Collector of molecular information, related to a single chemical object, that is deployed within the 3D builder. More...

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Public Member Functions
	ChemicalObjectModel ()
	Constructs an empty item. More...

	ChemicalObjectModel (DGraph molGraph, IAtomContainer fmol, TinkerMolecule tmol, String molName, ArrayList< ObjectPair > rotatableBnds, ArrayList< RingClosingAttractor > attractors, Map< RingClosingAttractor, Integer > attToAtmID, ArrayList< Set< ObjectPair > > allRCACombs, ArrayList< RingClosure > ringClosures, ArrayList< Integer > oldToNewOrder, ArrayList< Integer > newToOldOrder, Logger logger)
	Constructs an item specifying all its features. More...

	ChemicalObjectModel (DGraph molGraph, IAtomContainer fmol, TinkerMolecule tmol, String molName, ArrayList< ObjectPair > rotatableBnds, ArrayList< Integer > oldToNewOrder, ArrayList< Integer > newToOldOrder, Logger logger) throws DENOPTIMException
	Constructs a `Molecule3DBuilder` specifying all its features. More...

List< Integer >	getOldToNewOrder ()

List< Integer >	getNewToOldOrder ()

void	updateXYZFromINT () throws DENOPTIMException
	Converts currently loaded internal coordinates into Cartesian overwriting the current XYZ. More...

DGraph	getGraph ()
	Returns the graph representation of this molecule as it was originally generated by DEOPTIM. More...

IAtomContainer	getIAtomContainer ()
	Returns the CDK representation of the molecular system. More...

TinkerMolecule	getTinkerMolecule ()
	Returns the Tinker Internal Coordination representation of the molecule. More...

ArrayList< RingClosingAttractor >	getAttractorsList ()
	Returns the list of RuingClosingAttractors. More...

RingClosingAttractor	getAttractor (int i)
	Returns the attractor given its position in the list of attractors. More...

int	getAtmIdOfRCA (RingClosingAttractor rca)
	Returns the CDK atom number, 0 to (n-1), of the given RingClosingAttractor. More...

int	getTnkAtmIdOfRCA (RingClosingAttractor rca)
	Returns the Tinker atom number, 1 to n,of the given RingClosingAttractor. More...

ArrayList< Set< ObjectPair > >	getRCACombinations ()
	Returns the list of combinations of `RingClosingAttractor`. More...

ArrayList< ObjectPair >	getRotatableBonds ()
	Returns the list of rotatable bonds. More...

int	getNumberRotatableBonds ()
	Returns the size of the current list of rotatable bonds. More...

ArrayList< RingClosure >	getNewRingClosures ()
	Return the list of RingClosures that have been identified as closable head/tail of atom chains during RC-PSSROT conformational adaptation. More...

double	getNewRingClosuresQuality ()
	Return the overal evaluation of the whole list of RingClosures. More...

double	getAtomOverlapScore ()
	Return the atoms overlap score which is calculated for all atoms pairs not in 1-4 or lower relationship. More...

String	getName ()
	Return the name of this molecule. More...

void	addBond (IAtom atmA, IAtom atmB, RingClosure nRc, BondType bndTyp)
	Modify the molecule adding a cyclic bond between two atoms. More...

void	purgeListRotatableBonds () throws DENOPTIMException
	Remove the cyclic bonds from the list of rotatable bonds. More...

ChemicalObjectModel	deepcopy () throws DENOPTIMException
	Return a new Molecule3DBuilder having exactly the same features of this Molecule3DBuilder. More...

Private Member Functions
void	findAttractors ()

void	convertRingsToRCACombinations ()

Private Attributes
DGraph	molGraph
	DENOPTIM representation. More...

IAtomContainer	fmol
	CDK representation. More...

TinkerMolecule	tmol
	Tinker internal coordinates representation. More...

String	molName
	Reference name. More...

ArrayList< RingClosingAttractor >	attractors
	List of Ring Closing Attractors. More...

Map< RingClosingAttractor, Integer >	attToAtmID
	Relation between RingClosingAttractor and atom ID. More...

ArrayList< Set< ObjectPair > >	allRCACombs
	List of combinations of RingClosingAttractors (i.e., possible set of rings to create) More...

ArrayList< ObjectPair >	rotatableBnds
	List of rotatable bonds. More...

