- a -

a : denoptim.ga.EAUtilsTest, denoptim.graph.DGraphTest
acceptUnsetToSingeBOApprox : denoptim.programs.fragmenter.FragmenterParameters
activeTabsAndRefs : denoptim.gui.MainToolBar
activeTabsMenu : denoptim.gui.MainToolBar
activeViewer : denoptim.gui.VertexViewPanel
actvSrcAps : denoptim.fragspace.FragsCombinationIterator
addExplicitH : denoptim.programs.fragmenter.FragmenterParameters
ADDFUSEDRING : denoptim.utils.MutationType
additionalDocForParameters : denoptim.gui.FitnessParametersForm
ADDLINK : denoptim.utils.MutationType
ADDRING : denoptim.utils.MutationType
addTemplatesToLibraries : denoptim.programs.fitnessevaluator.FRParameters
advOptsBlock : denoptim.gui.FSEParametersForm, denoptim.gui.GAParametersForm
alignIn3D : denoptim.molecularmodeling.ThreeDimTreeBuilder
ALL_ELEMENTS : denoptim.constants.DENOPTIMConstants
ALL_METALS : denoptim.constants.DENOPTIMConstants
allAPClasses : denoptim.gui.CompatibilityMatrixForm
allAPClsInCPMap : denoptim.gui.CompatibilityMatrixForm
allAPMappings : denoptim.fragspace.APMapFinder
allAPRules : denoptim.gui.CompatibilityMatrixForm
allBChekBoxes : denoptim.gui.ScrollableJPupupMenu
allCapAPClasses : denoptim.gui.CompatibilityMatrixForm
allCompatLinks : denoptim.fragspace.GraphLinkFinder
allCoords : denoptim.fragmenter.ClusterableFragment
allData : denoptim.utils.SizeControlledSet
allIndividuals : denoptim.gui.GUIInspectGARun
allItems : denoptim.gui.GUIInspectFSERun
allMatches : denoptim.utils.ManySMARTSQuery
ALLOWED_ELEMENTS : denoptim.constants.DENOPTIMConstants
ALLOWED_EXTENSIONS : denoptim.constants.DENOPTIMConstants
allowedBridgeLength : denoptim.fragmenter.BridgeHeadFindingRule
allowedMutationTypes : denoptim.graph.Vertex
allParams : denoptim.gui.GUIPrepare
allPossibleChainIDs : denoptim.graph.rings.PathSubGraph
allRCACombs : denoptim.molecularmodeling.ChemicalObjectModel
allSrcAps : denoptim.fragspace.FragsCombinationIterator
alteredAPData : denoptim.gui.FragmentViewPanel, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel, denoptim.gui.VertexViewPanel
angs : denoptim.graph.rings.CyclicGraphHandler.ClosableConf
ANY : denoptim.graph.Edge.BondType
ap : denoptim.gui.GraphViewerPanel.JVertex
AP : denoptim.gui.GraphViewerPanel.JVertexType
apA : denoptim.graph.RelatedAPPair, denoptim.graph.simplified.UndirectedEdge
apB : denoptim.graph.RelatedAPPair, denoptim.graph.simplified.UndirectedEdge
APC : denoptim.gui.GraphViewerPanel.LabelType
apc0 : denoptim.programs.fragmenter.CuttingRule
APC1 : denoptim.fragspace.FragmentSpaceTest
apc1 : denoptim.programs.fragmenter.CuttingRule
APC2 : denoptim.fragspace.FragmentSpaceTest
APC3 : denoptim.fragspace.FragmentSpaceTest
APC4 : denoptim.fragspace.FragmentSpaceTest
APC5 : denoptim.fragspace.FragmentSpaceTest
APC6 : denoptim.fragspace.FragmentSpaceTest
APCA : denoptim.fragspace.APMapFinderTest, denoptim.fragspace.GraphLinkFinderTest, denoptim.ga.EAUtilsTest, denoptim.ga.GraphOperationsTest, denoptim.ga.PopulationTest, denoptim.graph.DGraphTest
APCAROMBRIDGE2EL : denoptim.graph.APClass
APCAROMBRIDGE3EL : denoptim.graph.APClass
APCAROMBRIDGE4EL : denoptim.graph.APClass
APCAROMBRIDGES : denoptim.graph.APClass
APCB : denoptim.fragspace.APMapFinderTest, denoptim.fragspace.GraphLinkFinderTest, denoptim.ga.EAUtilsTest, denoptim.ga.GraphOperationsTest, denoptim.ga.PopulationTest, denoptim.graph.DGraphTest
APCC : denoptim.fragspace.APMapFinderTest, denoptim.fragspace.GraphLinkFinderTest, denoptim.ga.EAUtilsTest, denoptim.ga.GraphOperationsTest, denoptim.ga.PopulationTest, denoptim.graph.DGraphTest
APCC1 : denoptim.fragspace.FragmentSpaceTest
