Utilities for molecule conversion. More...

Collaboration diagram for denoptim.utils.MoleculeUtils:

Static Public Member Functions
static double	getMolecularWeight (IAtomContainer mol) throws DENOPTIMException

static boolean	isDummy (IAtom atm)
	Checks if the given atom is a dummy atom based on the elemental symbol and the string used for dummy atom as a convention in DENOPTIM (uses `DENOPTIMConstants#DUMMYATMSYMBOL`. More...

static boolean	isElement (IAtom atom)
	Check element symbol corresponds to real element of Periodic Table. More...

static boolean	isElement (String symbol)
	Check element symbol corresponds to real element of Periodic Table. More...

static void	removeRCA (IAtomContainer mol)
	Replace any `PseudoAtom`s representing ring closing attractors with H. More...

static void	removeUsedRCA (IAtomContainer mol, DGraph graph, Logger logger) throws DENOPTIMException
	Replace used RCAs (i.e., those involved in `Ring`s) while adding the ring closing bonds. More...

static String	getSMILESForMolecule (IAtomContainer mol, Logger logger) throws DENOPTIMException
	Returns the SMILES representation of the molecule. More...

static IAtomContainer	generate2DCoordinates (IAtomContainer ac, Logger logger) throws DENOPTIMException
	Generates 2D coordinates for the molecule. More...

static String	getInChIKeyForMolecule (IAtomContainer mol, Logger logger) throws DENOPTIMException
	Generates the InChI key for the given atom container. More...

static String	getInChIKeyForMolecule (IAtomContainer mol, InchiOptions options, Logger logger) throws DENOPTIMException
	Generates the INCHI key for the molecule. More...

static int	getNumberOfRotatableBonds (IAtomContainer mol) throws DENOPTIMException
	Count number of rotatable bonds. More...

static int	getHeavyAtomCount (IAtomContainer mol)
	The heavy atom count. More...

static int	countAtomsOfElement (IAtomContainer mol, String symbol)
	Count atoms with the given elemental symbol. More...

static Map< Vertex, ArrayList< Integer > >	getVertexToAtomIdMap (ArrayList< Vertex > vertLst, IAtomContainer mol)
	Method to generate the map making in relation `DENOPTIMVertex` ID and atom index in the `IAtomContainer` representation of the chemical entity. More...

static void	moleculeToPNG (IAtomContainer mol, String filename, Logger logger) throws DENOPTIMException
	Generate a PNG image from molecule `mol` More...

static Point3d	getPoint3d (IAtom atm)
	Return the 3D coordinates, if present. More...

static void	setZeroImplicitHydrogensToAllAtoms (IAtomContainer iac)
	Sets zero implicit hydrogen count to all atoms. More...

static void	explicitHydrogens (IAtomContainer mol)
	Converts all the implicit hydrogens to explicit. More...

static void	ensureNoUnsetBondOrdersSilent (IAtomContainer iac)
	Sets bond order = single to all otherwise unset bonds. More...

static void	ensureNoUnsetBondOrders (IAtomContainer iac) throws CDKException
	Sets bond order = single to all otherwise unset bonds. More...

static String	missmatchingAromaticity (IAtomContainer mol)
	Looks for carbon atoms that are flagged as aromatic, but do not have any double bond and are, therefore, not properly Kekularized. More...

static int	numOfBondsWithBO (IAtom atm, IAtomContainer mol, IBond.Order order)
	Returns the number of bonds, with a certain bond order, surrounding the given atom. More...

static IAtomContainer	makeSameAs (IAtomContainer mol) throws DENOPTIMException
	Constructs a copy of an atom container, i.e., a molecule that reflects the one given in the input argument in terms of atom count, type, and geometric properties, and bond count and type. More...

static IAtom	makeSameAtomAs (IAtom oAtm)
	Method that constructs an atom that reflect the same atom given as parameter in terms of element symbol (or label, for pseudoatoms), and Cartesian coordinates, and most of the other attributes. More...

static IAtom	makeSameAtomAs (IAtom oAtm, boolean ignoreValence, boolean ignoreImplicitH)
	Method that constructs an atom that reflect the same atom given as parameter in terms of element symbol (or label, for pseudoatoms), and Cartesian coordinates, and most of the other attributes unless otherwise specified by the flags. More...

