.Fragment.getIAtomContainer(), denoptim.fragmenter.FragmenterTools.getMatchingBondsAllInOne(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.graph.Fragment.removeAtoms(), denoptim.graph.AttachmentPoint.setCutId(), and denoptim.graph.Vertex.BBType.UNDEFINED.

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◆ fragmentation() [4/4]

static List< Vertex > denoptim.fragmenter.FragmenterTools.fragmentation	(	IAtomContainer	mol,
		List< DGraph >	templates,
		int	maxBufferShellSize,
		Randomizer	randomizer,
		Logger	logger
	)		throws DENOPTIMException

static

Chops one chemical structure by applying the given fragmentation templates.

Parameters

mol	the molecule to fragment
templates	the template graphs to use for fragmentation
maxBufferShellSize	the maximum number of buffer shells to consider, i.e., the number of bonds to consider for including atoms around topology-critical atoms when trying to find a unique mapping between the template graph and the molecular structure.
randomizer	the randomizer to use for the fragmentation.
logger	the logger to use for logging messages.

Returns: the list of fragments

Exceptions

DENOPTIMException

Definition at line 501 of file FragmenterTools.java.

References denoptim.graph.Fragment.atoms(), denoptim.graph.Fragment.clone(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.fragmenter.FragmenterTools.exploreConnectivity(), denoptim.fragmenter.FragmenterTools.exploreDGraphForMappings(), denoptim.utils.MoleculeUtils.findUniqueAtomMappings(), denoptim.graph.Fragment.getAtomCount(), denoptim.graph.Fragment.getAttachmentPoints(), denoptim.graph.Fragment.getIAtomContainer(), denoptim.fragmenter.TopoTemplateProducer.getTemplateWithBufferShell(), denoptim.graph.Fragment.removeAtoms(), and denoptim.graph.Vertex.BBType.UNDEFINED.

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◆ fragmentationFromGraphs()

static boolean denoptim.fragmenter.FragmenterTools.fragmentationFromGraphs	(	File	input,
		FragmenterParameters	settings,
		File	output,
		Logger	logger
	)		throws DENOPTIMException, Exception

static

Performs fragmentation from graphs, i.e., extracts existing fragments from graphs (stored in a file).

No cutting rule is applied.

Parameters

input	the source of graphs.
settings	configurations including filtration criteria.
output	the file where to write extracted structures.
logger	where to direct log messages. This is typically different from the logger registered in the `FragmenterParameters`, which is the master logger, as we want thread-specific logging.

Returns: true if the extraction produced at least one fragment that survived post filtering, i.e., the output file does contain something.

Exceptions

Exception
DENOPTIMException

Definition at line 322 of file FragmenterTools.java.

References denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.files.FileFormat.VRTXSDF, and denoptim.io.DenoptimIO.writeVertexesToFile().

Referenced by denoptim.fragmenter.FragmenterTask.call().

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◆ getMatchingBondsAllInOne()

static Map< String, List< MatchedBond > > denoptim.fragmenter.FragmenterTools.getMatchingBondsAllInOne	(	IAtomContainer	mol,
		List< CuttingRule >	rules,
		Logger	logger
	)

staticpackage

Identification of the bonds matching a list of SMARTS queries.

Parameters

mol	chemical system to be analyzed
rules	priority-sorted list of cutting rules.
logger

Returns: the list of matches.

Definition at line 1247 of file FragmenterTools.java.

References denoptim.programs.fragmenter.MatchedBond.satisfiesRuleOptions.

Referenced by denoptim.fragmenter.FragmenterTools.fragmentation(), and denoptim.fragmenter.FragmenterToolsTest.testGetMatchingBonds().

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◆ getMWSlotIdentifier()

static String denoptim.fragmenter.FragmenterTools.getMWSlotIdentifier	(	Vertex	frag,
		int	slotSize
	)

static

Determines the name of the MW slot to use when comparing the given fragment with previously stored fragments.

Parameters

frag	the fragment for which we want the MW slot identifier.
slotSize	the size of the MW slot.

Returns: the MW slot identifier.

Definition at line 1835 of file FragmenterTools.java.

References denoptim.graph.Vertex.getIAtomContainer().

Referenced by denoptim.fragmenter.ConformerExtractorTask.ConformerExtractorTask(), denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), and denoptim.fragmenter.FragmenterToolsTest.testGetMWSlotIdentifier().

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◆ getRCVForAP()

static Vertex denoptim.fragmenter.FragmenterTools.getRCVForAP	(	AttachmentPoint	ap,
		APClass	rcvApClass
	)		throws DENOPTIMException

static

Definition at line 1849 of file FragmenterTools.java.

References denoptim.graph.Fragment.addAP(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.graph.rings.RingClosingAttractor.RCALABELPERAPCLASS, and denoptim.graph.Vertex.setAsRCV().