APCC2 : denoptim.fragspace.FragmentSpaceTest
APCD : denoptim.fragspace.APMapFinderTest, denoptim.fragspace.GraphLinkFinderTest, denoptim.ga.GraphOperationsTest, denoptim.ga.PopulationTest, denoptim.graph.DGraphTest
APCE : denoptim.fragspace.APMapFinderTest, denoptim.fragspace.GraphLinkFinderTest
APCF : denoptim.fragspace.GraphLinkFinderTest
apClass : denoptim.graph.AttachmentPoint
APCLASS : denoptim.graph.AttachmentPointTest, denoptim.graph.FragmentTest
apClass : denoptim.graph.rings.RingClosingAttractor
apClassBasedApproch : denoptim.fragspace.FragmentSpace
apClassCompatibilityMatrix : denoptim.fragspace.FragmentSpace
apClassesPerFrag : denoptim.fragspace.FragmentSpace
APCMAPAP2BO : denoptim.constants.DENOPTIMConstants
APCMAPCAPPING : denoptim.constants.DENOPTIMConstants
APCMAPCOMPRULE : denoptim.constants.DENOPTIMConstants
APCMAPFORBIDDENEND : denoptim.constants.DENOPTIMConstants
APCMAPIGNORE : denoptim.constants.DENOPTIMConstants
apCounter : denoptim.graph.DGraph
APCS : denoptim.fragspace.FragmentSpaceTest
APCSEP : denoptim.graph.FragmentTest
apcStringSyntax : denoptim.gui.GUIAPClassDefinitionDialog
APDATACHANGEEVENT : denoptim.gui.IVertexAPSelection
apId : denoptim.fragspace.IdFragmentAndAP
APID : denoptim.gui.GraphViewerPanel.LabelType
apLeft : denoptim.graph.rings.ChainLink
APORIGINALLENGTH : denoptim.constants.DENOPTIMConstants
appLogger : denoptim.logging.StaticLogger
apRight : denoptim.graph.rings.ChainLink
APRULE : denoptim.graph.AttachmentPointTest, denoptim.graph.FragmentTest
APSTAG : denoptim.constants.DENOPTIMConstants
APSUBRULE : denoptim.fragspace.FragmentSpaceTest, denoptim.graph.AttachmentPointTest, denoptim.graph.FragmentTest
apSymSetId : denoptim.fragspace.IdFragmentAndAP
apTable : denoptim.gui.FragmentViewPanel, denoptim.gui.GUIEmptyVertexMaker, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel
apTabModel : denoptim.gui.FragmentViewPanel, denoptim.gui.GUIEmptyVertexMaker, denoptim.gui.VertexAsGraphViewPanel, denoptim.gui.VertexAsTwoDimStructureViewPanel
apTabPanel : denoptim.gui.GUIEmptyVertexMaker
at : denoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel
atm : denoptim.graph.rings.RingClosingAttractor
atm0 : denoptim.programs.fragmenter.MatchedBond
atm1 : denoptim.programs.fragmenter.MatchedBond
ATMINUS : denoptim.graph.APClass
atmNb : denoptim.integration.tinker.TinkerAtom
atmNumStr : denoptim.graph.rings.PathSubGraph
atmOveralScore : denoptim.molecularmodeling.ChemicalObjectModel
ATMPROPAPS : denoptim.constants.DENOPTIMConstants
ATMPROPORIGINALATMID : denoptim.constants.DENOPTIMConstants
ATMPROPVERTEXID : denoptim.constants.DENOPTIMConstants
ATMPROPVERTEXPATH : denoptim.constants.DENOPTIMConstants
ATNEUTRAL : denoptim.graph.APClass
atomIds : denoptim.json.LWBond
atomOrderingScheme : denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
atomOrders : denoptim.utils.AtomOrganizer
atomPositionNumber : denoptim.graph.AttachmentPoint
atomPositionNumberInMol : denoptim.graph.AttachmentPoint
atoms : denoptim.integration.tinker.TinkerBond
ATOMSKEY : denoptim.json.IAtomContainerSerializer
atomsPathVAVB : denoptim.graph.rings.PathSubGraph
atomStr : denoptim.integration.tinker.TinkerAtom
ATPLUS : denoptim.graph.APClass
attA11 : denoptim.graph.rings.RingClosingAttractor
attA12 : denoptim.graph.rings.RingClosingAttractor
attB11 : denoptim.graph.rings.RingClosingAttractor
attB12 : denoptim.graph.rings.RingClosingAttractor
attractors : denoptim.molecularmodeling.ChemicalObjectModel
attToAtmID : denoptim.molecularmodeling.ChemicalObjectModel
attType : denoptim.graph.rings.RingClosingAttractor
AUTHORS : denoptim.logging.Version