static String	getSymbolOrLabel (IAtom atm)
	Gets either the elemental symbol (for standard atoms) of the label (for pseudo-atoms). More...

static String	getAtomRef (IAtom atm, IAtomContainer mol)

static Point3d	calculateCentroid (IAtomContainer mol)
	Calculated the centroid of the given molecule. More...

static IAtomContainer	extractIACForSubgraph (IAtomContainer wholeIAC, DGraph subGraph, DGraph wholeGraph, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Selects only the atoms that originate from a subgraph of a whole graph that originated the whole molecule given as parameter. More...

static int	getDimensions (IAtomContainer mol)
	Determines the dimensionality of the given chemical object. More...

Static Private Attributes
static final StructureDiagramGenerator	SDG

static final SmilesGenerator	SMGEN

static final IChemObjectBuilder	builder

Detailed Description

Utilities for molecule conversion.

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 93 of file MoleculeUtils.java.

Member Function Documentation

◆ calculateCentroid()

static Point3d denoptim.utils.MoleculeUtils.calculateCentroid ( IAtomContainer mol )

static

Calculated the centroid of the given molecule.

Parameters

mol

Returns: the centroid.

Definition at line 1026 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.getPoint3d().

Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.getRandomPoint(), and denoptim.utils.MoleculeUtilsTest.testCalculateCentroid().

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◆ countAtomsOfElement()

static int denoptim.utils.MoleculeUtils.countAtomsOfElement	(	IAtomContainer	mol,
		String	symbol
	)

static

Count atoms with the given elemental symbol.

Parameters

mol	Molecule to count atoms in.
symbol	the elemental symbol to look for.

Returns: the total number of those elements.

Definition at line 571 of file MoleculeUtils.java.

Referenced by denoptim.graph.TemplateTest.testGetIAtomContainer(), and denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex().

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◆ ensureNoUnsetBondOrders()

static void denoptim.utils.MoleculeUtils.ensureNoUnsetBondOrders ( IAtomContainer iac ) throws CDKException

static

Sets bond order = single to all otherwise unset bonds.

In case of failed kekulization this method reports a warning but does not throw an exception.

Parameters

iac	the container to process

Exceptions

CDKException

Definition at line 753 of file MoleculeUtils.java.

Referenced by denoptim.utils.MoleculeUtils.ensureNoUnsetBondOrdersSilent(), and denoptim.fragmenter.FragmenterTools.prepareMolToFragmentation().

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◆ ensureNoUnsetBondOrdersSilent()

static void denoptim.utils.MoleculeUtils.ensureNoUnsetBondOrdersSilent ( IAtomContainer iac )

static

Sets bond order = single to all otherwise unset bonds.

In case of failed kekulization this method reports a warning but does not throw an exception.

Parameters

iac	the container to process

Definition at line 725 of file MoleculeUtils.java.

References denoptim.logging.StaticLogger.appLogger, and denoptim.utils.MoleculeUtils.ensureNoUnsetBondOrders().

Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.utils.MoleculeUtils.getSMILESForMolecule(), and denoptim.utils.ManySMARTSQuery.ManySMARTSQuery().

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◆ explicitHydrogens()

static void denoptim.utils.MoleculeUtils.explicitHydrogens ( IAtomContainer mol )

static

Converts all the implicit hydrogens to explicit.

Definition at line 710 of file MoleculeUtils.java.

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

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◆ extractIACForSubgraph()

static IAtomContainer denoptim.utils.MoleculeUtils.extractIACForSubgraph	(	IAtomContainer	wholeIAC,
		DGraph	subGraph,
		DGraph	wholeGraph,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

static

Selects only the atoms that originate from a subgraph of a whole graph that originated the whole molecule given as parameter.

Parameters

wholeIAC the molecular representation of the whole graph. The atoms contained here are expected to be have the property DENOPTIMConstants#ATMPROPVERTEXID, which is used to identify which atoms originated from which vertex of the whole graph.

subGraph the portion of the whole graph for which we want the corresponding atoms. The vertexes are expected to have the DENOPTIMConstants#STOREDVID property that defines their original vertex ID in the whole graph. These labels are expected to be consistent with those in the property DENOPTIMConstants#ATMPROPVERTEXID of the wholeIAC parameter. Note that the current vertexID of each vertex can be different from the ID of the original vertex had in the while graph.