ArrayList< RingClosure >	newRingClosures
	List of new ring closing environments. More...

double	overalRCScore = Double.NaN
	Quality score of the list of RingClosures. More...

double	atmOveralScore = Double.NaN
	Atom overlap score (for atoms not is 1-4 or lower relationship) More...

Logger	logger
	Program-specific logger. More...

ArrayList< Integer >	oldToNewOrder

ArrayList< Integer >	newToOldOrder

Detailed Description

Collector of molecular information, related to a single chemical object, that is deployed within the 3D builder.

Author: Marco Foscato

Definition at line 63 of file ChemicalObjectModel.java.

Constructor & Destructor Documentation

◆ ChemicalObjectModel() [1/3]

denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel ( )

Constructs an empty item.

Definition at line 135 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.deepcopy().

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◆ ChemicalObjectModel() [2/3]

denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel	(	DGraph	molGraph,
		IAtomContainer	fmol,
		TinkerMolecule	tmol,
		String	molName,
		ArrayList< ObjectPair >	rotatableBnds,
		ArrayList< RingClosingAttractor >	attractors,
		Map< RingClosingAttractor, Integer >	attToAtmID,
		ArrayList< Set< ObjectPair > >	allRCACombs,
		ArrayList< RingClosure >	ringClosures,
		ArrayList< Integer >	oldToNewOrder,
		ArrayList< Integer >	newToOldOrder,
		Logger	logger
	)

Constructs an item specifying all its features.

Parameters

molGraph	the graph representation
fmol	the CDK molecular representation
tmol	the internal coordinates representation
molName	the reference name of this molecule
rotatableBnds	the list of rotatable bonds (as pairs of atom indexes)
attractors	all the ring closing attractors (RCA)
attToAtmID	the correspondence between RCA and atom index
allRCACombs	all combinations of compatible pairs of RCAs
ringClosures	the list of closed multi-fragment rings
logger	the tool to use for logging.

Definition at line 168 of file ChemicalObjectModel.java.

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◆ ChemicalObjectModel() [3/3]

denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel	(	DGraph	molGraph,
		IAtomContainer	fmol,
		TinkerMolecule	tmol,
		String	molName,
		ArrayList< ObjectPair >	rotatableBnds,
		ArrayList< Integer >	oldToNewOrder,
		ArrayList< Integer >	newToOldOrder,
		Logger	logger
	)		throws DENOPTIMException

Constructs a Molecule3DBuilder specifying all its features.

Parameters

molGraph	the graph representation
fmol	the CDK molecular representation
tmol	the internal coordinates representation
molName	the reference name of this molecule
rotatableBnds	the list of rotatable bonds (as pairs of atom
oldToNewOrder	indexes that allow to map the atom position before and after the reordering neede to make use of internal coordinates possible.
newToOldOrder	indexes that allow to map the atom position before and after the reordering neede to make use of internal coordinates possible.
logger	the tool dealing with log messages. indexes)

Definition at line 224 of file ChemicalObjectModel.java.

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Member Function Documentation

◆ addBond()

void denoptim.molecularmodeling.ChemicalObjectModel.addBond	(	IAtom	atmA,
		IAtom	atmB,
		RingClosure	nRc,
		BondType	bndTyp
	)

Modify the molecule adding a cyclic bond between two atoms.

This method is ONLY meant to add new cyclic bonds and requires that the pair of involved atoms comes with the object RingClosure.

Parameters

atmA	the first atom
atmA	the second atom
nRc	the RingClosure object describing the ring-closing arrangement of atoms.

Definition at line 670 of file ChemicalObjectModel.java.

References denoptim.integration.tinker.TinkerMolecule.addBond(), denoptim.molecularmodeling.ChemicalObjectModel.fmol, denoptim.graph.Edge.BondType.getCDKOrder(), denoptim.graph.Edge.BondType.hasCDKAnalogue(), and denoptim.molecularmodeling.ChemicalObjectModel.logger.

Referenced by denoptim.molecularmodeling.RingClosureTool.closeRings().

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◆ convertRingsToRCACombinations()

void denoptim.molecularmodeling.ChemicalObjectModel.convertRingsToRCACombinations ( )

private

Definition at line 290 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.allRCACombs, denoptim.molecularmodeling.ChemicalObjectModel.attractors, and denoptim.graph.rings.RingClosingAttractor.getRingUser().

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel().

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◆ deepcopy()

ChemicalObjectModel denoptim.molecularmodeling.ChemicalObjectModel.deepcopy ( ) throws DENOPTIMException

Return a new Molecule3DBuilder having exactly the same features of this Molecule3DBuilder.

