| Cdenoptim.graph.APClassTest | Unit test for APClass |
| Cdenoptim.fragspace.APMapFinder | An utility class to encapsulate the search for an AttachmentPoint-AttachmentPoint mapping |
| Cdenoptim.fragspace.APMapFinderTest | Unit test |
| Cdenoptim.utils.AtomOrganizer | Tool for re-organizing the list of atoms of an IAtomContainer |
| Cdenoptim.graph.AttachmentPointTest | Unit test for DENOPTIMAttachmentPoint |
| Cdenoptim.graph.Vertex.BBType | The type of building block |
| Cdenoptim.main.Behavior | Represents the behavior of the program at start-up |
| Cdenoptim.graph.Edge.BondType | Possible chemical bond types an edge can represent |
| Cdenoptim.fragmenter.BridgeHeadFindingRule | SMARTS-based rules to identify potential bridge head atoms for ring fusion operations |
| Cdenoptim.graph.CandidateLW | A light-weight candidate is a very low-demanding collection of data upon a specific candidate item |
| Cdenoptim.ga.EAUtils.CandidateSource | A chosen method for generation of new Candidates |
| Cdenoptim.utils.CartesianSpaceUtils | Utilities for working in the Cartesian space |
| Cdenoptim.combinatorial.CEBLUtils | Helper methods for the exploration of the fragment space |
| Cdenoptim.combinatorial.CheckPoint | Object collecting information needed to restart a FragSpaceExplorer job |
| Cdenoptim.molecularmodeling.ChemicalObjectModel | Collector of molecular information, related to a single chemical object, that is deployed within the 3D builder |
| ►CCloneable | |
| Cdenoptim.ga.Population | A collection of candidates |
| Cdenoptim.ga.XoverSite | This class collects the data identifying the subgraphs that would be swapped by a crossover event |
| Cdenoptim.graph.APClass | |
| Cdenoptim.graph.APMapping | Class representing a mapping between attachment points (APs) |
| Cdenoptim.graph.AttachmentPoint | An attachment point (AP) is a possibility to attach a Vertex onto the vertex holding the AP (i.e., the owner of the AP), this way forming a new Edge (i.e., the user of the AP) |
| Cdenoptim.graph.Candidate | A candidate is the combination of a denoptim graph with molecular representation and may include also fitness/error, and possibly other stuff |
| Cdenoptim.graph.DGraph | Container for the list of vertices and the edges that connect them |
| ►Cdenoptim.graph.Vertex | A vertex is a data structure that has an identity and holds a list of AttachmentPoints |
| Cdenoptim.graph.EmptyVertex | An empty vertex has the behaviors of a vertex, but has no molecular structure |
| Cdenoptim.graph.Fragment | Class representing a continuously connected portion of chemical object holding attachment points |
| Cdenoptim.graph.Template | |
| Cdenoptim.graph.rings.ChainLink | ChainLink represents a vertex in a closable chain |
| Cdenoptim.graph.rings.ClosableChain | ClosableChain represents a chain of fragments (chain links) that is closable (or candidate closable) |
| Cdenoptim.integration.tinker.TinkerAtom | Based on the code from ffx.kenai.com Michael J |
| Cdenoptim.integration.tinker.TinkerBond | |
| Cdenoptim.integration.tinker.TinkerMolecule | |
| Cdenoptim.graph.rings.CyclicGraphHandler.ClosableConf | Utility class to handle the simultaneous closeness condition |
| Cdenoptim.fragmenter.ClusterableFragmentTest | Unit test for fragmenter's tools |
| Cdenoptim.combinatorial.CombinatorialExplorerByLayer | Generates all combinators of fragments by means of asynchronous threads |
| ►CComparable | |
| Cdenoptim.graph.APClass | |
| Cdenoptim.graph.AttachmentPoint | An attachment point (AP) is a possibility to attach a Vertex onto the vertex holding the AP (i.e., the owner of the AP), this way forming a new Edge (i.e., the user of the AP) |
| Cdenoptim.graph.Candidate | A candidate is the combination of a denoptim graph with molecular representation and may include also fitness/error, and possibly other stuff |
| Cdenoptim.integration.tinker.ConformationalSearchPSSROT | Toolkit to perform conformational search via Tinker PSSROT program |
| Cdenoptim.fragmenter.ConformerExtractorTaskTest | Unit test for fragmenter's tools |
| Cdenoptim.utils.ConnectedLigand | A ConnectedLigand is just an atom with an explicit field reporting the number of connected atoms |
| Cdenoptim.graph.Template.ContractLevel | Enum specifying to what extent the template's inner graph can be changed |
| Cdenoptim.logging.CounterID | Identifier of a counter |
| Cdenoptim.utils.CrossoverType | Types of crossover defined |
| Cdenoptim.programs.fragmenter.CuttingRule | A cutting rule with three SMARTS queries (atom 1, bond, atom2) and options |
| Cdenoptim.graph.rings.CyclicGraphHandler | This is a tool to identify and manage vertices' connections not included in the DGraph, which is a spanning tree, thus connections that identify cyclic paths in the graph |
