The RingClosingAttractor represent the available valence/connection that allows to close a ring. More...

Collaboration diagram for denoptim.graph.rings.RingClosingAttractor:

Public Member Functions
	RingClosingAttractor ()
	Constructor for an empty RingClosingAttractor. More...

	RingClosingAttractor (IAtom atm, IAtomContainer mol)
	Constructor for a `RingClosingAttractor` corresponding to an atom in an `IAtomContainer`. More...

boolean	isAttractor ()
	Checks whether the constructed RingClosingAttractor does corresponds to a RingClosingAttractor in the molecular representation. More...

boolean	isCompatible (RingClosingAttractor other)
	Evaluate compatibility between this RingClosingAttractor and another one. More...

String	getType ()
	Get the type of RingClosingAttractor. More...

IAtom	getIAtom ()
	Get the atom corresponding to this RingClosingAttractor in the molecular representation. More...

void	setIAtom (IAtom atm)
	Change the reference to the atom in the molecular representation. More...

IAtom	getSrcAtom ()
	Get the atom in the parent fragment that holds the attachment point occupied by this RingClosingAttractor. More...

APClass	getApClass ()
	Get the class of the Attachment Point occupied (i.e., in the parent fragment) by this RingClosingAttractor, if any. More...

BondType	getRCBondType ()
	Get the type of bond this attractor is meant to close. More...

Ring	getRingUser ()
	Get the reference to the graph representation of the ring this attractor is meant to close. More...

void	setUsed ()
	Set this RingClosingAttractor to 'used'. More...

boolean	isUsed ()
	Check if this RingClosingAttractor has been used to close a ring and is not available any more. More...

Double	getParamA11 ()

Double	getParamB11 ()

Double	getParamA12 ()

Double	getParamB12 ()

String	toString ()

Static Public Attributes
static final HashMap< APClass, String >	RCALABELPERAPCLASS
	Conventional labels for attractor pseudoatom. More...

static final Set< APClass >	RCAAPCLASSSET
	Recognized `APClass` for `RingClosingAttractor`. More...

static final Map< APClass, APClass >	RCAAPCMAP
	Recognized `APClass`es on `RingClosingAttractor` and compatible types. More...

static final Map< String, String >	RCATYPEMAP
	Recognized types of `RingClosingAttractor` and compatible types. More...

Package Attributes
final Map< String, Double >	paramAR11
	Parameter A for points in 1,1 relationship. More...

final Map< String, Double >	paramBR11
	Parameter B for points in 1,1 relationship. More...

final Map< String, Double >	paramAR12
	Parameter A for points in 1,2 relationship. More...

final Map< String, Double >	paramBR12
	Parameter B for points in 1,2 relationship. More...

Private Attributes
Double	attA11 = 0.0
	Parameter A for 1,1 interaction. More...

Double	attB11 = 0.0
	Parameter B for 1,1 interaction. More...

Double	attA12 = 0.0
	Parameter A for 1,2 interaction. More...

Double	attB12 = 0.0
	Parameter B for 1,2 interaction. More...

String	attType = "none"
	Type of this attractor. More...

IAtom	atm
	Pseudo atom representing RingClosingAttractor in molecule. More...

IAtom	src
	Atom hosting the RingClosingAttractor. More...

APClass	apClass
	Class of the Attachment Point represented by this RCA. More...

BondType	bndTyp
	Type of ring-closing bond that this ring-closing attractor is there to create. More...

Ring	ringUser
	Reference to the graph `Ring` that represent the intention to close a ring of vertices in DENOPTIM's graph representation of the chemical object. More...

boolean	used = false
	Flag: this RingClosingAttractor is used to close a ring. More...

Detailed Description

The RingClosingAttractor represent the available valence/connection that allows to close a ring.

The RingClosingAttractor is a fragment that has one real attachment point and a virtual one reserved for forming a new bond with another RingClosingAttractor that belongs to the same atom chain thus forming a ring.