Returns: a new container with the requested substructure

Exceptions

DENOPTIMException

Definition at line 1060 of file MoleculeUtils.java.

References denoptim.graph.Fragment.addAPOnAtom(), denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.graph.Fragment.bonds(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.Fragment.getAtom(), denoptim.graph.Fragment.getIAtomContainer(), denoptim.graph.AttachmentPoint.getIndexInOwner(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.constants.DENOPTIMConstants.LINKAPS, denoptim.utils.MoleculeUtils.makeSameAs(), denoptim.graph.Fragment.removeAtom(), denoptim.graph.Fragment.removeBond(), denoptim.graph.AttachmentPoint.setProperty(), denoptim.constants.DENOPTIMConstants.STOREDVID, denoptim.graph.Fragment.updateAPs(), and denoptim.io.DenoptimIO.writeGraphToSDF().

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

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◆ generate2DCoordinates()

static IAtomContainer denoptim.utils.MoleculeUtils.generate2DCoordinates	(	IAtomContainer	ac,
		Logger	logger
	)		throws DENOPTIMException

static

Generates 2D coordinates for the molecule.

Parameters

ac	the molecule to layout.
logger	program-specific logger.

Returns: A new molecule laid out in 2D. If the molecule already has 2D coordinates then it is returned unchanged. If layout fails then null is returned.

Exceptions

denoptim.exception.DENOPTIMException

Definition at line 384 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.builder, denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.utils.DummyAtomHandler.removeDummyInHapto(), denoptim.utils.MoleculeUtils.removeRCA(), and denoptim.utils.MoleculeUtils.SDG.

Referenced by denoptim.utils.MoleculeUtils.moleculeToPNG().

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◆ getAtomRef()

static String denoptim.utils.MoleculeUtils.getAtomRef	(	IAtom	atm,
		IAtomContainer	mol
	)

static

Returns: a string with the element symbol and the atom number (1-based) of the given atom.

Definition at line 1014 of file MoleculeUtils.java.

Referenced by denoptim.utils.MoleculeUtils.missmatchingAromaticity().

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◆ getDimensions()

static int denoptim.utils.MoleculeUtils.getDimensions ( IAtomContainer mol )

static

Determines the dimensionality of the given chemical object.

Parameters

mol	the given chemical object

Returns: dimensionality of this object: 2, or 3, or -1 if neither 2 nor 3.

Definition at line 1219 of file MoleculeUtils.java.

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

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◆ getHeavyAtomCount()

static int denoptim.utils.MoleculeUtils.getHeavyAtomCount ( IAtomContainer mol )

static

The heavy atom count.

Parameters

mol	Molecule to count heavy atoms in

Returns: heavy atom count

Definition at line 550 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.getSymbolOrLabel(), and denoptim.utils.MoleculeUtils.isElement().

Referenced by denoptim.graph.DGraph.checkConsistency(), and denoptim.graph.Fragment.getHeavyAtomsCount().

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◆ getInChIKeyForMolecule() [1/2]

static String denoptim.utils.MoleculeUtils.getInChIKeyForMolecule	(	IAtomContainer	mol,
		InchiOptions	options,
		Logger	logger
	)		throws DENOPTIMException

static

Generates the INCHI key for the molecule.

Parameters

mol	the molecule
logger	program-specific logger.

Returns: the InchiKey. null if error

Exceptions

denoptim.exception.DENOPTIMException

Definition at line 467 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.builder, denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.utils.DummyAtomHandler.removeDummyInHapto(), and denoptim.utils.MoleculeUtils.removeRCA().

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◆ getInChIKeyForMolecule() [2/2]

static String denoptim.utils.MoleculeUtils.getInChIKeyForMolecule	(	IAtomContainer	mol,
		Logger	logger
	)		throws DENOPTIMException

static

Generates the InChI key for the given atom container.

By default we produce a non-standard InChI using the flags InchiFlag#AuxNone, InchiFlag#RecMet, and InchiFlag#SUU.

Parameters

mol	the molecule
logger	program-specific logger.

