denoptim.graph.APClass Class Reference

Inheritance diagram for denoptim.graph.APClass:

Collaboration diagram for denoptim.graph.APClass:

Classes
class	APClassDeserializer

Public Member Functions
	APClass ()
	Constructor for an empty APClass. More...
String	getRule ()
int	getSubClass ()
BondType	getBondType ()
String	toString ()
	Do not use this to make SDF representations. More...
String	toSDFString ()
boolean	isCPMapCompatibleWith (APClass other, FragmentSpace fragSpace)
	Check compatibility as defined in the compatibility matrix considering this AP as source and the other as target. More...
int	compareTo (APClass o)
APClass	clone ()
	WARNING: this method does NOT clone! It just returns the reference to this. More...
boolean	equals (Object o)

Static Public Member Functions
static APClass	make (String ruleAndSubclass) throws DENOPTIMException
	Creates an APClass if it does not exist already, or returns the reference to the existing instance. More...
static APClass	make (String rule, int subClass) throws DENOPTIMException
	Constructor for an APClass with default bond type (i.e., BondType#DEFAULTBT). More...
static APClass	make (String ruleAndSubclass, BondType bt) throws DENOPTIMException
	Constructor for a fully defined APClass. More...
static APClass	make (String rule, int subClass, BondType bt) throws DENOPTIMException
	Constructor for a fully defined APClass. More...
static List< String >	getAllAPClassesAsString ()
	Returns the list of the names of all APClasses. More...
static boolean	isValidAPSubCLassString (String s)
	Evaluate the given string as a candidate for attachment point subclass, i.e., the attachment point class component discriminating the two sides of a bond being broken to yield two attachment points. More...
static boolean	isValidAPRuleString (String s)
	Evaluates the given string as a candidate attachment point rule, i.e., as name of a fragmentation rule that generates attachment points. More...
static boolean	isValidAPClassString (String s)
	Evaluate is a candidate string can be used as APClass. More...

Static Public Attributes
static Set< APClass >	uniqueAPClasses = new HashSet<APClass>()
	Set unique APClasses. More...
static final String	ATPLUS = "ATplus"
	String defining a conventional APClass. More...
static final String	ATMINUS = "ATminus"
	String defining a conventional APClass. More...
static final String	ATNEUTRAL = "ATneutral"
	String defining a conventional APClass. More...
static final APClass	RCACLASSPLUS
	Conventional class of attachment points on ring-closing vertexes. More...
static final APClass	RCACLASSMINUS
	Conventional class of attachment points on ring-closing vertexes. More...
static final APClass	RCACLASSNEUTRAL
	Conventional class of attachment points on ring-closing vertexes. More...
static final BondType	DEFAULTBT = BondType.SINGLE
	Default bond type for all but APClasses of RCVs. More...

Private Member Functions
void	setBondType (BondType bt)
void	setRule (String rule)
void	setSubClass (int sumClass)

Static Private Member Functions
static APClass	getUnique (String rule, int subClass, BondType bt)
	Checks if there is already a instance with the given members, if not it created one. More...

Private Attributes
String	rule
	The main feature of the APClass. More...
int	subClass
	The secondary feature of the APClass. More...
BondType	bndTyp = DEFAULTBT
	Bond type to use when converting edge users into formal bonds. More...

Static Private Attributes
static final Object	uniqueAPClassesLock = new Object()
	Synchronization lock. More...

Detailed Description

Definition at line 40 of file APClass.java.

Constructor & Destructor Documentation

APClass()

denoptim.graph.APClass.APClass

(

)

Constructor for an empty APClass.

Definition at line 116 of file APClass.java.

Referenced by denoptim.graph.APClass.getUnique().

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Member Function Documentation

clone()

APClass denoptim.graph.APClass.clone

(

)

WARNING: this method does NOT clone! It just returns the reference to this.

We have this method to avoid any attempt to actual cloning of an APClass.

Definition at line 481 of file APClass.java.

Referenced by denoptim.graph.AttachmentPoint.clone().

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compareTo()

int denoptim.graph.APClass.compareTo

(

APClass

o

)

Definition at line 463 of file APClass.java.

References denoptim.graph.APClass.rule, and denoptim.graph.APClass.subClass.