| Cdenoptim.files.FileFormat.DataKind | The kind of data found in a file |
| Cdenoptim.constants.DENOPTIMConstants | General set of constants used in DENOPTIM |
| Cdenoptim.json.DENOPTIMgson | Class for de/serializing DENOPTIM graphs from/to JSON format |
| Cdenoptim.json.DENOPTIMgsonTest | Unit test for DENOPTIMgson |
| Cdenoptim.io.DenoptimIO | Utility methods for input/output |
| Cdenoptim.io.DenoptimIOTest | Unit test for input/output |
| Cdenoptim.fitness.DescriptorForFitness | This is a reference to a specific descriptor value |
| Cdenoptim.fitness.DescriptorUtils | |
| Cdenoptim.fitness.DescriptorUtilsTest | Unit test for descriptor utils |
| Cdenoptim.graph.DGraphTest | Unit test for DENOPTIMGraph |
| Cdenoptim.gui.DNPSpringLayout< denoptim.gui.GraphViewerPanel.JVertex, denoptim.gui.GraphViewerPanel.JEdge > | |
| Cdenoptim.utils.DummyAtomHandler | Toll to add/remove dummy atoms from linearities or multi-hapto sites |
| Cdenoptim.fragmenter.DynamicCentroidCluster | A cluster with a centroid that can be updated after definition of the cluster |
| Cdenoptim.fragmenter.DynamicCentroidClusterTest | Unit test for fragmenter's tools |
| Cdenoptim.ga.EAUtils | Helper methods for the genetic algorithm |
| Cdenoptim.ga.EAUtilsTest | Unit test |
| Cdenoptim.graph.Edge | This class represents the edge between two vertices |
| Cdenoptim.graph.EdgeQuery | A query for edges: a list of properties that target edges should possess in order to match this query |
| Cdenoptim.graph.EdgeTest | Unit test for DENOPTIMEdge |
| Cdenoptim.utils.GraphEdit.EditTask | Defined the kind of graph editing task |
| Cdenoptim.ga.EvolutionaryAlgorithm | DENOPTIM's evolutionary algorithm |
| ►CException | |
| Cdenoptim.exception.DENOPTIMException | |
| Cdenoptim.files.UndetectedFileFormatException | Exception thrown when the format of a file is not recognized |
| Cdenoptim.integration.tinker.TinkerException | Exceptions resulting from a failure of Tinker |
| Cdenoptim.exception.ExceptionUtils | |
| Cdenoptim.ga.GraphOperationsTest.ExtractPatternCase | |
| Cdenoptim.files.FileAndFormat | A file with a conventional representation of its format |
| Cdenoptim.files.FileFormat | File formats identified by DENOPTIM |
| Cdenoptim.files.FileUtils | |
| Cdenoptim.fitness.FitnessExpressionParser | Class parsing fitness expression by means of Expression Language |
| Cdenoptim.fitness.FitnessExpressionParserTest | Unit test for parser of fitness-defining expressions |
| Cdenoptim.fitness.FitnessProvider | DENOPTIM's (internal) fitness provider calculates the value of Variables that are used in an expression for calculating a single numerical results, i.e., the fitness |
| Cdenoptim.fitness.FitnessProviderTest | Unit test for internal fitness provider |
| Cdenoptim.utils.FormulaUtils | Utilities for manipulating molecular formulas |
| Cdenoptim.utils.FormulaUtilsTest | Unit test for tools manipulating molecular formulae |
| Cdenoptim.programs.fitnessevaluator.FPRunner | Runs a fitness provider task as defined in the static parameters |
| Cdenoptim.ga.GraphOperations.FragForClosabChains | Private class representing a selected closable chain of fragments |
| Cdenoptim.graph.FragIsomorphEdge | |
| Cdenoptim.graph.FragIsomorphNode | |
| Cdenoptim.fragmenter.FragmentAlignement | Class performing the alignment of Fragments |
| Cdenoptim.fragmenter.FragmentAlignementTest | Unit test for fragmenter's tools |
| Cdenoptim.fragmenter.FragmentClusterer | |
| Cdenoptim.fragmenter.FragmentClustererTest | Unit test for fragmenter's tools |
| Cdenoptim.fragmenter.FragmenterTools | |
| Cdenoptim.fragmenter.FragmenterToolsTest | Unit test for fragmenter's tools |
| Cdenoptim.graph.FragmentIsomorphismInspector | |
| Cdenoptim.graph.FragmentIsomorphismInspectorTest | Unit test for isomorphism inspector |
| Cdenoptim.fragspace.FragmentSpace | Class defining a space of building blocks |
| Cdenoptim.fragspace.FragmentSpaceTest | Unit test for fragment space |
| Cdenoptim.fragspace.FragmentSpaceUtils | Utility class for the fragment space |
| Cdenoptim.graph.FragmentTest | Unit test for DENOPTIMFragment |
| Cdenoptim.fragspace.FragsCombinationIterator | Factory of combination of fragments |
| Cdenoptim.programs.denovo.GAParametersTest | Unit test |
| Cdenoptim.utils.GeneralUtils | General utilities |
| Cdenoptim.utils.GenUtilsTest | Unit test |
| Cdenoptim.utils.GraphConversionTool | Tool to convert string into graphs and into molecular representation |
| Cdenoptim.utils.GraphConversionToolTest | Unit test for GraphConversionTool |
| Cdenoptim.utils.GraphEdit | Definition of a graph editing task |
| Cdenoptim.fragspace.GraphLinkFinder | An utility class to encapsulate the search for vertexes that satisfy constraints |
| Cdenoptim.fragspace.GraphLinkFinderTest | Unit test |