Returns: the InchiKey. null if error

Exceptions

denoptim.exception.DENOPTIMException

Definition at line 447 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.getInChIKeyForMolecule().

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.graph.DGraph.checkConsistency(), denoptim.utils.MoleculeUtils.getInChIKeyForMolecule(), and denoptim.ga.EAUtils.setupRings().

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◆ getMolecularWeight()

static double denoptim.utils.MoleculeUtils.getMolecularWeight ( IAtomContainer mol ) throws DENOPTIMException

static

Definition at line 104 of file MoleculeUtils.java.

Referenced by denoptim.graph.DGraph.checkConsistency().

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◆ getNumberOfRotatableBonds()

static int denoptim.utils.MoleculeUtils.getNumberOfRotatableBonds ( IAtomContainer mol ) throws DENOPTIMException

static

Count number of rotatable bonds.

Parameters

mol	molecule to count rotatable bonds in

Returns: number of rotatable bonds

Exceptions

DENOPTIMException

Definition at line 524 of file MoleculeUtils.java.

Referenced by denoptim.graph.DGraph.checkConsistency().

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◆ getPoint3d()

static Point3d denoptim.utils.MoleculeUtils.getPoint3d ( IAtom atm )

static

Return the 3D coordinates, if present.

If only 2D coords exist, then it returns the 2D projected in 3D space. If neither 3D nor 2D are present returns [0, 0, 0].

Parameters

atm	the atom to analyze.

Returns: a not null.

Definition at line 673 of file MoleculeUtils.java.

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges(), denoptim.utils.MoleculeUtils.calculateCentroid(), denoptim.gui.GUIVertexInspector.convertAtomToAP(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.utils.MoleculeUtils.extractIACForSubgraph(), denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.utils.DummyAtomHandler.getDummyInSafeDirection(), denoptim.gui.FragmentViewPanel.getLoadedStructure(), denoptim.graph.FragIsomorphNode.getPoint3d(), denoptim.fragmenter.FragmenterTools.getRCPForAP(), denoptim.json.IAtomContainerSerializer.serialize(), denoptim.json.DENOPTIMgsonTest.testIAtomContainerToJSONAndBack(), denoptim.json.DENOPTIMgsonTest.testMolecularFragmentSerialization(), denoptim.json.DENOPTIMgsonTest.testTemplateSerialization(), and denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer().

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◆ getSMILESForMolecule()

static String denoptim.utils.MoleculeUtils.getSMILESForMolecule	(	IAtomContainer	mol,
		Logger	logger
	)		throws DENOPTIMException

static

Returns the SMILES representation of the molecule.

All atoms are expected to be explicit, as we set the count of implicit H to zero for all atoms.

Parameters

mol	the molecule
logger	program.specific logger.

Returns: smiles string

Exceptions

DENOPTIMException

Definition at line 330 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.builder, denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.utils.MoleculeUtils.ensureNoUnsetBondOrdersSilent(), denoptim.utils.DummyAtomHandler.removeDummy(), denoptim.utils.DummyAtomHandler.removeDummyInHapto(), denoptim.utils.MoleculeUtils.removeRCA(), denoptim.utils.MoleculeUtils.setZeroImplicitHydrogensToAllAtoms(), denoptim.utils.MoleculeUtils.SMGEN, and denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.graph.DGraph.checkConsistency(), denoptim.gui.FragmentViewPanel.getLoadedStructure(), and denoptim.ga.EAUtils.setupRings().

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◆ getSymbolOrLabel()

static String denoptim.utils.MoleculeUtils.getSymbolOrLabel ( IAtom atm )

static

Gets either the elemental symbol (for standard atoms) of the label (for pseudo-atoms).

Other classes implementing IAtom are not considered. This method is a response to the change from CDK-1.* to CDK-2.*. In the old CDK-1.* the getSymbol() method of IAtom would return the label for a PseudoAtom, but this behavior is not retained in newer versions.

Parameters

atm

Returns: either the element symbol of the label

Definition at line 979 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.isElement().