Exceptions

DENOPTIMException

Definition at line 751 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.attractors, denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.graph.DGraph.clone(), denoptim.integration.tinker.TinkerMolecule.clone(), denoptim.integration.tinker.TinkerMolecule.deepCopy(), denoptim.molecularmodeling.ChemicalObjectModel.getAtmIdOfRCA(), denoptim.molecularmodeling.ChemicalObjectModel.logger, denoptim.molecularmodeling.ChemicalObjectModel.molName, denoptim.molecularmodeling.ChemicalObjectModel.newToOldOrder, and denoptim.molecularmodeling.ChemicalObjectModel.oldToNewOrder.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptAllRingClosures(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ findAttractors()

void denoptim.molecularmodeling.ChemicalObjectModel.findAttractors ( )

private

Definition at line 274 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.attractors, denoptim.molecularmodeling.ChemicalObjectModel.attToAtmID, denoptim.molecularmodeling.ChemicalObjectModel.fmol, and denoptim.graph.rings.RingClosingAttractor.isAttractor().

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel().

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◆ getAtmIdOfRCA()

int denoptim.molecularmodeling.ChemicalObjectModel.getAtmIdOfRCA ( RingClosingAttractor rca )

Returns the CDK atom number, 0 to (n-1), of the given RingClosingAttractor.

Definition at line 521 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.attToAtmID.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.deepcopy().

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◆ getAtomOverlapScore()

double denoptim.molecularmodeling.ChemicalObjectModel.getAtomOverlapScore ( )

Return the atoms overlap score which is calculated for all atoms pairs not in 1-4 or lower relationship.

Definition at line 613 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.atmOveralScore, denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, and denoptim.molecularmodeling.ChemicalObjectModel.fmol.

Referenced by denoptim.molecularmodeling.RingClosureTool.RingClosedMolComparator.compare().

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◆ getAttractor()

RingClosingAttractor denoptim.molecularmodeling.ChemicalObjectModel.getAttractor ( int i )

Returns the attractor given its position in the list of attractors.

Definition at line 509 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.attractors.

◆ getAttractorsList()

ArrayList< RingClosingAttractor > denoptim.molecularmodeling.ChemicalObjectModel.getAttractorsList ( )

Returns the list of RuingClosingAttractors.

Definition at line 498 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.attractors.

◆ getGraph()

DGraph denoptim.molecularmodeling.ChemicalObjectModel.getGraph ( )

Returns the graph representation of this molecule as it was originally generated by DEOPTIM.

No change is expected after ring-closing step

Definition at line 465 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.molGraph.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getIAtomContainer()

IAtomContainer denoptim.molecularmodeling.ChemicalObjectModel.getIAtomContainer ( )

Returns the CDK representation of the molecular system.

Definition at line 476 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.fmol.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptAllRingClosures(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getName()

String denoptim.molecularmodeling.ChemicalObjectModel.getName ( )

Return the name of this molecule.

Definition at line 653 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.molName.

◆ getNewRingClosures()

ArrayList< RingClosure > denoptim.molecularmodeling.ChemicalObjectModel.getNewRingClosures ( )

Return the list of RingClosures that have been identified as closable head/tail of atom chains during RC-PSSROT conformational adaptation.

Definition at line 581 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.newRingClosures.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptAllRingClosures(), and denoptim.molecularmodeling.RingClosureTool.RingClosedMolComparator.compare().

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◆ getNewRingClosuresQuality()

double denoptim.molecularmodeling.ChemicalObjectModel.getNewRingClosuresQuality ( )

Return the overal evaluation of the whole list of RingClosures.

Definition at line 592 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.newRingClosures, and denoptim.molecularmodeling.ChemicalObjectModel.overalRCScore.

Referenced by denoptim.molecularmodeling.RingClosureTool.RingClosedMolComparator.compare().

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◆ getNewToOldOrder()

List< Integer > denoptim.molecularmodeling.ChemicalObjectModel.getNewToOldOrder ( )

Definition at line 267 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.newToOldOrder.

◆ getNumberRotatableBonds()

int denoptim.molecularmodeling.ChemicalObjectModel.getNumberRotatableBonds ( )

Returns the size of the current list of rotatable bonds.

Definition at line 569 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.rotatableBnds.