| Cdenoptim.ga.GraphOperations | Collection of operators meant to alter graphs and associated utilities |
| Cdenoptim.ga.GraphOperationsTest | Unit test |
| Cdenoptim.graph.GraphPattern | |
| Cdenoptim.utils.GraphUtils | Utilities for graphs |
| Cdenoptim.gui.GUIFileOpener | File opener for DENOPTIM GUI |
| Cdenoptim.gui.GUIFileSaver | GUI component to provide pathname where to save stuff |
| Cdenoptim.gui.GUIPreferences | The collection of tunable preferences |
| ►Cdenoptim.fitness.IDenoptimDescriptor | This interface forces descriptors that are not defined in the CDK ontology to provide information that would otherwise be found in the ontology |
| Cdenoptim.fitness.descriptors.SocketProvidedDescriptor | Sends the request to produce a numerical descriptor to a defined socket and receives back the response |
| Cdenoptim.fitness.descriptors.TanimotoMolSimilarity | Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter |
| Cdenoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure | Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter, and using a given list of substructures |
| Cdenoptim.fragspace.IdFragmentAndAP | Data structure containing information that identifies a single AP of a vertex/fragment |
| Cdenoptim.gui.ILoadFragSpace | Implemented by GUI components that want to allow user-driven loading of the fragment space |
| ►Cdenoptim.gui.IParametersForm | Interface for parameter forms |
| ►Cdenoptim.gui.ParametersForm | General structure of a form for collecting input parameters of various nature |
| Cdenoptim.gui.FSEParametersForm | Form collecting input parameters for a combinatorial/virtual screening experiment performed by FragSpaceExplorer |
| Cdenoptim.gui.FSParametersForm | Form collecting input parameters for defining the fragment space |
| Cdenoptim.gui.FitnessParametersForm | Form collecting input parameters for a setting-up the fitness provider |
| Cdenoptim.gui.GAParametersForm | Form collecting input parameters for a genetic algorithm experiment |
| Cdenoptim.gui.GUIPrepareFitnessRunner.InputForm | |
| ►Cdenoptim.gui.IVertexAPSelection | Interface for all vertex viewers that intend to allow selection of attachment points |
| Cdenoptim.gui.FragmentViewPanel | A panel with a molecular viewer and attachment point table |
| Cdenoptim.gui.VertexAsGraphViewPanel | A panel to visualize a vertex as a graph component with attachment point table |
| Cdenoptim.gui.VertexAsTwoDimStructureViewPanel | A panel to visualize a vertex as two-dimensional chemical structure with attachment point table |
| Cdenoptim.gui.GraphViewerPanel.JEdge | An edge in the JUNG Graph |
| Cdenoptim.gui.JUNGGraphSnapshot | This class collects information on how a graph was displayed in a JUNG visialisation server (i.e., node positions and visible labels) |
| Cdenoptim.gui.GraphViewerPanel.JVertex | Vertex in the JUNG Graph |
| Cdenoptim.gui.GraphViewerPanel.JVertexType | |
| Cdenoptim.gui.GraphViewerPanel.LabelType | |
| Cdenoptim.json.LWAtom | A light-weight atom representation to facilitate json serialization of IAtom |
| Cdenoptim.json.LWBond | A light-weight bond representation to facilitate json serialization of IBond |
| Cdenoptim.main.Main | Entry point of any kind of run of the DENOPTIM program |
| Cdenoptim.main.MainTest | |
| Cdenoptim.utils.ManySMARTSQuery | Container of lists of atoms matching a list of SMARTS |
| Cdenoptim.programs.fragmenter.MatchedBond | |
| Cdenoptim.utils.MathUtils | Some useful math operations |
| Cdenoptim.molecularmodeling.MMBuilderUtils | Utilities for molecular models builder |
| Cdenoptim.utils.MoleculeUtils | Utilities for molecule conversion |
| Cdenoptim.utils.MoleculeUtilsTest | Unit test for DENOPTIMMoleculeUtils |
| Cdenoptim.molecularmodeling.MultiMolecularModelBuilder | |
| Cdenoptim.utils.MutationType | Types of mutation defined in relation to what happens to the target vertex (i.e., the actual mutation site), and the child vertices, i.e., any vertices reachable by a directed path from the target vertex |
| Cdenoptim.graph.simplified.Node | This class represents a subgraph feature that defined the structure of a graph |
| Cdenoptim.graph.simplified.NodeConnection | This class represents an edge that is undirected and ignores attachment points |
| Cdenoptim.utils.ObjectPair | This class is the equivalent of the Pair data structure used in C++ Although AbstractMap.SimpleImmutableEntry<K,V>> is available it does not have a setValue method |
| Cdenoptim.programs.genetweeker.GeneOpsRunnerParameters.Operator | Testable Operators |
| ►Cdenoptim.task.ParallelAsynchronousTaskExecutor | Runs tasks parallel in asynchronous fashion |
| Cdenoptim.fragmenter.ParallelConformerExtractionAlgorithm | Runs threads that extract the most representative conformer of fragments given as input |