Author: Marco Foscato

Definition at line 48 of file RingClosingAttractor.java.

Constructor & Destructor Documentation

◆ RingClosingAttractor() [1/2]

denoptim.graph.rings.RingClosingAttractor.RingClosingAttractor ( )

Constructor for an empty RingClosingAttractor.

Definition at line 258 of file RingClosingAttractor.java.

◆ RingClosingAttractor() [2/2]

denoptim.graph.rings.RingClosingAttractor.RingClosingAttractor	(	IAtom	atm,
		IAtomContainer	mol
	)

Constructor for a RingClosingAttractor corresponding to an atom in an IAtomContainer.

Note that any atom can be used to construct a RingClosingAttractor, but only the elemental symbol stored in RingClosingAttractor#RCATYPEMAP are recognized and trigger the perception of the candidate atom as a RingClosingAttractor. In which case the isAttractor() method will return true.

Parameters

atm	the atom candidate to become a `RingClosingAttractor`.
mol	the molecule containing the candidate atom.

Definition at line 279 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.atm, denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.graph.rings.RingClosingAttractor.isAttractor(), denoptim.graph.rings.RingClosingAttractor.paramAR11, denoptim.graph.rings.RingClosingAttractor.paramAR12, denoptim.graph.rings.RingClosingAttractor.paramBR11, denoptim.graph.rings.RingClosingAttractor.paramBR12, denoptim.constants.DENOPTIMConstants.RCAPROPAPCTORCA, denoptim.constants.DENOPTIMConstants.RCAPROPCHORDBNDTYP, denoptim.constants.DENOPTIMConstants.RCAPROPRINGUSER, and denoptim.graph.rings.RingClosingAttractor.RCATYPEMAP.

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Member Function Documentation

◆ getApClass()

APClass denoptim.graph.rings.RingClosingAttractor.getApClass ( )

Get the class of the Attachment Point occupied (i.e., in the parent fragment) by this RingClosingAttractor, if any.

Returns: the attachment point class

Definition at line 397 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.apClass.

◆ getIAtom()

IAtom denoptim.graph.rings.RingClosingAttractor.getIAtom ( )

Get the atom corresponding to this RingClosingAttractor in the molecular representation.

Returns: the dummy atom

Definition at line 359 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.atm.

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

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◆ getParamA11()

Double denoptim.graph.rings.RingClosingAttractor.getParamA11 ( )

Returns: the parameter A for interactions with atoms/RCA in 1,1 relationship.

Definition at line 459 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.attA11.

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

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◆ getParamA12()

Double denoptim.graph.rings.RingClosingAttractor.getParamA12 ( )

Returns: the parameter A for interactions with atoms/RCA in 1,2 relationship.

Definition at line 483 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.attA12.

◆ getParamB11()

Double denoptim.graph.rings.RingClosingAttractor.getParamB11 ( )

Returns: the parameter B for interactions with atoms/RCA in 1,1 relationship.

Definition at line 471 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.attB11.

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

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◆ getParamB12()

Double denoptim.graph.rings.RingClosingAttractor.getParamB12 ( )

Returns: the parameter B for interactions with atoms/RCA in 1,2 relationship.

Definition at line 495 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.attB12.

◆ getRCBondType()

BondType denoptim.graph.rings.RingClosingAttractor.getRCBondType ( )

Get the type of bond this attractor is meant to close.

Returns: the type of ring-closing bond.

Definition at line 409 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.bndTyp.

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

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◆ getRingUser()

Ring denoptim.graph.rings.RingClosingAttractor.getRingUser ( )

Get the reference to the graph representation of the ring this attractor is meant to close.

Returns: the ring in the graph representation, or null.

Definition at line 422 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.ringUser.

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

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◆ getSrcAtom()

IAtom denoptim.graph.rings.RingClosingAttractor.getSrcAtom ( )

Get the atom in the parent fragment that holds the attachment point occupied by this RingClosingAttractor.