Referenced by denoptim.graph.AttachmentPoint.comparePropertiesTo(), and denoptim.graph.Fragment.identifySymmetryRelatedAPSets().

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equals()

boolean denoptim.graph.APClass.equals

(

Object

o

)

Definition at line 488 of file APClass.java.

Referenced by denoptim.ga.GraphOperations.addRing(), denoptim.fragspace.FragmentSpace.getCappingGroupsWithAPClass(), denoptim.fragspace.FragmentSpace.getCappingVertexWithAPClass(), denoptim.programs.fragmenter.CuttingRule.getComplementaryAPClass(), denoptim.fragspace.FragmentSpace.getRCVsWithAPClass(), and denoptim.graph.APClassTest.testEquals().

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getAllAPClassesAsString()

static List< String > denoptim.graph.APClass.getAllAPClassesAsString ( )

static

Returns the list of the names of all APClasses.

Returns

Definition at line 303 of file APClass.java.

References denoptim.graph.APClass.uniqueAPClasses.

Referenced by denoptim.gui.GUIVertexInspector.choseOrCreateNewAPClass().

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getBondType()

BondType denoptim.graph.APClass.getBondType

(

)

Returns

the bond type associated with this APClass

Definition at line 341 of file APClass.java.

References denoptim.graph.APClass.bndTyp.

Referenced by denoptim.graph.AttachmentPoint.getBondType(), denoptim.graph.DGraph.removeSingleVertexAndWeld(), denoptim.graph.AttachmentPointTest.testParsingofSdfAPString(), and denoptim.graph.simplified.UndirectedEdge.UndirectedEdge().

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getRule()

String denoptim.graph.APClass.getRule

(

)

Returns

the main part of this APClass, which typically corresponds to name of the fragmentation rule that generated attachment point with this APClass.

Definition at line 321 of file APClass.java.

References denoptim.graph.APClass.rule.

Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.CompatibilityRuleLine().

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getSubClass()

int denoptim.graph.APClass.getSubClass

(

)

Returns

the secondary part of this APClass, which typically corresponds to the discriminating factor that distinguishes between asymmetric fragments.

Definition at line 332 of file APClass.java.

References denoptim.graph.APClass.subClass.

getUnique()

static APClass denoptim.graph.APClass.getUnique ( String  rule, int  subClass, BondType  bt  )

staticprivate

Checks if there is already a instance with the given members, if not it created one.

In either case, returns the reference to that instance of APClass.

Parameters

rule
subClass

Returns

reference to the APClass instance with the given members.

Definition at line 242 of file APClass.java.

References denoptim.graph.APClass.APClass(), denoptim.graph.APClass.bndTyp, denoptim.graph.rings.RingClosingAttractor.RCAAPCLASSSET, denoptim.graph.APClass.rule, denoptim.graph.APClass.setBondType(), denoptim.graph.APClass.setRule(), denoptim.graph.APClass.setSubClass(), denoptim.graph.APClass.subClass, denoptim.graph.APClass.uniqueAPClasses, and denoptim.graph.APClass.uniqueAPClassesLock.

Referenced by denoptim.graph.APClass.APClassDeserializer.deserialize(), and denoptim.graph.APClass.make().

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isCPMapCompatibleWith()

boolean denoptim.graph.APClass.isCPMapCompatibleWith	(	APClass	other,
		FragmentSpace	fragSpace
	)

Check compatibility as defined in the compatibility matrix considering this AP as source and the other as target.

Parameters

other	AP.
the	fragment space that defines APClass compatibility rules.

Returns

true is APs of these two classes are allowed to form new vertex-vertex connections where this AP is source and other is target.

Definition at line 455 of file APClass.java.

References denoptim.fragspace.FragmentSpace.getCompatibleAPClasses().

Referenced by denoptim.fragspace.APMapFinder.findMappingCompatibileAPs(), denoptim.fragspace.GraphLinkFinder.GraphLinkFinder(), denoptim.ga.GraphOperations.isCrossoverPossible(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithClass(), and denoptim.fragspace.FragmentSpaceTest.testGetFragAPsCompatibleWithTheseAPs().

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isValidAPClassString()

static boolean denoptim.graph.APClass.isValidAPClassString ( String  s )

static

Evaluate is a candidate string can be used as APClass.

This method checks whether the string reflects the expected syntax of an APClass string

Returns

true if the given string can be used as attachment point class.