| Cdenoptim.fragmenter.ParallelFragmentationAlgorithm | Fragments a list of chemical systems by running parallel fragmentation tasks |
| Cdenoptim.fragmenter.ParallelFragmentationAlgorithmTest | Unit test for fparallel ragmentation algorithm components |
| Cdenoptim.programs.RunTimeParameters.ParametersType | Identifier of the type of parameters |
| Cdenoptim.graph.rings.PathClosabilityTools | Tool box for determining whether a chain of atoms, i.e., a path, can be folded as to form a ring-closing bond that transforms the open chain in a ring |
| Cdenoptim.graph.rings.PathClosabilityToolsTest | Unit test for path closability tools |
| Cdenoptim.graph.rings.PathSubGraph | This object represents a path in a DGraph |
| Cdenoptim.graph.rings.PathSubGraphTest | Unit test for PathSubGraph |
| Cdenoptim.ga.PopulationTest | Unit test |
| Cdenoptim.gui.GAParametersForm.ProbabilityFuncitonShape | The identifiers of probability function shapes that are available |
| Cdenoptim.task.ProcessHandler | |
| Cdenoptim.integration.python.Py4JGetawayServer | A tool that start a Py4J gateway server that can listens to calls from Python and translate JAVA objects to make their functionality available to in the Python environment |
| Cdenoptim.graph.rings.RandomCombOfRingIteratorTest | Unit test for the iterator over random combination of rings |
| Cdenoptim.utils.Randomizer | Tool to generate random numbers and random decisions |
| Cdenoptim.utils.RandomizerTest | Unit test |
| Cdenoptim.graph.RelatedAPPair | Class representing a pair of AttachmentPoints related by some property that is defined by string |
| Cdenoptim.graph.RelatedAPPairTest | |
| Cdenoptim.graph.Ring | This class represents the closure of a ring in a spanning tree |
| Cdenoptim.graph.rings.RingClosingAttractor | The RingClosingAttractor represent the available valence/connection that allows to close a ring |
| Cdenoptim.utils.RingClosingUtils | Toolbox useful when dealing with Ring Closing Attractors and ring closures |
| Cdenoptim.graph.rings.RingClosure | RingClosure represents the arrangement of atoms and PseudoAtoms identifying the head and tail of a chain of atoms |
| Cdenoptim.graph.rings.RingClosureFinder | Tool to explore the conformational space of chains of atoms and identify ring closing conformations |
| Cdenoptim.graph.rings.RingClosuresArchive | Data structure to store and handle information about sub-structures (i.e., chains of fragments) and ring closure capability |
| Cdenoptim.molecularmodeling.RingClosureTool | Toolkit to perform ring closing conformational search |
| Cdenoptim.graph.rings.RingSizeManager | Utility class to calculate and manage the alternative ring sizes achievable by formation of Rings |
| Cdenoptim.graph.rings.RingSizeManagerTest | Unit test for ring size manager |
| Cdenoptim.graph.RingTest | Unit test |
| Cdenoptim.utils.RotationalSpaceUtils | Tool box for definition and management of the rotational space, which is given by the list of rotatable bonds |
| ►CRunnable | |
| Cdenoptim.ga.ExternalCmdsListener | Service that watches the interface folder (i.e., see GAParameters#interfaceDir) for instructions coming from outside the JVM |
| Cdenoptim.gui.GUI | Graphical User Interface of the DENOPTIM package |
| ►Cdenoptim.programs.RunTimeParameters | Collection of parameters controlling the behavior of the software |
| Cdenoptim.fitness.FitnessParameters | Settings defining the calculation of fitness |
| Cdenoptim.fragspace.FragmentSpaceParameters | Parameters defining the fragment space |
| Cdenoptim.graph.rings.RingClosureParameters | Parameters and setting related to handling ring closures |
| Cdenoptim.programs.combinatorial.CEBLParameters | Parameters controlling execution of the combinatorial algorithm for exploration of a fragment space by layer (CEBL) |
| Cdenoptim.programs.denovo.GAParameters | Parameters for genetic algorithm |
| Cdenoptim.programs.fitnessevaluator.FRParameters | Parameters controlling execution of FitnessRunner |
| Cdenoptim.programs.fragmenter.FragmenterParameters | Parameters controlling execution of the fragmenter |
| Cdenoptim.programs.genetweeker.GeneOpsRunnerParameters | Parameters controlling execution of TestOperator |
| Cdenoptim.programs.grapheditor.GraphEdParameters | Parameters controlling execution of GraphEditor |
| Cdenoptim.programs.graphlisthandler.GraphListsHandlerParameters | Parameters controlling execution of GraphEditor |
| Cdenoptim.programs.isomorphism.IsomorphismParameters | Parameters controlling execution of Isomorphism main class |
| Cdenoptim.programs.mol2graph.Mol2GraphParameters | Parameters controlling execution of GraphEditor |
| Cdenoptim.programs.moldecularmodelbuilder.MMBuilderParameters | Parameters for the conformer generator (3D builder) |
| Cdenoptim.main.Main.RunType | Types of runs that can be requested to the DENOPTIM Main class |