◆ getOldToNewOrder()

List< Integer > denoptim.molecularmodeling.ChemicalObjectModel.getOldToNewOrder ( )

Definition at line 260 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.oldToNewOrder.

◆ getRCACombinations()

ArrayList< Set< ObjectPair > > denoptim.molecularmodeling.ChemicalObjectModel.getRCACombinations ( )

Returns the list of combinations of RingClosingAttractor.

This method require that there are Rings in the DGraph representation of this object.

Definition at line 547 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.allRCACombs.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptAllRingClosures(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getRotatableBonds()

ArrayList< ObjectPair > denoptim.molecularmodeling.ChemicalObjectModel.getRotatableBonds ( )

Returns the list of rotatable bonds.

Definition at line 558 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.rotatableBnds.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getTinkerMolecule()

TinkerMolecule denoptim.molecularmodeling.ChemicalObjectModel.getTinkerMolecule ( )

Returns the Tinker Internal Coordination representation of the molecule.

Definition at line 487 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.tmol.

◆ getTnkAtmIdOfRCA()

int denoptim.molecularmodeling.ChemicalObjectModel.getTnkAtmIdOfRCA ( RingClosingAttractor rca )

Returns the Tinker atom number, 1 to n,of the given RingClosingAttractor.

Definition at line 533 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.attToAtmID.

◆ purgeListRotatableBonds()

void denoptim.molecularmodeling.ChemicalObjectModel.purgeListRotatableBonds ( ) throws DENOPTIMException

Remove the cyclic bonds from the list of rotatable bonds.

Exceptions

DENOPTIMException

Definition at line 706 of file ChemicalObjectModel.java.

References denoptim.molecularmodeling.ChemicalObjectModel.fmol, denoptim.molecularmodeling.ChemicalObjectModel.logger, and denoptim.molecularmodeling.ChemicalObjectModel.rotatableBnds.

◆ updateXYZFromINT()

void denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT ( ) throws DENOPTIMException

Converts currently loaded internal coordinates into Cartesian overwriting the current XYZ.

Definition at line 325 of file ChemicalObjectModel.java.

References denoptim.utils.MathUtils.distance(), denoptim.constants.DENOPTIMConstants.FLOATCOMPARISONTOLERANCE, denoptim.molecularmodeling.ChemicalObjectModel.fmol, denoptim.integration.tinker.TinkerMolecule.getAtom(), denoptim.integration.tinker.TinkerAtom.getAtomNeighbours(), denoptim.integration.tinker.TinkerAtom.getDistAngle(), denoptim.molecularmodeling.ChemicalObjectModel.logger, denoptim.integration.tinker.TinkerAtom.moveTo(), denoptim.utils.MathUtils.normDist(), and denoptim.molecularmodeling.ChemicalObjectModel.tmol.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel().

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Member Data Documentation

◆ allRCACombs

ArrayList<Set<ObjectPair> > denoptim.molecularmodeling.ChemicalObjectModel.allRCACombs

private

List of combinations of RingClosingAttractors (i.e., possible set of rings to create)

Definition at line 99 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.convertRingsToRCACombinations(), and denoptim.molecularmodeling.ChemicalObjectModel.getRCACombinations().

◆ atmOveralScore

double denoptim.molecularmodeling.ChemicalObjectModel.atmOveralScore = Double.NaN

private

Atom overlap score (for atoms not is 1-4 or lower relationship)

Definition at line 119 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.getAtomOverlapScore().

◆ attractors

ArrayList<RingClosingAttractor> denoptim.molecularmodeling.ChemicalObjectModel.attractors

private

List of Ring Closing Attractors.

Definition at line 88 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.convertRingsToRCACombinations(), denoptim.molecularmodeling.ChemicalObjectModel.deepcopy(), denoptim.molecularmodeling.ChemicalObjectModel.findAttractors(), denoptim.molecularmodeling.ChemicalObjectModel.getAttractor(), and denoptim.molecularmodeling.ChemicalObjectModel.getAttractorsList().

◆ attToAtmID

Map<RingClosingAttractor,Integer> denoptim.molecularmodeling.ChemicalObjectModel.attToAtmID

private

Relation between RingClosingAttractor and atom ID.

Definition at line 93 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.findAttractors(), denoptim.molecularmodeling.ChemicalObjectModel.getAtmIdOfRCA(), and denoptim.molecularmodeling.ChemicalObjectModel.getTnkAtmIdOfRCA().