Returns: the atom to which this attractor is attached

Definition at line 384 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.src.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.RingClosureTool.closeRings().

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◆ getType()

String denoptim.graph.rings.RingClosingAttractor.getType ( )

Get the type of RingClosingAttractor.

Returns: the type of RingClosingAttractor.

Definition at line 346 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.attType.

◆ isAttractor()

boolean denoptim.graph.rings.RingClosingAttractor.isAttractor ( )

Checks whether the constructed RingClosingAttractor does corresponds to a RingClosingAttractor in the molecular representation.

Returns: true if this is a real RingClosingAttractor

Definition at line 320 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.molecularmodeling.ChemicalObjectModel.findAttractors(), denoptim.utils.RingClosingUtils.findAttractors(), and denoptim.graph.rings.RingClosingAttractor.RingClosingAttractor().

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◆ isCompatible()

boolean denoptim.graph.rings.RingClosingAttractor.isCompatible ( RingClosingAttractor other )

Evaluate compatibility between this RingClosingAttractor and another one.

Returns: true is this and the other RingClosingAttractor are compatible.

Definition at line 333 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.attType, and denoptim.graph.rings.RingClosingAttractor.RCATYPEMAP.

Referenced by denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs().

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◆ isUsed()

boolean denoptim.graph.rings.RingClosingAttractor.isUsed ( )

Check if this RingClosingAttractor has been used to close a ring and is not available any more.

Returns: true if already used

Definition at line 447 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.used.

◆ setIAtom()

void denoptim.graph.rings.RingClosingAttractor.setIAtom ( IAtom atm )

Change the reference to the atom in the molecular representation.

Parameters

atm	the new reference

Definition at line 371 of file RingClosingAttractor.java.

References denoptim.graph.rings.RingClosingAttractor.atm.

◆ setUsed()

void denoptim.graph.rings.RingClosingAttractor.setUsed ( )

Set this RingClosingAttractor to 'used'.

Once the 'used' flag is set this RingClosingAttractor cannot be used to close rings any more

Definition at line 434 of file RingClosingAttractor.java.

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

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◆ toString()

String denoptim.graph.rings.RingClosingAttractor.toString ( )

Returns: the string representation of this attractor

Definition at line 506 of file RingClosingAttractor.java.

References denoptim.utils.MoleculeUtils.getSymbolOrLabel().

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Member Data Documentation

◆ apClass

APClass denoptim.graph.rings.RingClosingAttractor.apClass

private

Class of the Attachment Point represented by this RCA.

Definition at line 149 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getApClass().

◆ atm

IAtom denoptim.graph.rings.RingClosingAttractor.atm

private

Pseudo atom representing RingClosingAttractor in molecule.

Definition at line 139 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getIAtom(), denoptim.graph.rings.RingClosingAttractor.RingClosingAttractor(), and denoptim.graph.rings.RingClosingAttractor.setIAtom().

◆ attA11

Double denoptim.graph.rings.RingClosingAttractor.attA11 = 0.0

private

Parameter A for 1,1 interaction.

Definition at line 114 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getParamA11().

◆ attA12

Double denoptim.graph.rings.RingClosingAttractor.attA12 = 0.0

private

Parameter A for 1,2 interaction.

Definition at line 124 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getParamA12().

◆ attB11

Double denoptim.graph.rings.RingClosingAttractor.attB11 = 0.0

private

Parameter B for 1,1 interaction.

Definition at line 119 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getParamB11().

◆ attB12

Double denoptim.graph.rings.RingClosingAttractor.attB12 = 0.0

private

Parameter B for 1,2 interaction.

Definition at line 129 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getParamB12().

◆ attType

String denoptim.graph.rings.RingClosingAttractor.attType = "none"

private

Type of this attractor.