| Cdenoptim.fragmenter.ScaffoldingPolicy | Defines how to define the scaffold vertex of a graph |
| Cdenoptim.gui.ScrollableJPupupMenu | A popup menu' that has a fixed size and can be scrolled to see menu items that do not fit into the fixed-size panel |
| Cdenoptim.ga.SeelctionHelperTest | Unit test |
| Cdenoptim.ga.SelectionHelper | Class that offers methods to performs fitness-driven selection of candidates |
| Cdenoptim.files.SingletonFileAccess | Singleton for synchronizing multi-thread safe file access |
| Cdenoptim.utils.SizeControlledSet | Class meant to collect unique strings without leading to memory overflow |
| Cdenoptim.utils.SizeControlledSetTest | Unit test for SizeControlledSet |
| Cdenoptim.io.SMILESListFormatTest | Unit test for SMILES List Format |
| Cdenoptim.gui.GUIPreferences.SMITo3DEngine | Available engines used to do SMILES-to-3D conversion |
| Cdenoptim.fitness.descriptors.SocketProvidedDescriptorTest | Unit test for descriptor SocketProvidedDescriptor |
| Cdenoptim.logging.StaticLogger | Logger class for DENOPTIM |
| Cdenoptim.task.StaticTaskManager | Manager for tasks submitted by the GUI |
| Cdenoptim.utils.StatUtils | Utilities for calculating basic statistics |
| Cdenoptim.graph.DGraph.StringFormat | Identifier for the format of string representations of a graph |
| Cdenoptim.graph.SymmetricAPsTest | |
| ►Cdenoptim.graph.SymmetricSet< AttachmentPoint > | |
| Cdenoptim.graph.SymmetricAPs | A collection of AttachmentPoints that are related by a relation that we call "symmetry", even though this class does not define what such relation is |
| ►Cdenoptim.graph.SymmetricSet< Vertex > | |
| Cdenoptim.graph.SymmetricVertexes | A collection of Vertexs that are related by a relation that we call "symmetry", even though this class does not define what such relation is |
| Cdenoptim.graph.SymmetricSetWithMode | Class coupling a reference to a SymmetricSet with a string that we call "mode" and can is used to store any sort of information |
| Cdenoptim.graph.SymmetricSetWithModeTest | |
| Cdenoptim.fitness.descriptors.TanimotoMolSimilarityTest | Unit test for descriptor TanimotoMolSimilarity |
| Cdenoptim.task.TasksBatchManager | Class that manages the submission of a batch of tasks |
| Cdenoptim.utils.TaskUtils | Utilities for tasks |
| Cdenoptim.graph.TemplateTest | Unit test for DENOPTIMTemplate |
| Cdenoptim.fragspace.FragmentSpaceTest.TestCase | |
| ►CThread | |
| Cdenoptim.fitness.descriptors.SocketProvidedDescriptorTest.MySocketServer | |
| Cdenoptim.fitness.descriptors.SocketProvidedDescriptorTest.RequestHandler | |
| Cdenoptim.task.StaticTaskManager.ShutDownHook | Shutdown hook that stops all child tasks upon shutdown of JavaVM |
| Cdenoptim.task.StreamGobbler | See http://www.javaworld.com/jw-12-2000/jw-1229-traps.html?page=4 |
| Cdenoptim.molecularmodeling.ThreeDimTreeBuilder | Tool to build build three-dimensional (3D) tree-like molecular structures from DGraph |
| Cdenoptim.molecularmodeling.ThreeDimTreeBuilderTest | Unit test for TreeBuilder3D |
| Cdenoptim.integration.tinker.TinkerConstants | General set of constants used to deal with Tinker |
| Cdenoptim.integration.tinker.TinkerUtils | Toolbox of utilities for Tinker style molecular representation |
| Cdenoptim.graph.simplified.UndirectedEdge | This class represents an undirected version of the edge between two vertices |
| Cdenoptim.graph.UndirectedEdgeRelationTest | Unit test for UndirectedEdge |
| Cdenoptim.gui.Utils | |
| Cdenoptim.fitness.Variable | A variable in the expression defining the fitness |
| Cdenoptim.logging.Version | Class handling DENOPTIM's version identifier for headers |
| Cdenoptim.graph.VertexQuery | Query for searching vertices |
| Cdenoptim.graph.VertexTest | Unit test for DENOPTIMVertex |
| Cdenoptim.graph.Vertex.VertexType | Flag declaring the type of Vertex implementation |
| Cdenoptim.ga.Population.XoverSitesAmongCandidates | A data structure collecting crossover-compatible sites |
| Cdenoptim.ga.XoverSiteTest | Unit test |
| ►CAbstractMolecularDescriptor | |
| Cdenoptim.fitness.descriptors.SocketProvidedDescriptor | Sends the request to produce a numerical descriptor to a defined socket and receives back the response |
| Cdenoptim.fitness.descriptors.TanimotoMolSimilarity | Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter |
| Cdenoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure | Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter, and using a given list of substructures |
| ►CAbstractPopupGraphMousePlugin | |
| Cdenoptim.gui.GraphViewerPanel.PopupGraphMousePlugin | |
| ►CActionListener | |
| Cdenoptim.gui.GUICardPanel.removeCardActionListener | Remove the card from the deck of cards and takes care of removing also the entry in the list of active tabs |