Referenced by denoptim.graph.DGraph.checkConsistency(), denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability(), denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.graph.FragIsomorphNode.FragIsomorphNode(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.utils.MoleculeUtils.getHeavyAtomCount(), denoptim.integration.tinker.TinkerUtils.getICFromIAC(), denoptim.graph.Fragment.getJGraphFragIsomorphism(), denoptim.integration.tinker.TinkerUtils.getThirdRefAtomId(), denoptim.utils.MoleculeUtils.isDummy(), denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), denoptim.utils.MoleculeUtils.makeSameAtomAs(), denoptim.utils.DummyAtomHandler.removeDummy(), denoptim.utils.DummyAtomHandler.removeDummyInHapto(), denoptim.utils.MoleculeUtils.removeRCA(), denoptim.graph.rings.RingClosingAttractor.RingClosingAttractor(), denoptim.json.IAtomContainerSerializer.serialize(), denoptim.json.DENOPTIMgsonTest.testIAtomContainerToJSONAndBack(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_linearities(), denoptim.json.DENOPTIMgsonTest.testMolecularFragmentSerialization(), denoptim.json.DENOPTIMgsonTest.testTemplateSerialization(), denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates(), and denoptim.graph.rings.RingClosingAttractor.toString().

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◆ getVertexToAtomIdMap()

static Map< Vertex, ArrayList< Integer > > denoptim.utils.MoleculeUtils.getVertexToAtomIdMap	(	ArrayList< Vertex >	vertLst,
		IAtomContainer	mol
	)

static

Method to generate the map making in relation DENOPTIMVertex ID and atom index in the IAtomContainer representation of the chemical entity.

Note that the IAtomContainer must have been generated from the DENOPTIMGraph that contains the required DENOPTIMVertexs.

Parameters

vertLst	the list of `DENOPTIMVertex` to find
mol	the molecular representation

Returns: the map of atom indexes per each DENOPTIMVertex ID

Definition at line 595 of file MoleculeUtils.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManager.initialize(), and denoptim.utils.MoleculeUtils.removeUsedRCA().

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◆ isDummy()

static boolean denoptim.utils.MoleculeUtils.isDummy ( IAtom atm )

static

Checks if the given atom is a dummy atom based on the elemental symbol and the string used for dummy atom as a convention in DENOPTIM (uses DENOPTIMConstants#DUMMYATMSYMBOL.

For detecting dummy atoms beyond DENOPTIM's convention, use DummyAtomHandler.

Parameters

atm

Returns: true if the symbol of the atom indicates this is a dummy atom according to DENOPTIM's convention.

Definition at line 134 of file MoleculeUtils.java.

References denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, and denoptim.utils.MoleculeUtils.getSymbolOrLabel().

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities().

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◆ isElement() [1/2]

static boolean denoptim.utils.MoleculeUtils.isElement ( IAtom atom )

static

Check element symbol corresponds to real element of Periodic Table.

Parameters

atom to check.

Returns: true if the element symbol correspond to an atom in the periodic table.

Definition at line 149 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.isElement().

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.utils.MoleculeUtils.getHeavyAtomCount(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.utils.MoleculeUtils.isElement(), denoptim.utils.MoleculeUtils.makeSameAtomAs(), denoptim.programs.fragmenter.CuttingRule.satisfiesOptions(), and denoptim.json.LWAtom.toIAtom().

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◆ isElement() [2/2]

static boolean denoptim.utils.MoleculeUtils.isElement ( String symbol )

static

Check element symbol corresponds to real element of Periodic Table.

Parameters

symbol of the element to check

Returns: true if the element symbol correspond to an atom in the periodic table.

Definition at line 164 of file MoleculeUtils.java.

◆ makeSameAs()

static IAtomContainer denoptim.utils.MoleculeUtils.makeSameAs ( IAtomContainer mol ) throws DENOPTIMException

static

Constructs a copy of an atom container, i.e., a molecule that reflects the one given in the input argument in terms of atom count, type, and geometric properties, and bond count and type.

Other properties are not copied.

Parameters

mol	the container to copy.

Returns: the chemical-copy of the input argument.

Exceptions

DENOPTIMException if there are bonds involving more than two atoms.

Definition at line 860 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.builder, and denoptim.utils.MoleculeUtils.makeSameAtomAs().