Definition at line 134 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getType(), and denoptim.graph.rings.RingClosingAttractor.isCompatible().

◆ bndTyp

BondType denoptim.graph.rings.RingClosingAttractor.bndTyp

private

Type of ring-closing bond that this ring-closing attractor is there to create.

Definition at line 155 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getRCBondType().

◆ paramAR11

final Map<String,Double> denoptim.graph.rings.RingClosingAttractor.paramAR11

package

Initial value:

= new HashMap<String,Double>() {
        
        private static final long serialVersionUID = 1L;
 
        {
            put("ATP", 1.0);
            put("ATM", 1.0);
            put("ATN", 1.0);
        };
    }

Parameter A for points in 1,1 relationship.

Definition at line 53 of file RingClosingAttractor.java.

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

◆ paramAR12

final Map<String,Double> denoptim.graph.rings.RingClosingAttractor.paramAR12

package

Initial value:

= new HashMap<String,Double>() {
        
        private static final long serialVersionUID = 1L;
        {
            put("ATP", 5.0);
            put("ATM", 5.0);
            put("ATN", 5.0);
        };
    }

Parameter A for points in 1,2 relationship.

Definition at line 84 of file RingClosingAttractor.java.

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

◆ paramBR11

final Map<String,Double> denoptim.graph.rings.RingClosingAttractor.paramBR11

package

Initial value:

= new HashMap<String,Double>() {
        
        private static final long serialVersionUID = 1L;
        {
            put("ATP", 1.0);
            put("ATM", 1.0);
            put("ATN", 1.0);
        };
    }

Parameter B for points in 1,1 relationship.

Definition at line 69 of file RingClosingAttractor.java.

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

◆ paramBR12

final Map<String,Double> denoptim.graph.rings.RingClosingAttractor.paramBR12

package

Initial value:

= new HashMap<String,Double>() {
        
        private static final long serialVersionUID = 1L;
        {
            put("ATP", 7.0);
            put("ATM", 7.0);
            put("ATN", 7.0);
        };  
    }

Parameter B for points in 1,2 relationship.

Definition at line 99 of file RingClosingAttractor.java.

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

◆ RCAAPCLASSSET

final Set<APClass> denoptim.graph.rings.RingClosingAttractor.RCAAPCLASSSET

static

Initial value:

= 
            new HashSet<APClass>(){
                
                private static final long serialVersionUID = 1L;
    
                {
                    add(APClass.RCACLASSPLUS);
                    add(APClass.RCACLASSMINUS);
                    add(APClass.RCACLASSNEUTRAL);
                }}

Recognized APClass for RingClosingAttractor.

Definition at line 193 of file RingClosingAttractor.java.

Referenced by denoptim.graph.Vertex.convertIACToVertex(), denoptim.graph.Fragment.Fragment(), denoptim.graph.APClass.getUnique(), and denoptim.graph.Vertex.newVertexFromLibrary().

◆ RCAAPCMAP

final Map<APClass,APClass> denoptim.graph.rings.RingClosingAttractor.RCAAPCMAP

static

Initial value:

=
            new HashMap<APClass,APClass>() 
    {
        
        private static final long serialVersionUID = 3L;
    
        {
            put(APClass.RCACLASSPLUS, APClass.RCACLASSMINUS);
            put(APClass.RCACLASSMINUS, APClass.RCACLASSPLUS);
            put(APClass.RCACLASSNEUTRAL, APClass.RCACLASSNEUTRAL);
        };
    }

Recognized APClasses on RingClosingAttractor and compatible types.

This is equivalent to RCATYPEMAP but is expressed in terms of APClass instead of pseudoatom label.

Definition at line 212 of file RingClosingAttractor.java.

Referenced by denoptim.ga.GraphOperations.addRing().