| Cdenoptim.gui.GUIGraphHandler.showHideLabelsListener | |
| Cdenoptim.gui.ParametersForm.CmbFieldChange | |
| ►CArrayList | |
| Cdenoptim.ga.Population | A collection of candidates |
| Cdenoptim.graph.SymmetricSet< T > | Class representing a list of references pointing to instances that are related by some conventional criterion that is referred to as "symmetry
relation" |
| ►CBasicAtomGenerator | |
| Cdenoptim.gui.VertexAsTwoDimStructureViewPanel.AtomOrAPGenerator | |
| ►CCallable | |
| ►Cdenoptim.task.Task | A task that can throw exceptions |
| Cdenoptim.fragmenter.ConformerExtractorTask | Task that analyzes an isomorphic family of fragments to identify the most representative fragment (i.e., the champion) |
| Cdenoptim.fragmenter.FragmenterTask | Task that performs the various steps in the process that prepares chemical structured to be chopped, chops them, and post-process the resulting fragments |
| ►Cdenoptim.task.FitnessTask | Task that assesses the fitness of a given graph |
| Cdenoptim.combinatorial.GraphBuildingTask | Task that builds a graph by appending a given combination of fragments onto a given list of attachment points of a given root graph |
| Cdenoptim.ga.OffspringEvaluationTask | Task that calls the fitness provider for an offspring that can become a member of the current population |
| Cdenoptim.programs.fitnessevaluator.FitnessEvaluationTask | Task that calls the fitness provider |
| ►Cdenoptim.task.ProgramTask | Task structure for any of the main programs in the denoptim project, such as genetic algorithm and combinatorial exploration of fragment spaces |
| Cdenoptim.programs.combinatorial.FragSpaceExplorer | Combinatorial exploration of the fragment space |
| Cdenoptim.programs.denovo.GARunner | Programs that runs de novo design by a genetic algorithm |
| Cdenoptim.programs.fitnessevaluator.FitnessRunner | Stand-alone fitness provider |
| Cdenoptim.programs.fragmenter.Fragmenter | Tool to create fragments by chopping 2D/3D chemical structures |
| Cdenoptim.programs.genetweeker.GeneOpsRunner | Tool to run genetic operations in a stand-alone fashion, i.e., outside of a genetic algorithm run |
| Cdenoptim.programs.grapheditor.GraphEditor | Tool for editing DGraphs |
| Cdenoptim.programs.graphlisthandler.GraphListsHandler | Tool for handling lists of graphs |
| Cdenoptim.programs.isomorphism.Isomorphism | Tool to perform isomorphism analysis on DGraphs |
| Cdenoptim.programs.mol2graph.Mol2Graph | Tool for creating DGraphs from molecules |
| Cdenoptim.programs.moldecularmodelbuilder.MolecularModelBuilder | Builder of molecular models |
| ►CChangeListener | |
| Cdenoptim.gui.GUIGraphHandler.GraphSpinnerChangeEvent | |
| Cdenoptim.gui.GUIVertexInspector.VrtxSpinnerChangeEvent | |
| Cdenoptim.gui.GUIVertexSelector.VrtxSpinnerChangeEvent | |
| Cdenoptim.gui.ParametersForm.RdbFieldChange | |
| ►CClusterable | |
| Cdenoptim.fragmenter.ClusterableFragment | Represents a fragment that can be clustered based on the 3*N coordinate of atoms and attachment points, i.e., N is the sum of atoms and attachment points |
| ►CComparator | |
| Cdenoptim.graph.AttachmentPointComparator | Comparator for DENOPTIMAttachmentPoints |
| Cdenoptim.gui.GUIInspectGARun.PlottedCandidatesComparator | |
| Cdenoptim.molecularmodeling.RingClosureTool.RingClosedMolComparator | Compares the Molecule3DBuilder afters ring closing-biased conformational adaptation |
| Cdenoptim.utils.ConnectedLigandComparator | Compare two ConnectedLigand according to the number of connected atoms and the mass number |
| ►CDefaultMutableTreeNode | |
| Cdenoptim.gui.FitnessParametersForm.DescriptorTreeNode | |
| ►CDistanceMeasure | |
| Cdenoptim.fragmenter.FragmentClusterer.DistanceAsRMSD | Distance in terms of RMSD between sets of 3D points expressed as a single vector of coordinates [x1,y1,z1,x2,y2,z2,...xN,yN,zN] |
| ►CDocumentListener | |
| Cdenoptim.gui.ParametersForm.FieldListener | |
| ►CELContext | |
| Cdenoptim.fitness.FitnessExpressionParser.CustomVariableDefiningContext | In this context we only need to know that "Variable" is mapped to the class Variable |
| Cdenoptim.fitness.FitnessExpressionParser.VariableDefiningContext | This is the context on which we read a fitness expression, and parse it to identify all variables in the expression |
| ►CExclusionStrategy | |
| Cdenoptim.json.DENOPTIMgson.DENOPTIMExclusionStrategy | |
| Cdenoptim.json.DENOPTIMgson.DENOPTIMExclusionStrategyNoAPMap | |
| ►CFormatter | |
| Cdenoptim.logging.HTMLLogFormatter | |
| ►CFunction | |
| Cdenoptim.gui.DNPSpringLayout< V, E >.RecreateKnownPositions | |
| Cdenoptim.gui.GraphViewerPanel.EdgeDrawPaintTransformer | |
| Cdenoptim.gui.GraphViewerPanel.EdgeLabelTransformer | |
| Cdenoptim.gui.GraphViewerPanel.EdgeStrokeTransformer | |
| Cdenoptim.gui.GraphViewerPanel.VertexFillPaintTransformer | |
