denoptim.fragmenter.FragmenterTools Class Reference

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	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< 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	getRCPForAP (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...

Detailed Description

Definition at line 52 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 71 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 660 of file FragmenterTools.java.

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

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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 620 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 979 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 998 of file FragmenterTools.java.

References denoptim.graph.Fragment.atoms(), denoptim.programs.fragmenter.FragmenterParameters.doRejectWeirdIsotopes, denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.graph.Vertex.getAllAPClasses(), denoptim.graph.Fragment.getAttachmentPoints(), denoptim.utils.FormulaUtils.getElementalanalysis(), denoptim.programs.fragmenter.FragmenterParameters.getFragRejectionSMARTS(), denoptim.programs.fragmenter.FragmenterParameters.getFragRetentionSMARTS(), denoptim.graph.Fragment.getIAtomContainer(), denoptim.programs.fragmenter.FragmenterParameters.getMaxFragHeavyAtomCount(), denoptim.utils.ManySMARTSQuery.getMessage(), denoptim.programs.fragmenter.FragmenterParameters.getMinFragHeavyAtomCount(), denoptim.utils.ManySMARTSQuery.getNumMatchesOfQuery(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.programs.fragmenter.FragmenterParameters.getRejectedAPClassCombinations(), denoptim.programs.fragmenter.FragmenterParameters.getRejectedAPClasses(), denoptim.programs.fragmenter.FragmenterParameters.getRejectedElements(), denoptim.programs.fragmenter.FragmenterParameters.getRejectedFormulaLessThan(), denoptim.programs.fragmenter.FragmenterParameters.getRejectedFormulaMoreThan(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.utils.ManySMARTSQuery.hasProblems(), denoptim.utils.MoleculeUtils.isElement(), and denoptim.programs.fragmenter.FragmenterParameters.isWorkingIn3D().

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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 219 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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fragmentation() [1/2]

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 312 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().

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

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fragmentation() [2/2]

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 406 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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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 695 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 1283 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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getRCPForAP()

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

static

Definition at line 1297 of file FragmenterTools.java.

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

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 766 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(), 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 828 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 151 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.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