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Fragment.clone(), denoptim.graph.Template.clone(), denoptim.utils.MoleculeUtils.extractIACForSubgraph(), denoptim.graph.Fragment.Fragment(), denoptim.graph.Candidate.fromAtomContainerNoGraph(), and denoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel.TwoDimStructurePanel().

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◆ makeSameAtomAs() [1/2]

static IAtom denoptim.utils.MoleculeUtils.makeSameAtomAs ( IAtom oAtm )

static

Method that constructs an atom that reflect the same atom given as parameter in terms of element symbol (or label, for pseudoatoms), and Cartesian coordinates, and most of the other attributes.

This method copies valence and implicit H count, in addition to most of the fields accessible via IAtom. Use makeSameAtomAs(IAtom, boolean, boolean) to have the option to exclude valence and implicit H count. This is basically a cloning method that ignores some fields.

Parameters

oAtm	the original

Returns: the copy of the original

Definition at line 899 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.makeSameAtomAs().

Referenced by denoptim.utils.AtomOrganizer.makeReorderedCopy(), denoptim.utils.MoleculeUtils.makeSameAs(), and denoptim.utils.MoleculeUtils.makeSameAtomAs().

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◆ makeSameAtomAs() [2/2]

static IAtom denoptim.utils.MoleculeUtils.makeSameAtomAs	(	IAtom	oAtm,
		boolean	ignoreValence,
		boolean	ignoreImplicitH
	)

static

Method that constructs an atom that reflect the same atom given as parameter in terms of element symbol (or label, for pseudoatoms), and Cartesian coordinates, and most of the other attributes unless otherwise specified by the flags.

This is basically a cloning method that ignores some fields.

Parameters

oAtm	the original
ignoreValence	if `true` the returned atom will have null valence
ignoreImplicitH	if `true` the returned atom will have null implicit hydrogen count.

Returns: the copy of the original

Definition at line 919 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.getSymbolOrLabel(), and denoptim.utils.MoleculeUtils.isElement().

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◆ missmatchingAromaticity()

static String denoptim.utils.MoleculeUtils.missmatchingAromaticity ( IAtomContainer mol )

static

Looks for carbon atoms that are flagged as aromatic, but do not have any double bond and are, therefore, not properly Kekularized.

Parameters

mol	the molecule to analyze.

Returns: a non-empty string if there is any carbon atom that does not look properly Kekularized.

Definition at line 775 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.getAtomRef(), and denoptim.utils.MoleculeUtils.numOfBondsWithBO().

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◆ moleculeToPNG()

static void denoptim.utils.MoleculeUtils.moleculeToPNG	(	IAtomContainer	mol,
		String	filename,
		Logger	logger
	)		throws DENOPTIMException

static

Generate a PNG image from molecule mol

Parameters

mol	generate molecule PNG from
filename	name of file to store generated PNG as
logger	program-specific logger.

Exceptions

DENOPTIMException

Definition at line 639 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.generate2DCoordinates().

Referenced by denoptim.task.FitnessTask.runFitnessProvider().

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◆ numOfBondsWithBO()

static int denoptim.utils.MoleculeUtils.numOfBondsWithBO	(	IAtom	atm,
		IAtomContainer	mol,
		IBond.Order	order
	)

static

Returns the number of bonds, with a certain bond order, surrounding the given atom.

Parameters

atm	the atom to look at
mol	its container
order	the bond order to count.

Returns: the number of bonds with that order.

Definition at line 837 of file MoleculeUtils.java.

Referenced by denoptim.utils.MoleculeUtils.missmatchingAromaticity().

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◆ removeRCA()

static void denoptim.utils.MoleculeUtils.removeRCA ( IAtomContainer mol )

static

Replace any PseudoAtoms representing ring closing attractors with H.

No change in coordinates, but any reference to the original atom, beyond those managed internally to the CDK library, will be broken.

Parameters

mol	Molecule to replace `PseudoAtom`s of.

Definition at line 190 of file MoleculeUtils.java.

References denoptim.utils.MoleculeUtils.getSymbolOrLabel(), and denoptim.graph.rings.RingClosingAttractor.RCATYPEMAP.