Definition at line 412 of file APClass.java.

References denoptim.graph.APClass.isValidAPRuleString(), denoptim.graph.APClass.isValidAPSubCLassString(), and denoptim.constants.DENOPTIMConstants.SEPARATORAPPROPSCL.

Referenced by denoptim.gui.GUIAPClassDefinitionDialog.GUIAPClassDefinitionDialog(), and denoptim.graph.APClass.make().

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isValidAPRuleString()

static boolean denoptim.graph.APClass.isValidAPRuleString ( String  s )

static

Evaluates the given string as a candidate attachment point rule, i.e., as name of a fragmentation rule that generates attachment points.

Parameters

s	the string to evaluate

Returns

true if the given string can be used as attachment point rule.

Definition at line 396 of file APClass.java.

Referenced by denoptim.gui.GUIVertexInspector.ensureGoodAPRuleString(), denoptim.graph.APClass.isValidAPClassString(), denoptim.graph.APClass.make(), and denoptim.graph.APClassTest.testIsValidAPRuleString().

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isValidAPSubCLassString()

static boolean denoptim.graph.APClass.isValidAPSubCLassString ( String  s )

static

Evaluate the given string as a candidate for attachment point subclass, i.e., the attachment point class component discriminating the two sides of a bond being broken to yield two attachment points.

Parameters

s	the string to evaluate

Returns

true if the given string can be used as

Definition at line 381 of file APClass.java.

Referenced by denoptim.graph.APClass.isValidAPClassString(), and denoptim.graph.APClassTest.testIsValidAPSubCLassString().

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make() [1/4]

static APClass denoptim.graph.APClass.make ( String  rule, int  subClass  ) throws DENOPTIMException

static

Constructor for an APClass with default bond type (i.e., BondType#DEFAULTBT).

Checks if there is already a instance with the given rule name and subclass, if not it created one. In either case, returns the reference to that instance of APClass. This method does not define the bond type that should be used to make bonds when using the attachment point belonging to the specified class. Therefore, it creates an incomplete class definition. To create a complete one, use make(String, int, BondType).

Parameters

rule	the APClass rule, i.e., a string identifier that typically corresponds to the name of the cutting rule used to break a bond.
subClass	the integer identifier of the "side" of the bond broken to make an attachment point.

Exceptions

DENOPTIMException

Definition at line 169 of file APClass.java.

References denoptim.graph.APClass.DEFAULTBT, denoptim.graph.APClass.make(), denoptim.graph.APClass.rule, and denoptim.graph.APClass.subClass.

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make() [2/4]

static APClass denoptim.graph.APClass.make ( String  rule, int  subClass, BondType  bt  ) throws DENOPTIMException

static

Constructor for a fully defined APClass.

Checks if there is already a instance with the given members, if not it created one. In either case, returns the reference to that instance of APClass.

Parameters

rule	the APClass rule, i.e., a string identifier that typically corresponds to the name of the cutting rule used to break a bond.
subClass	the integer identifier of the "side" of the bond broken to make an attachment point.
bt	the bond type to be used when converting edges using APs of this APClass into bonds, if any.

Exceptions

DENOPTIMException

Definition at line 221 of file APClass.java.

References denoptim.graph.APClass.getUnique(), denoptim.graph.APClass.isValidAPRuleString(), denoptim.graph.APClass.rule, and denoptim.graph.APClass.subClass.

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make() [3/4]

static APClass denoptim.graph.APClass.make ( String  ruleAndSubclass ) throws DENOPTIMException

static

Creates an APClass if it does not exist already, or returns the reference to the existing instance.

This method does not define the bond type that should be used to make bonds when using the attachment point belonging to the specified class. Therefore, it creates an incomplete class definition. To create a complete one, use make(String, int, BondType).

Parameters

ruleAndSubclass

the string representing the APClass name in terms of 'rule' and 'subclass', where the first is typically the name of the cutting rule that generated the attachment point, and the second is the integer desymmetrizing the two attachment points created by braking asymmetric bonds.

Exceptions

DENOPTIMException

when syntax of the string is not correct.

Definition at line 136 of file APClass.java.

References denoptim.graph.APClass.isValidAPClassString(), denoptim.graph.APClass.make(), and denoptim.constants.DENOPTIMConstants.SEPARATORAPPROPSCL.