| Cdenoptim.gui.GraphViewerPanel.VertexLabelTransformer | |
| Cdenoptim.gui.GraphViewerPanel.VertexShapePaintTransformer | |
| ►CFunction | |
| Cdenoptim.graph.DGraph.EdgeFinder | Utility to make selection of edges to a vertex tunable by a parameter |
| ►CHashMap | |
| Cdenoptim.fragspace.FragsCombination | Data structure identifying a combination of one or more pairs of attachment points located on specific fragments/vertices |
| Cdenoptim.logging.Monitor | A collection of counters user to count actions taken by the evolutionary algorithm |
| ►CIChemFormatMatcher | |
| Cdenoptim.io.SMILESListFormat | Class for recognizing file containing a list of SMILES |
| ►CIMolecularDescriptor | |
| Cdenoptim.fitness.descriptors.SocketProvidedDescriptor | Sends the request to produce a numerical descriptor to a defined socket and receives back the response |
| Cdenoptim.fitness.descriptors.TanimotoMolSimilarity | Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter |
| Cdenoptim.fitness.descriptors.TanimotoMolSimilarityBySubstructure | Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter, and using a given list of substructures |
| ►CIterator | |
| Cdenoptim.graph.rings.RandomCombOfRingsIterator | A class for iterating over sets of ring combinations generated by considering any constrain and setting defined in the fragment space and ring-closure settings and by randomly picking candidates when no criterion can be used to take an informed decision |
| Cdenoptim.io.IteratingAtomContainerReader | An iterator that take IAtomContainers from a file, possibly using an available iterating reader, or, if such reader does not exist, reads the whole file and collects the containers exposing the iterator over the list of containers |
| ►CJButton | |
| Cdenoptim.gui.CuttingRulesSelectionDialog.SMARTSVisualizationButton | A button that opens a modal dialog displaying the PNGs with a visual representation of SMARTS queries that are selected in the table given upon construction |
| ►CJDialog | |
| ►Cdenoptim.gui.GUIModalDialog | |
| ►Cdenoptim.gui.CuttingRulesSelectionDialog | A modal dialog to define parameters for fragmentation and fragment filtering |
| Cdenoptim.gui.MolToGraphParametersDialog | |
| Cdenoptim.gui.FSParamsDialog | A modal dialog to define a fragment space and load it |
| Cdenoptim.gui.FitnessParametersForm.AtomSpecExpressionDefinition | |
| Cdenoptim.gui.FitnessParametersForm.ParametrizedDescriptorDefinition | |
| Cdenoptim.gui.GUIAPClassDefinitionDialog | |
| Cdenoptim.gui.GUIEmptyVertexMaker | |
| Cdenoptim.gui.GUIGraphHandler.ConfigTemplateDialog | Dialog to configure one or more templates |
| Cdenoptim.gui.GUIInspectGARun.GenerationChoiceDialog | Modal dialog that asks the user for a generation number |
| Cdenoptim.gui.GUIPreferencesDialog | |
| Cdenoptim.gui.GUIVertexSelector | A modal dialog with a viewer that understands the different types of DENOPTIM vertex and allows to select vertices and, if needed, attachment points |
| ►CJMenuBar | |
| Cdenoptim.gui.MainToolBar | Main tool bar of the DENOPTIM graphical user interface |
| ►CJMenuItem | |
| Cdenoptim.gui.MainToolBar.RecentFileItem | |
| ►CJPanel | |
| Cdenoptim.gui.ButtonsBar | Standardised horizontal bar with padded components, which are meant to be JButtons |
| Cdenoptim.gui.CompatibilityMatrixForm | |
| Cdenoptim.gui.CompatibilityMatrixForm.CompatRulesHeader | |
| Cdenoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine | Single line in the list of APClass compatibility rules |
| Cdenoptim.gui.CompatibilityMatrixForm.TargetAPClassToken | |
| ►Cdenoptim.gui.GUICardPanel | Class of GUI panels meant to occupy one card in the deck-of-cards layout of the main panel |
| Cdenoptim.gui.GUICompatibilityMatrixTab | A panel for handling of compatibility matrix |
| Cdenoptim.gui.GUIGraphHandler | A panel that understands DENOPTIM graphs and allows to create and edit them |
| Cdenoptim.gui.GUIInspectFSERun | A panel that allows to inspect the output of an combinatorial experiment exploring a fragment space |
| Cdenoptim.gui.GUIInspectGARun | A panel that allows to inspect the output of an artificial evolution experiment |
| ►Cdenoptim.gui.GUIPrepare | Class representing the general structure of a form including a specific set of parameter collections |
| Cdenoptim.gui.GUIPrepareFSERun | Master form containing all sub-forms that need to be filled to define the input parameters for FragSpaceExplorer |
| Cdenoptim.gui.GUIPrepareFitnessRunner | Form that allows to test the configuration of a fitness provider |
| Cdenoptim.gui.GUIPrepareGARun | Master form containing all sub-forms that need to be filled to define the input parameters for DenoptimGA |
| Cdenoptim.gui.GUITextReader | A panel that allows to print the content of a text file into a GUI tab |