◆ RCALABELPERAPCLASS

final HashMap<APClass,String> denoptim.graph.rings.RingClosingAttractor.RCALABELPERAPCLASS

static

Initial value:

= 
            new HashMap<APClass,String>(){
                
                private static final long serialVersionUID = 1L;
    
            {
                try {
                    put(APClass.RCACLASSPLUS, "ATP");
                    put(APClass.RCACLASSMINUS, "ATM");
                    put(APClass.RCACLASSNEUTRAL, "ATN");
                } catch (Throwable t)
                {
                    
                }
            }}

Conventional labels for attractor pseudoatom.

Definition at line 172 of file RingClosingAttractor.java.

Referenced by denoptim.fragspace.FragmentSpace.getPolarizedRCV(), denoptim.fragmenter.FragmenterTools.getRCPForAP(), denoptim.graph.rings.RingSizeManagerTest.makeTestGraphA(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass(), and denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass().

◆ RCATYPEMAP

final Map<String,String> denoptim.graph.rings.RingClosingAttractor.RCATYPEMAP

static

Initial value:

=
            new HashMap<String,String>() 
    {
        
        private static final long serialVersionUID = 3L;
    
        {
            put(RCALABELPERAPCLASS.get(APClass.RCACLASSPLUS), 
                    RCALABELPERAPCLASS.get(APClass.RCACLASSMINUS));
            put(RCALABELPERAPCLASS.get(APClass.RCACLASSMINUS), 
                    RCALABELPERAPCLASS.get(APClass.RCACLASSPLUS));
            put(RCALABELPERAPCLASS.get(APClass.RCACLASSNEUTRAL), 
                    RCALABELPERAPCLASS.get(APClass.RCACLASSNEUTRAL));
        };
    }

Recognized types of RingClosingAttractor and compatible types.

This is equivalent to RingClosingAttractor#RCAAPCMAP but is expressed in terms of pseudoatom label. instead of APClass.

Definition at line 233 of file RingClosingAttractor.java.

Referenced by denoptim.graph.DGraph.checkConsistency(), denoptim.utils.ConnectedLigand.ConnectedLigand(), denoptim.graph.rings.RingClosingAttractor.isCompatible(), denoptim.utils.MoleculeUtils.removeRCA(), and denoptim.graph.rings.RingClosingAttractor.RingClosingAttractor().

◆ ringUser

Ring denoptim.graph.rings.RingClosingAttractor.ringUser

private

Reference to the graph Ring that represent the intention to close a ring of vertices in DENOPTIM's graph representation of the chemical object.

Definition at line 162 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getRingUser().

◆ src

IAtom denoptim.graph.rings.RingClosingAttractor.src

private

Atom hosting the RingClosingAttractor.

Definition at line 144 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.getSrcAtom().

◆ used

boolean denoptim.graph.rings.RingClosingAttractor.used = false

private

Flag: this RingClosingAttractor is used to close a ring.

Definition at line 167 of file RingClosingAttractor.java.

Referenced by denoptim.graph.rings.RingClosingAttractor.isUsed().

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

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

Public Member Functions

Static Public Attributes

Package Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RingClosingAttractor() [1/2]

◆ RingClosingAttractor() [2/2]

Member Function Documentation

◆ getApClass()

◆ getIAtom()

◆ getParamA11()

◆ getParamA12()

◆ getParamB11()

◆ getParamB12()

◆ getRCBondType()

◆ getRingUser()

◆ getSrcAtom()

◆ getType()

◆ isAttractor()

◆ isCompatible()

◆ isUsed()

◆ setIAtom()

◆ setUsed()

◆ toString()

Member Data Documentation

◆ apClass

◆ atm

◆ attA11

◆ attA12

◆ attB11

◆ attB12

◆ attType

◆ bndTyp

◆ paramAR11

◆ paramAR12

◆ paramBR11

◆ paramBR12

◆ RCAAPCLASSSET

◆ RCAAPCMAP

◆ RCALABELPERAPCLASS

◆ RCATYPEMAP

◆ ringUser

◆ src

◆ used