Referenced by denoptim.ga.EAUtils.appendVertexesToGraphFollowingEdges(), denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.gui.GUIVertexInspector.choseOrCreateNewAPClass(), denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.CompatibilityRuleLine(), denoptim.gui.GUIVertexInspector.convertAtomToAP(), denoptim.programs.fragmenter.CuttingRule.CuttingRule(), denoptim.graph.TemplateTest.getAmideFragment(), denoptim.graph.TemplateTest.getCH2Fragment(), denoptim.graph.TemplateTest.getOHFragment(), denoptim.gui.GUIEmptyVertexMaker.GUIEmptyVertexMaker(), denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), denoptim.graph.rings.RingClosureParameters.interpretKeyword(), denoptim.graph.APClass.make(), denoptim.graph.FragmentTest.makeFragment(), denoptim.graph.FragmentTest.makeFragmentA(), denoptim.graph.FragmentTest.makeFragmentB(), denoptim.graph.FragmentTest.makeFragmentC(), denoptim.graph.FragmentIsomorphismInspectorTest.makePathologicalFragment(), denoptim.graph.rings.PathSubGraphTest.makeTestGraphA(), denoptim.graph.rings.RingSizeManagerTest.makeTestGraphA(), denoptim.graph.DGraphTest.makeTestGraphA2(), denoptim.graph.rings.PathSubGraphTest.makeTestGraphB(), denoptim.fragspace.APMapFinderTest.prepare(), denoptim.fragspace.GraphLinkFinderTest.prepare(), denoptim.ga.EAUtilsTest.prepare(), denoptim.ga.GraphOperationsTest.prepare(), denoptim.ga.PopulationTest.prepare(), denoptim.graph.DGraphTest.prepare(), denoptim.graph.AttachmentPoint.processSdfString(), denoptim.io.DenoptimIO.readCompatibilityMatrix(), denoptim.io.DenoptimIO.readRCCompatibilityMatrix(), denoptim.graph.AttachmentPoint.setAPClass(), denoptim.ga.GraphOperationsTest.setUpClass(), denoptim.graph.TemplateTest.testAddAP_after_setInnerGraph_throwsException(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.graph.AttachmentPointTest.testClone(), denoptim.graph.VertexTest.testClone(), denoptim.fragmenter.FragmentClustererTest.testCluster(), denoptim.fragmenter.FragmentClustererTest.testCluster2(), denoptim.graph.APClassTest.testCompareTo(), denoptim.graph.AttachmentPointTest.testConstructorsAndSDFString(), denoptim.graph.AttachmentPointTest.testConstructorsAndSDFStringNoDirVec(), denoptim.molecularmodeling.ThreeDimTreeBuilderTest.testConversionTo3dTree(), denoptim.graph.FragmentTest.testConversionToIAC(), denoptim.graph.APClassTest.testEquals(), denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), denoptim.ga.GraphOperationsTest.testExtendGraph(), denoptim.fragmenter.ConformerExtractorTaskTest.testExtractClusterableFragments(), denoptim.fragmenter.FragmenterToolsTest.testFilterFragment(), denoptim.fragspace.APMapFinderTest.testFindMappingCompatibileAPs(), denoptim.graph.DGraphTest.testFindVertex(), denoptim.graph.VertexTest.testFromToJSON_withSymmetricAPs(), denoptim.fragmenter.DynamicCentroidClusterTest.testGetCentroid(), denoptim.graph.AttachmentPointTest.testGetLinkedAP(), denoptim.fragmenter.FragmentAlignementTest.testGetMinimumRMSD(), denoptim.fragmenter.DynamicCentroidClusterTest.testGetNearestToCentroid(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass(), denoptim.graph.SymmetricAPsTest.testGetSameAsThis(), denoptim.fragmenter.ClusterableFragmentTest.testGetTransformedCopy(), denoptim.graph.FragmentTest.testHandlingAPsAsObjOrProperty(), denoptim.graph.AttachmentPointTest.testHasConnectedSrcAtom(), denoptim.graph.AttachmentPointTest.testHasSameSrcAtom(), denoptim.io.DenoptimIOTest.testIOEmptyVertex(), denoptim.graph.AttachmentPointTest.testIsSrcInUser(), denoptim.graph.APClassTest.testListContains(), denoptim.io.DenoptimIOTest.testReadAllAPClasses(), denoptim.graph.DGraphTest.testRemoveUnusedRCVs(), denoptim.graph.SymmetricAPsTest.testSameAs(), denoptim.graph.AttachmentPointTest.testSameAs_DiffAPClass(), denoptim.graph.TemplateTest.testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs(), denoptim.fragmenter.ClusterableFragmentTest.testSetNaturalNodeOrder(), denoptim.graph.AttachmentPointTest.testSortAPs(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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make() [4/4]