| Cdenoptim.gui.GUIVertexInspector | A panel with a viewer capable of visualising DENOPTIM fragments and allows to create and edit fragments |
| Cdenoptim.gui.HomePanel | The home panel contains shortcuts buttons to perform the most common tasks |
| Cdenoptim.gui.GUIGraphHandler.ConfigTemplateDialog.TemplateConfiguration | Utility class for a form to configure a template via the GUI |
| Cdenoptim.gui.GUIMainPanel | The main panel is a deck of cards that occupies all the GUI frame |
| Cdenoptim.gui.GraphViewerPanel | A Panel that holds the JUNG representation of a graph |
| Cdenoptim.gui.JmolPanel | |
| Cdenoptim.gui.ParametersForm | General structure of a form for collecting input parameters of various nature |
| Cdenoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel | Panel dealing with the painting of 2D chemical representation |
| Cdenoptim.gui.VertexViewPanel | A panel for visualizing vertices |
| ►CJPopupMenu | |
| Cdenoptim.gui.GraphViewerPanel.GraphOptsPopup | |
| ►CJsonDeserializer | |
| Cdenoptim.graph.APClass.APClassDeserializer | |
| Cdenoptim.graph.DGraph.DENOPTIMGraphDeserializer | |
| Cdenoptim.graph.Vertex.DENOPTIMVertexDeserializer | |
| Cdenoptim.json.IAtomContainerDeserializer | Deserialisation of collections of both light-weight atoms and bonds into a CDK IAtomContainer |
| ►CJsonSerializer | |
| Cdenoptim.graph.APTreeMap.APMapSerializer | Method that serializes this class without creating loops of references |
| Cdenoptim.graph.DGraph.DENOPTIMGraphSerializer | We expect unique IDs for vertices |
| Cdenoptim.graph.Edge.DENOPTIMEdgeSerializer | |
| Cdenoptim.graph.Ring.DENOPTIMRingSerializer | |
| Cdenoptim.graph.SymmetricAPs.SymmetricAPsSerializer | |
| Cdenoptim.graph.SymmetricVertexes.SymmetricVertexesSerializer | |
| Cdenoptim.json.IAtomContainerSerializer | Class to serialise CDK's IAtomContainer in a simplified manner |
| ►CJSplitPane | |
| Cdenoptim.gui.FragmentViewPanel | A panel with a molecular viewer and attachment point table |
| Cdenoptim.gui.GraphVertexMolViewerPanel | A panel that collects three viewers: |
| Cdenoptim.gui.MoleculeViewPanel | A panel with a molecular viewer and data table |
| Cdenoptim.gui.VertexAsGraphViewPanel | A panel to visualize a vertex as a graph component with attachment point table |
| Cdenoptim.gui.VertexAsTwoDimStructureViewPanel | A panel to visualize a vertex as two-dimensional chemical structure with attachment point table |
| ►CJSVGCanvas | |
| Cdenoptim.gui.CuttingRulesSelectionDialog.MyJSVGCanvas | Special canvas that overrides the set interpretation of mouse+key input to achieve a simplified zoom/pan capability using only BUTTON1 and SHIFT or CTRL keys |
| ►CLinkedHashMap | |
| Cdenoptim.graph.APMapping | Class representing a mapping between attachment points (APs) |
| Cdenoptim.graph.APTreeMap | Attachment point mapping where keys are sorted by natural ordering, i.e., by AttachmentPoint#compareTo(AttachmentPoint) |
| ►CMouseListener | |
| Cdenoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine | Single line in the list of APClass compatibility rules |
| Cdenoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel | Panel dealing with the painting of 2D chemical representation |
| ►CMouseMotionListener | |
| Cdenoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel | Panel dealing with the painting of 2D chemical representation |
| ►CMouseWheelListener | |
| Cdenoptim.gui.VertexAsTwoDimStructureViewPanel.TwoDimStructurePanel | Panel dealing with the painting of 2D chemical representation |
| ►COptions | |
| Cdenoptim.main.CLIOptions | |
| ►CPropertyChangeListener | |
| Cdenoptim.gui.CompatibilityMatrixForm.TrgRemovalListener | Listens for clicks that require removal of a compatible APClass (i.e., the target APClass) from the existing rule of a source APClass |
| Cdenoptim.gui.GraphVertexMolViewerPanel.MouseModeChoiceListener | Listener for identifying the node on which the user has clicked and load the corresponding fragment into the fragment viewer pane |
| Cdenoptim.gui.GraphVertexMolViewerPanel.NodeClickedListener | Listener for identifying the node on which the user has clicked and load the corresponding fragment into the fragment viewer pane |
| ►CSerializable | |
| Cdenoptim.graph.rings.RingClosingConformations | Serializable object to store/get a list of conformations that allow to close a ring from an open chain of atoms |
| ►CSpringLayout2 | |
| Cdenoptim.gui.DNPSpringLayout< V, E > | This layout extends the SpringLayout to change its behaviour |
| ►CTableModelListener | |
| Cdenoptim.gui.FragmentViewPanel.PausableTableModelListener | |
| Cdenoptim.gui.ParametersForm.TabFieldChange | |
| Cdenoptim.gui.VertexAsGraphViewPanel.PausableTableModelListener | |
| Cdenoptim.gui.VertexAsTwoDimStructureViewPanel.PausableTableModelListener | |
1.9.4