| ▼Ndenoptim | |
| ►Ncombinatorial | |
| CCEBLUtils | Helper methods for the exploration of the fragment space |
| CCheckPoint | Object collecting information needed to restart a FragSpaceExplorer job |
| CCombinatorialExplorerByLayer | Generates all combinators of fragments by means of asynchronous threads |
| CGraphBuildingTask | Task that builds a graph by appending a given combination of fragments onto a given list of attachment points of a given root graph |
| ►Nconstants | |
| CDENOPTIMConstants | General set of constants used in DENOPTIM |
| ►Nexception | |
| CDENOPTIMException | |
| CExceptionUtils | |
| ►Nfiles | |
| CFileAndFormat | A file with a conventional representation of its format |
| ►CFileFormat | File formats identified by DENOPTIM |
| CDataKind | The kind of data found in a file |
| CFileUtils | |
| CSingletonFileAccess | Singleton for synchronizing multi-thread safe file access |
| CUndetectedFileFormatException | Exception thrown when the format of a file is not recognized |
| ►Nfitness | |
| ►Ndescriptors | |
| CSocketProvidedDescriptor | Sends the request to produce a numerical descriptor to a defined socket and receives back the response |
| ►CSocketProvidedDescriptorTest | Unit test for descriptor SocketProvidedDescriptor |
| CMySocketServer | |
| CRequestHandler | |
| CTanimotoMolSimilarity | Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter |
| CTanimotoMolSimilarityBySubstructure | Calculates the molecular similarity against a target compound the fingerprint of which is given as parameter, and using a given list of substructures |
| CTanimotoMolSimilarityTest | Unit test for descriptor TanimotoMolSimilarity |
| CDescriptorForFitness | This is a reference to a specific descriptor value |
| CDescriptorUtils | |
| CDescriptorUtilsTest | Unit test for descriptor utils |
| ►CFitnessExpressionParser | Class parsing fitness expression by means of Expression Language |
| CCustomVariableDefiningContext | In this context we only need to know that "Variable" is mapped to the class Variable |
| CVariableDefiningContext | This is the context on which we read a fitness expression, and parse it to identify all variables in the expression |
| CFitnessExpressionParserTest | Unit test for parser of fitness-defining expressions |
| CFitnessParameters | Settings defining the calculation of fitness |
| CFitnessProvider | 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 |
| CFitnessProviderTest | Unit test for internal fitness provider |
| CIDenoptimDescriptor | This interface forces descriptors that are not defined in the CDK ontology to provide information that would otherwise be found in the ontology |
| CVariable | A variable in the expression defining the fitness |
| ►Nfragmenter | |
| CBridgeHeadFindingRule | SMARTS-based rules to identify potential bridge head atoms for ring fusion operations |
| CClusterableFragment | 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 |
| CClusterableFragmentTest | Unit test for fragmenter's tools |
| CConformerExtractorTask | Task that analyzes an isomorphic family of fragments to identify the most representative fragment (i.e., the champion) |
| CConformerExtractorTaskTest | Unit test for fragmenter's tools |
| CDynamicCentroidCluster | A cluster with a centroid that can be updated after definition of the cluster |
| CDynamicCentroidClusterTest | Unit test for fragmenter's tools |
| CFragmentAlignement | Class performing the alignment of Fragments |
| CFragmentAlignementTest | Unit test for fragmenter's tools |
| ►CFragmentClusterer | |
| CDistanceAsRMSD | 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] |
| CFragmentClustererTest | Unit test for fragmenter's tools |
| CFragmenterTask | Task that performs the various steps in the process that prepares chemical structured to be chopped, chops them, and post-process the resulting fragments |
| CFragmenterTools | |
| CFragmenterToolsTest | Unit test for fragmenter's tools |
| CParallelConformerExtractionAlgorithm | Runs threads that extract the most representative conformer of fragments given as input |
| CParallelFragmentationAlgorithm | Fragments a list of chemical systems by running parallel fragmentation tasks |
| CParallelFragmentationAlgorithmTest | Unit test for fparallel ragmentation algorithm components |
| CScaffoldingPolicy | Defines how to define the scaffold vertex of a graph |