◆ fmol

IAtomContainer denoptim.molecularmodeling.ChemicalObjectModel.fmol

private

CDK representation.

Definition at line 73 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.addBond(), denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.findAttractors(), denoptim.molecularmodeling.ChemicalObjectModel.getAtomOverlapScore(), denoptim.molecularmodeling.ChemicalObjectModel.getIAtomContainer(), denoptim.molecularmodeling.ChemicalObjectModel.purgeListRotatableBonds(), and denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT().

◆ logger

Logger denoptim.molecularmodeling.ChemicalObjectModel.logger

private

Program-specific logger.

Definition at line 124 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.addBond(), denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.deepcopy(), denoptim.molecularmodeling.ChemicalObjectModel.purgeListRotatableBonds(), and denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT().

◆ molGraph

DGraph denoptim.molecularmodeling.ChemicalObjectModel.molGraph

private

DENOPTIM representation.

Definition at line 68 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), and denoptim.molecularmodeling.ChemicalObjectModel.getGraph().

◆ molName

String denoptim.molecularmodeling.ChemicalObjectModel.molName

private

Reference name.

Definition at line 83 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.deepcopy(), and denoptim.molecularmodeling.ChemicalObjectModel.getName().

◆ newRingClosures

ArrayList<RingClosure> denoptim.molecularmodeling.ChemicalObjectModel.newRingClosures

private

List of new ring closing environments.

Definition at line 109 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.getNewRingClosures(), and denoptim.molecularmodeling.ChemicalObjectModel.getNewRingClosuresQuality().

◆ newToOldOrder

ArrayList<Integer> denoptim.molecularmodeling.ChemicalObjectModel.newToOldOrder

private

Definition at line 127 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.deepcopy(), and denoptim.molecularmodeling.ChemicalObjectModel.getNewToOldOrder().

◆ oldToNewOrder

ArrayList<Integer> denoptim.molecularmodeling.ChemicalObjectModel.oldToNewOrder

private

Definition at line 126 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.deepcopy(), and denoptim.molecularmodeling.ChemicalObjectModel.getOldToNewOrder().

◆ overalRCScore

double denoptim.molecularmodeling.ChemicalObjectModel.overalRCScore = Double.NaN

private

Quality score of the list of RingClosures.

Definition at line 114 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.getNewRingClosuresQuality().

◆ rotatableBnds

ArrayList<ObjectPair> denoptim.molecularmodeling.ChemicalObjectModel.rotatableBnds

private

List of rotatable bonds.

Definition at line 104 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.getNumberRotatableBonds(), denoptim.molecularmodeling.ChemicalObjectModel.getRotatableBonds(), and denoptim.molecularmodeling.ChemicalObjectModel.purgeListRotatableBonds().

◆ tmol

TinkerMolecule denoptim.molecularmodeling.ChemicalObjectModel.tmol

private

Tinker internal coordinates representation.

Definition at line 78 of file ChemicalObjectModel.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), denoptim.molecularmodeling.ChemicalObjectModel.getTinkerMolecule(), and denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT().

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

/github/workspace/src/main/java/denoptim/molecularmodeling/ChemicalObjectModel.java

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ChemicalObjectModel() [1/3]

◆ ChemicalObjectModel() [2/3]

◆ ChemicalObjectModel() [3/3]

Member Function Documentation

◆ addBond()

◆ convertRingsToRCACombinations()

◆ deepcopy()

◆ findAttractors()

◆ getAtmIdOfRCA()

◆ getAtomOverlapScore()

◆ getAttractor()

◆ getAttractorsList()

◆ getGraph()

◆ getIAtomContainer()

◆ getName()

◆ getNewRingClosures()

◆ getNewRingClosuresQuality()

◆ getNewToOldOrder()

◆ getNumberRotatableBonds()

◆ getOldToNewOrder()

◆ getRCACombinations()

◆ getRotatableBonds()

◆ getTinkerMolecule()

◆ getTnkAtmIdOfRCA()

◆ purgeListRotatableBonds()

◆ updateXYZFromINT()

Member Data Documentation

◆ allRCACombs

◆ atmOveralScore

◆ attractors

◆ attToAtmID

◆ fmol

◆ logger

◆ molGraph

◆ molName

◆ newRingClosures

◆ newToOldOrder

◆ oldToNewOrder

◆ overalRCScore

◆ rotatableBnds

◆ tmol