static APClass denoptim.graph.APClass.make ( String  ruleAndSubclass, BondType  bt  ) throws DENOPTIMException

static

Constructor for a fully defined APClass.

Checks if there is already a instance with the given members, if not it created one. In either case, returns the reference to that instance of APClass.

Parameters

ruleAndSubclass	the string representing the APClass name in terms of 'rule' and 'subclass', where the first is typically the name of the cutting rule that generated the attachment point, and the second is the integer desymmetrizing the two attachment points created by braking asymmetric bonds.
bt	the bond type to be used when converting edges using APs of this APClass into bonds, if any.

Exceptions

DENOPTIMException

Definition at line 191 of file APClass.java.

References denoptim.graph.APClass.isValidAPClassString(), denoptim.graph.APClass.make(), and denoptim.constants.DENOPTIMConstants.SEPARATORAPPROPSCL.

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setBondType()

void denoptim.graph.APClass.setBondType ( BondType  bt )

private

Definition at line 281 of file APClass.java.

Referenced by denoptim.graph.APClass.getUnique().

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setRule()

void denoptim.graph.APClass.setRule ( String  rule )

private

Definition at line 287 of file APClass.java.

References denoptim.graph.APClass.rule.

Referenced by denoptim.graph.APClass.getUnique().

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setSubClass()

void denoptim.graph.APClass.setSubClass ( int  sumClass )

private

Definition at line 293 of file APClass.java.

Referenced by denoptim.graph.APClass.getUnique().

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toSDFString()

String denoptim.graph.APClass.toSDFString

(

)

Returns

a string with a format compatible with reporting APClasses in text files (e.g., compatibility matrix files) and SDF files (e.g., SDF with fragments).

Definition at line 364 of file APClass.java.

References denoptim.graph.APClass.bndTyp, denoptim.graph.APClass.rule, and denoptim.graph.APClass.subClass.

Referenced by denoptim.graph.AttachmentPoint.getSingleAPStringSDF().

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toString()

String denoptim.graph.APClass.toString

(

)

Do not use this to make SDF representations.

Use toSDFString() instead.

Returns

a string meant for human reading. E.g., "Rule:0".

Definition at line 352 of file APClass.java.

References denoptim.graph.APClass.rule, and denoptim.graph.APClass.subClass.

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.CompatibilityRuleLine(), denoptim.graph.FragIsomorphNode.FragIsomorphNode(), denoptim.graph.DGraph.hasForbiddenEnd(), denoptim.gui.GraphViewerPanel.JEdge.JEdge(), denoptim.gui.CompatibilityMatrixForm.TargetAPClassToken.matchesAPClass(), denoptim.graph.simplified.Node.Node(), denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.renderIfMatches(), and denoptim.gui.CompatibilityMatrixForm.TargetAPClassToken.TargetAPClassToken().

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Member Data Documentation

ATMINUS

final String denoptim.graph.APClass.ATMINUS = "ATminus"

static

String defining a conventional APClass.

Definition at line 73 of file APClass.java.

ATNEUTRAL

final String denoptim.graph.APClass.ATNEUTRAL = "ATneutral"

static

String defining a conventional APClass.

Definition at line 78 of file APClass.java.

ATPLUS

final String denoptim.graph.APClass.ATPLUS = "ATplus"

static

String defining a conventional APClass.

Definition at line 68 of file APClass.java.

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

bndTyp

BondType denoptim.graph.APClass.bndTyp = DEFAULTBT

private

Bond type to use when converting edge users into formal bonds.

Definition at line 104 of file APClass.java.

Referenced by denoptim.graph.APClass.getBondType(), denoptim.graph.APClass.getUnique(), and denoptim.graph.APClass.toSDFString().