| CTopoTemplateProducer | |
| ►Nfragspace | |
| CAPMapFinder | An utility class to encapsulate the search for an AttachmentPoint-AttachmentPoint mapping |
| CAPMapFinderTest | Unit test |
| CFragmentSpace | Class defining a space of building blocks |
| CFragmentSpaceParameters | Parameters defining the fragment space |
| ►CFragmentSpaceTest | Unit test for fragment space |
| CTestCase | |
| CFragmentSpaceUtils | Utility class for the fragment space |
| CFragsCombination | Data structure identifying a combination of one or more pairs of attachment points located on specific fragments/vertices |
| CFragsCombinationIterator | Factory of combination of fragments |
| CGraphLinkFinder | An utility class to encapsulate the search for vertexes that satisfy constraints |
| CGraphLinkFinderTest | Unit test |
| CIdFragmentAndAP | Data structure containing information that identifies a single AP of a vertex/fragment |
| ►Nga | |
| ►CEAUtils | Helper methods for the genetic algorithm |
| CCandidateSource | A chosen method for generation of new Candidates |
| CEAUtilsTest | Unit test |
| CEvolutionaryAlgorithm | DENOPTIM's evolutionary algorithm |
| CExternalCmdsListener | Service that watches the interface folder (i.e., see GAParameters#interfaceDir) for instructions coming from outside the JVM |
| ►CGraphOperations | Collection of operators meant to alter graphs and associated utilities |
| CFragForClosabChains | Private class representing a selected closable chain of fragments |
| ►CGraphOperationsTest | Unit test |
| CExtractPatternCase | |
| COffspringEvaluationTask | Task that calls the fitness provider for an offspring that can become a member of the current population |
| ►CPopulation | A collection of candidates |
| CXoverSitesAmongCandidates | A data structure collecting crossover-compatible sites |
| CPopulationTest | Unit test |
| CSeelctionHelperTest | Unit test |
| CSelectionHelper | Class that offers methods to performs fitness-driven selection of candidates |
| CXoverSite | This class collects the data identifying the subgraphs that would be swapped by a crossover event |
| CXoverSiteTest | Unit test |
| ►Ngraph | |
| ►Nrings | |
| CChainLink | ChainLink represents a vertex in a closable chain |
| CClosableChain | ClosableChain represents a chain of fragments (chain links) that is closable (or candidate closable) |
| ►CCyclicGraphHandler | 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 |
| CClosableConf | Utility class to handle the simultaneous closeness condition |
| CPathClosabilityTools | 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 |
| CPathClosabilityToolsTest | Unit test for path closability tools |
| CPathSubGraph | This object represents a path in a DGraph |
| CPathSubGraphTest | Unit test for PathSubGraph |
| CRandomCombOfRingIteratorTest | Unit test for the iterator over random combination of rings |
| CRandomCombOfRingsIterator | 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 |
| CRingClosingAttractor | The RingClosingAttractor represent the available valence/connection that allows to close a ring |
| CRingClosingConformations | Serializable object to store/get a list of conformations that allow to close a ring from an open chain of atoms |
| CRingClosure | RingClosure represents the arrangement of atoms and PseudoAtoms identifying the head and tail of a chain of atoms |
| CRingClosureFinder | Tool to explore the conformational space of chains of atoms and identify ring closing conformations |
| CRingClosureParameters | Parameters and setting related to handling ring closures |
| CRingClosuresArchive | Data structure to store and handle information about sub-structures (i.e., chains of fragments) and ring closure capability |
| CRingSizeManager | Utility class to calculate and manage the alternative ring sizes achievable by formation of Rings |
| CRingSizeManagerTest | Unit test for ring size manager |
| ►Nsimplified | |
| CNode | This class represents a subgraph feature that defined the structure of a graph |
| CNodeConnection | This class represents an edge that is undirected and ignores attachment points |
| CUndirectedEdge | This class represents an undirected version of the edge between two vertices |
| ►CAPClass | |
| CAPClassDeserializer | |
| CAPClassTest | Unit test for APClass |
| CAPMapping | Class representing a mapping between attachment points (APs) |