Referenced by denoptim.utils.RotationalSpaceUtils.defineRotatableBonds(), denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability(), denoptim.utils.MoleculeUtils.generate2DCoordinates(), denoptim.utils.MoleculeUtils.getInChIKeyForMolecule(), and denoptim.utils.MoleculeUtils.getSMILESForMolecule().

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◆ removeUsedRCA()

static void denoptim.utils.MoleculeUtils.removeUsedRCA	(	IAtomContainer	mol,
		DGraph	graph,
		Logger	logger
	)		throws DENOPTIMException

static

Replace used RCAs (i.e., those involved in Rings) while adding the ring closing bonds.

Does not alter the graph.

Parameters

mol	the molecular representation to be updated
graph	the corresponding graph representation

Exceptions

DENOPTIMException

Definition at line 224 of file MoleculeUtils.java.

References denoptim.graph.Edge.BondType.getCDKOrder(), denoptim.utils.MoleculeUtils.getVertexToAtomIdMap(), and denoptim.graph.Edge.BondType.hasCDKAnalogue().

Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), and denoptim.gui.GraphVertexMolViewerPanel.updateMolevularViewer().

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◆ setZeroImplicitHydrogensToAllAtoms()

static void denoptim.utils.MoleculeUtils.setZeroImplicitHydrogensToAllAtoms ( IAtomContainer iac )

static

Sets zero implicit hydrogen count to all atoms.

Parameters

iac	the container to process

Definition at line 698 of file MoleculeUtils.java.

Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.graph.Fragment.Fragment(), denoptim.utils.MoleculeUtils.getSMILESForMolecule(), denoptim.utils.ManySMARTSQuery.ManySMARTSQuery(), and denoptim.fragmenter.FragmenterTools.prepareMolToFragmentation().

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Member Data Documentation

◆ builder

final IChemObjectBuilder denoptim.utils.MoleculeUtils.builder

staticprivate

Initial value:

=

SilentChemObjectBuilder.getInstance()

Definition at line 99 of file MoleculeUtils.java.

Referenced by denoptim.utils.MoleculeUtils.generate2DCoordinates(), denoptim.utils.MoleculeUtils.getInChIKeyForMolecule(), denoptim.utils.MoleculeUtils.getSMILESForMolecule(), and denoptim.utils.MoleculeUtils.makeSameAs().

◆ SDG

final StructureDiagramGenerator denoptim.utils.MoleculeUtils.SDG

staticprivate

Initial value:

=

new StructureDiagramGenerator()

Definition at line 95 of file MoleculeUtils.java.

Referenced by denoptim.utils.MoleculeUtils.generate2DCoordinates().

◆ SMGEN

final SmilesGenerator denoptim.utils.MoleculeUtils.SMGEN

staticprivate

Initial value:

= new SmilesGenerator(

SmiFlavor.Generic)

Definition at line 97 of file MoleculeUtils.java.

Referenced by denoptim.utils.MoleculeUtils.getSMILESForMolecule().

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

/github/workspace/src/main/java/denoptim/utils/MoleculeUtils.java

Static Public Member Functions

Static Private Attributes

Detailed Description

Member Function Documentation

◆ calculateCentroid()

◆ countAtomsOfElement()

◆ ensureNoUnsetBondOrders()

◆ ensureNoUnsetBondOrdersSilent()

◆ explicitHydrogens()

◆ extractIACForSubgraph()

◆ generate2DCoordinates()

◆ getAtomRef()

◆ getDimensions()

◆ getHeavyAtomCount()

◆ getInChIKeyForMolecule() [1/2]

◆ getInChIKeyForMolecule() [2/2]

◆ getMolecularWeight()

◆ getNumberOfRotatableBonds()

◆ getPoint3d()

◆ getSMILESForMolecule()

◆ getSymbolOrLabel()

◆ getVertexToAtomIdMap()

◆ isDummy()

◆ isElement() [1/2]

◆ isElement() [2/2]

◆ makeSameAs()

◆ makeSameAtomAs() [1/2]

◆ makeSameAtomAs() [2/2]

◆ missmatchingAromaticity()

◆ moleculeToPNG()

◆ numOfBondsWithBO()

◆ removeRCA()

◆ removeUsedRCA()

◆ setZeroImplicitHydrogensToAllAtoms()

Member Data Documentation

◆ builder

◆ SDG

◆ SMGEN