DEFAULTBT

final BondType denoptim.graph.APClass.DEFAULTBT = BondType.SINGLE

static

Default bond type for all but APClasses of RCVs.

Definition at line 109 of file APClass.java.

Referenced by denoptim.graph.APClass.APClassDeserializer.deserialize(), denoptim.graph.AttachmentPoint.getBondType(), denoptim.gui.GUIAPClassDefinitionDialog.GUIAPClassDefinitionDialog(), denoptim.graph.APClass.make(), denoptim.graph.APClassTest.testListContains(), and denoptim.graph.AttachmentPointTest.testParsingofSdfAPString().

RCACLASSMINUS

final APClass denoptim.graph.APClass.RCACLASSMINUS

static

Initial value:

= getUnique(ATMINUS, 0, 
            BondType.ANY)

Conventional class of attachment points on ring-closing vertexes.

Polarized (-) case.

Definition at line 91 of file APClass.java.

Referenced by denoptim.ga.EAUtils.appendVertexesToGraphFollowingEdges(), denoptim.fragspace.FragmentSpace.getPolarizedRCV(), denoptim.graph.rings.RingSizeManagerTest.makeTestGraphA(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.molecularmodeling.ThreeDimTreeBuilderTest.testConversionTo3dTree(), denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass(), and denoptim.graph.DGraphTest.testRemoveUnusedRCVs().

RCACLASSNEUTRAL

final APClass denoptim.graph.APClass.RCACLASSNEUTRAL

static

Initial value:

= getUnique(ATNEUTRAL, 0, 
            BondType.ANY)

Conventional class of attachment points on ring-closing vertexes.

Unpolarized, neutral case.

Definition at line 98 of file APClass.java.

RCACLASSPLUS

final APClass denoptim.graph.APClass.RCACLASSPLUS

static

Initial value:

= getUnique(ATPLUS, 0, 
            BondType.ANY)

Conventional class of attachment points on ring-closing vertexes.

Polarized (+) case.

Definition at line 84 of file APClass.java.

Referenced by denoptim.fragspace.FragmentSpace.getPolarizedRCV(), denoptim.graph.rings.RingSizeManagerTest.makeTestGraphA(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.molecularmodeling.ThreeDimTreeBuilderTest.testConversionTo3dTree(), denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsForAPClass(), denoptim.fragspace.FragmentSpaceTest.testGetRCVsWithAPClass(), and denoptim.graph.DGraphTest.testRemoveUnusedRCVs().

rule

String denoptim.graph.APClass.rule

private

The main feature of the APClass.

This would usually correspond to the cutting rule that generated APs belonging to this class.

Definition at line 46 of file APClass.java.

Referenced by denoptim.graph.APClass.compareTo(), denoptim.graph.APClass.APClassDeserializer.deserialize(), denoptim.graph.APClass.getRule(), denoptim.graph.APClass.getUnique(), denoptim.graph.APClass.make(), denoptim.graph.APClass.setRule(), denoptim.graph.APClass.toSDFString(), and denoptim.graph.APClass.toString().

subClass

int denoptim.graph.APClass.subClass

private

The secondary feature of the APClass.

This would usually distinguish the two asymmetric sides of a bond but upon fragmentation

Definition at line 52 of file APClass.java.

Referenced by denoptim.graph.APClass.compareTo(), denoptim.graph.APClass.APClassDeserializer.deserialize(), denoptim.graph.APClass.getSubClass(), denoptim.graph.APClass.getUnique(), denoptim.graph.APClass.make(), denoptim.graph.APClass.toSDFString(), and denoptim.graph.APClass.toString().

uniqueAPClasses

Set<APClass> denoptim.graph.APClass.uniqueAPClasses = new HashSet<APClass>()

static

Set unique APClasses.

Definition at line 57 of file APClass.java.

Referenced by denoptim.graph.APClass.APClassDeserializer.deserialize(), denoptim.graph.APClass.getAllAPClassesAsString(), and denoptim.graph.APClass.getUnique().

uniqueAPClassesLock

final Object denoptim.graph.APClass.uniqueAPClassesLock = new Object()

staticprivate

Synchronization lock.

Used to guard alteration of the set of unique APClasses.

Definition at line 63 of file APClass.java.

Referenced by denoptim.graph.APClass.getUnique().

---

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

• /github/workspace/src/main/java/denoptim/graph/APClass.java