| ►CAPTreeMap | Attachment point mapping where keys are sorted by natural ordering, i.e., by AttachmentPoint#compareTo(AttachmentPoint) |
| CAPMapSerializer | Method that serializes this class without creating loops of references |
| CAttachmentPoint | 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) |
| CAttachmentPointComparator | Comparator for DENOPTIMAttachmentPoints |
| CAttachmentPointQuery | Query for searching AttachmentPoints |
| CAttachmentPointQueryTest | Unit tests for AttachmentPointQuery#matches(AttachmentPoint) |
| CAttachmentPointTest | Unit test for DENOPTIMAttachmentPoint |
| CCandidate | A candidate is the combination of a denoptim graph with molecular representation and may include also fitness/error, and possibly other stuff |
| CCandidateLW | A light-weight candidate is a very low-demanding collection of data upon a specific candidate item |
| ►CDGraph | Container for the list of vertices and the edges that connect them |
| CDENOPTIMGraphDeserializer | |
| CDENOPTIMGraphSerializer | We expect unique IDs for vertices |
| CEdgeFinder | Utility to make selection of edges to a vertex tunable by a parameter |
| CStringFormat | Identifier for the format of string representations of a graph |
| CDGraphTest | Unit test for DENOPTIMGraph |
| ►CEdge | This class represents the edge between two vertices |
| CBondType | Possible chemical bond types an edge can represent |
| CDENOPTIMEdgeSerializer | |
| CEdgeQuery | A query for edges: a list of properties that target edges should possess in order to match this query |
| CEdgeQueryTest | Unit tests for EdgeQuery#matches(Edge) |
| CEdgeTest | Unit test for DENOPTIMEdge |
| CEmptyVertex | An empty vertex has the behaviors of a vertex, but has no molecular structure |
| CFragIsomorphEdge | |
| CFragIsomorphNode | |
| CFragment | Class representing a continuously connected portion of chemical object holding attachment points |
| CFragmentIsomorphismInspector | |
| CFragmentIsomorphismInspectorTest | Unit test for isomorphism inspector |
| CFragmentTest | Unit test for DENOPTIMFragment |
| CGraphPattern | |
| CRelatedAPPair | Class representing a pair of AttachmentPoints related by some property that is defined by string |
| CRelatedAPPairTest | |
| ►CRing | This class represents the closure of a ring in a spanning tree |
| CDENOPTIMRingSerializer | |
| CRingTest | Unit test |
| ►CSymmetricAPs | 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 |
| CSymmetricAPsSerializer | |
| CSymmetricAPsTest | |
| CSymmetricSet | Class representing a list of references pointing to instances that are related by some conventional criterion that is referred to as "symmetry
relation" |
| CSymmetricSetWithMode | Class coupling a reference to a SymmetricSet with a string that we call "mode" and can is used to store any sort of information |
| CSymmetricSetWithModeTest | |
| ►CSymmetricVertexes | 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 |
| CSymmetricVertexesSerializer | |
| ►CTemplate | |
| CContractLevel | Enum specifying to what extent the template's inner graph can be changed |
| CTemplateTest | Unit test for DENOPTIMTemplate |
| CUndirectedEdgeRelationTest | Unit test for UndirectedEdge |
| ►CVertex | A vertex is a data structure that has an identity and holds a list of AttachmentPoints |
| CBBType | The type of building block |
| CDENOPTIMVertexDeserializer | |
| CVertexType | Flag declaring the type of Vertex implementation |
| CVertexQuery | Query for searching vertices |
| CVertexQueryTest | Unit tests for VertexQuery#matches(Vertex) |
| CVertexTest | Unit test for DENOPTIMVertex |
| ►Ngui | |
| CButtonsBar | Standardised horizontal bar with padded components, which are meant to be JButtons |
| ►CCompatibilityMatrixForm | |
| CCompatibilityRuleLine | Single line in the list of APClass compatibility rules |
| CCompatRulesHeader | |
| CTargetAPClassToken | |
| CTrgRemovalListener | Listens for clicks that require removal of a compatible APClass (i.e., the target APClass) from the existing rule of a source APClass |
| ►CCuttingRulesSelectionDialog | A modal dialog to define parameters for fragmentation and fragment filtering |
| CMyJSVGCanvas | 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 |
| CSMARTSVisualizationButton | 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 |
| ►CDNPSpringLayout | This layout extends the SpringLayout to change its behaviour |