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

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◆ manageFragmentCollection() [1/2]

static void denoptim.fragmenter.FragmenterTools.manageFragmentCollection	(	File	input,
		FragmenterParameters	settings,
		File	output,
		Logger	logger
	)		throws DENOPTIMException, IOException, IllegalArgumentException, UndetectedFileFormatException

static

Management of fragments: includes application of fragment filters, rejection rules, and collection rules (also of isomorphic fragments, thus management of duplicates) to manipulate collection of fragments.

Definition at line 1318 of file FragmenterTools.java.

References denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), denoptim.graph.Vertex.BBType.UNDEFINED, denoptim.files.FileFormat.VRTXSDF, and denoptim.io.DenoptimIO.writeVertexesToFile().

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.fragmenter.FragmenterTools.fragmentationFromGraphs(), and denoptim.fragmenter.FragmenterTools.manageFragmentCollection().

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◆ manageFragmentCollection() [2/2]

static void denoptim.fragmenter.FragmenterTools.manageFragmentCollection	(	Vertex	frag,
		int	fragCounter,
		FragmenterParameters	settings,
		List< Vertex >	collector,
		Logger	logger
	)		throws DENOPTIMException, IllegalArgumentException, UndetectedFileFormatException, IOException

static

Management of fragments: includes application of fragment filters, rejection rules, and collection rules (also of isomorphic fragments, thus management of duplicates) to manipulate collection of fragments.

Parameters

frag	the fragment to analyze now. This is a fragment that is candidates to enter the collection of fragments.
fragCounter	fragment index. Used only for logging purposes.
settings	configuration of the filters and methods uses throughout the fragmentation and pre-/post-processing of fragments.
collector	where accepted fragments are collected. This is the collection of fragment where we want to put `frag`.
logger	where to direct all log.

Exceptions

DENOPTIMException
IllegalArgumentException
UndetectedFileFormatException
IOException

Definition at line 1380 of file FragmenterTools.java.

References denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.utils.MoleculeUtils.getDimensions(), denoptim.graph.Fragment.getIAtomContainer(), denoptim.fragmenter.FragmenterTools.getMWSlotIdentifier(), denoptim.graph.Vertex.getProperty(), denoptim.constants.DENOPTIMConstants.ISOMORPHICFAMILYID, denoptim.io.DenoptimIO.readVertexes(), denoptim.graph.Vertex.setProperty(), denoptim.graph.Vertex.BBType.UNDEFINED, denoptim.files.FileFormat.VRTXSDF, and denoptim.io.DenoptimIO.writeVertexToFile().

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◆ prepareMolToFragmentation()

static boolean denoptim.fragmenter.FragmenterTools.prepareMolToFragmentation	(	IAtomContainer	mol,
		FragmenterParameters	settings,
		int	index
	)

static

Do any pre-processing on a IAtomContainer meant to be fragmented.

These are DENOPTIM specific manipulations, in particular meant to comply to requirements to write SDF files: unset bond orders can only be used in query-type files. So types 4 and 8 are not expected to be found (but CSD uses them...). Also, it deals with implicit H formalism according to the given settings.

Parameters

mol	the system that this method prepares to fragmentation.
settings	the settings controlling how the molecule is prepared.
index	identifies the given `IAtomContainer` in a collection of systems to work on. This is used only for logging.

Definition at line 162 of file FragmenterTools.java.

References denoptim.programs.fragmenter.FragmenterParameters.acceptUnsetToSingeBO(), denoptim.programs.fragmenter.FragmenterParameters.addExplicitH, denoptim.utils.MoleculeUtils.ensureNoUnsetBondOrders(), denoptim.utils.MoleculeUtils.explicitHydrogens(), denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS, denoptim.programs.RunTimeParameters.getLogger(), and denoptim.utils.MoleculeUtils.setZeroImplicitHydrogensToAllAtoms().

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), and denoptim.fragmenter.ParallelFragmentationAlgorithm.splitInputForThreads().

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

/github/workspace/src/main/java/denoptim/fragmenter/FragmenterTools.java

Static Public Member Functions

Static Package Functions

Static Private Member Functions

Detailed Description

Member Function Documentation

◆ checkElementalAnalysisAgainstFormula()

◆ exploreConnectivity()

◆ exploreDGraphForMappings()

◆ exploreHapticity()

◆ filterFragment() [1/2]

◆ filterFragment() [2/2]

◆ filterStrucutresBySMARTS()

◆ findPointAlignedWithTmpl()

◆ fragmentation() [1/4]

◆ fragmentation() [2/4]

◆ fragmentation() [3/4]

◆ fragmentation() [4/4]

◆ fragmentationFromGraphs()

◆ getMatchingBondsAllInOne()

◆ getMWSlotIdentifier()

◆ getRCVForAP()

◆ manageFragmentCollection() [1/2]

◆ manageFragmentCollection() [2/2]

◆ prepareMolToFragmentation()