| CRecreateKnownPositions | |
| ►CFitnessParametersForm | Form collecting input parameters for a setting-up the fitness provider |
| CAtomSpecExpressionDefinition | |
| CDescriptorTreeNode | |
| CParametrizedDescriptorDefinition | |
| ►CFragmentViewPanel | A panel with a molecular viewer and attachment point table |
| CPausableTableModelListener | |
| CFSEParametersForm | Form collecting input parameters for a combinatorial/virtual screening experiment performed by FragSpaceExplorer |
| CFSParametersForm | Form collecting input parameters for defining the fragment space |
| CFSParamsDialog | A modal dialog to define a fragment space and load it |
| ►CGAParametersForm | Form collecting input parameters for a genetic algorithm experiment |
| CProbabilityFuncitonShape | The identifiers of probability function shapes that are available |
| ►CGraphVertexMolViewerPanel | A panel that collects three viewers: |
| CMouseModeChoiceListener | Listener for identifying the node on which the user has clicked and load the corresponding fragment into the fragment viewer pane |
| CNodeClickedListener | Listener for identifying the node on which the user has clicked and load the corresponding fragment into the fragment viewer pane |
| ►CGraphViewerPanel | A Panel that holds the JUNG representation of a graph |
| CEdgeDrawPaintTransformer | |
| CEdgeLabelTransformer | |
| CEdgeStrokeTransformer | |
| CGraphOptsPopup | |
| CJEdge | An edge in the JUNG Graph |
| CJVertex | Vertex in the JUNG Graph |
| CJVertexType | |
| CLabelType | |
| CPopupGraphMousePlugin | |
| CVertexFillPaintTransformer | |
| CVertexLabelTransformer | |
| CVertexShapePaintTransformer | |
| CGUI | Graphical User Interface of the DENOPTIM package |
| CGUIAPClassDefinitionDialog | |
| CGUIAtomSelectionDialog | A dialog window meant only to select atoms one or multiple times |
| ►CGUICardPanel | Class of GUI panels meant to occupy one card in the deck-of-cards layout of the main panel |
| CremoveCardActionListener | Remove the card from the deck of cards and takes care of removing also the entry in the list of active tabs |
| CGUICompatibilityMatrixTab | A panel for handling of compatibility matrix |
| CGUIEmptyVertexMaker | |
| CGUIFileOpener | File opener for DENOPTIM GUI |
| CGUIFileSaver | GUI component to provide pathname where to save stuff |
| ►CGUIGraphHandler | A panel that understands DENOPTIM graphs and allows to create and edit them |
| ►CConfigTemplateDialog | Dialog to configure one or more templates |
| CTemplateConfiguration | Utility class for a form to configure a template via the GUI |
| CGraphSpinnerChangeEvent | |
| CshowHideLabelsListener | |
| CGUIInspectFSERun | A panel that allows to inspect the output of an combinatorial experiment exploring a fragment space |
| ►CGUIInspectGARun | A panel that allows to inspect the output of an artificial evolution experiment |
| CGenerationChoiceDialog | Modal dialog that asks the user for a generation number |
| CPlottedCandidatesComparator | |
| CGUIMainPanel | The main panel is a deck of cards that occupies all the GUI frame |
| CGUIModalDialog | |
| ►CGUIPreferences | The collection of tunable preferences |
| CSMITo3DEngine | Available engines used to do SMILES-to-3D conversion |
| CGUIPreferencesDialog | |
| CGUIPrepare | Class representing the general structure of a form including a specific set of parameter collections |
| ►CGUIPrepareFitnessRunner | Form that allows to test the configuration of a fitness provider |
| CInputForm | |
| CGUIPrepareFSERun | Master form containing all sub-forms that need to be filled to define the input parameters for FragSpaceExplorer |
| CGUIPrepareGARun | Master form containing all sub-forms that need to be filled to define the input parameters for DenoptimGA |
| CGUITextReader | A panel that allows to print the content of a text file into a GUI tab |
| ►CGUIVertexInspector | A panel with a viewer capable of visualising DENOPTIM fragments and allows to create and edit fragments |
| CVrtxSpinnerChangeEvent | |
| ►CGUIVertexSelector | A modal dialog with a viewer that understands the different types of DENOPTIM vertex and allows to select vertices and, if needed, attachment points |
| CVrtxSpinnerChangeEvent | |
| CHomePanel | The home panel contains shortcuts buttons to perform the most common tasks |
| CILoadFragSpace | Implemented by GUI components that want to allow user-driven loading of the fragment space |
| CIParametersForm | Interface for parameter forms |
| CIVertexAPSelection | Interface for all vertex viewers that intend to allow selection of attachment points |
| CJmolPanel | |
| CJUNGGraphSnapshot | This class collects information on how a graph was displayed in a JUNG visialisation server (i.e., node positions and visible labels) |
| ►CMainToolBar | Main tool bar of the DENOPTIM graphical user interface |
| CRecentFileItem | |
| CMoleculeViewPanel | A panel with a molecular viewer and data table |
| CMolToGraphParametersDialog | |
| ►CParametersForm | General structure of a form for collecting input parameters of various nature |
| CCmbFieldChange | |
| CFieldListener | |
| CRdbFieldChange | |
| CTabFieldChange | |
| CScrollableJPupupMenu | 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 |
| CUtils | |
| ►CVertexAsGraphViewPanel | A panel to visualize a vertex as a graph component with attachment point table |
| CPausableTableModelListener | |
| ►CVertexAsTwoDimStructureViewPanel | A panel to visualize a vertex as two-dimensional chemical structure with attachment point table |
| CAtomOrAPGenerator | |
| CPausableTableModelListener | |
| CTwoDimStructurePanel | Panel dealing with the painting of 2D chemical representation |
| CVertexViewPanel | A panel for visualizing vertices |
| ►Nintegration | |
| ►Npython | |
| CPy4JGetawayServer | 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 |
| ►Nrcoserver | |
| CRCOSocketServerClient | Sends the request to produce a socket server running the RingClosingMM service |
| CRCOSocketServerClientTest | Unit test for RCOSocketServerClient |
| ►Ntinker | |
| CConformationalSearchPSSROT | Tool to perform conformational search via Tinker PSSROT program |
| CTinkerAtom | Based on the code from ffx.kenai.com Michael J |
| CTinkerBond | |
| CTinkerConstants | General set of constants used to deal with Tinker |
| CTinkerException | Exceptions resulting from a failure of Tinker |
| CTinkerUtils | Toolbox of utilities for Tinker style molecular representation |
| CTinkerUtilsTest | Unit test for TinkerUtils |
| ►Nio | |
| ►CDenoptimIO | Utility methods for input/output |
| CPartlySilencedChemObjReaderErrorHandler | This differs from DefaultChemObjectReaderErrorHandler just by ignoring messages about invalid symbol |
| CDenoptimIOTest | Unit test for input/output |
| CIteratingAtomContainerReader | 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 |
| CSMILESListFormat | Class for recognizing file containing a list of SMILES |
| CSMILESListFormatTest | Unit test for SMILES List Format |
| ►Njson | |
| ►CDENOPTIMgson | Class for de/serializing DENOPTIM graphs from/to JSON format |
| CDENOPTIMExclusionStrategy | |
| CDENOPTIMExclusionStrategyNoAPMap | |
| CDENOPTIMgsonTest | Unit test for DENOPTIMgson |
| CIAtomContainerDeserializer | Deserialisation of collections of both light-weight atoms and bonds into a CDK IAtomContainer |
| CIAtomContainerSerializer | Class to serialise CDK's IAtomContainer in a simplified manner |
| CLWAtom | A light-weight atom representation to facilitate json serialization of IAtom |
| CLWBond | A light-weight bond representation to facilitate json serialization of IBond |
| ►Nlogging | |
| CCounterID | Identifier of a counter |
| CHTMLLogFormatter | |
| CMonitor | A collection of counters user to count actions taken by the evolutionary algorithm |
| CStaticLogger | Logger class for DENOPTIM |
| CVersion | Class handling DENOPTIM's version identifier for headers |
| ►Nmain | |
| CBehavior | Represents the behavior of the program at start-up |
| CCLIOptions | |
| ►CMain | Entry point of any kind of run of the DENOPTIM program |
| CRunType | Types of runs that can be requested to the DENOPTIM Main class |
| CMainTest | |
| ►Nmolecularmodeling | |
| ►Nzmatrix | |
| CZMatrix | Representation of an atom container's geometry with internal coordinates |
| CZMatrixAtom | Representation of an atom in the ZMatrix |
| CZMatrixAtomTest | Unit test for ZMatrixAtom |
| CZMatrixBond | Representation of a bond in the ZMatrix |
| CZMatrixBondTest | Unit test for ZMatrixAtom |
| CZMatrixTest | Unit test for ZMatrix |
| CChemicalObjectModel | Collector of molecular information, related to a single chemical object, that is deployed within the 3D builder |
| CChemicalObjectModelTest | Unit test for ChemicalObjectModel |
| CMMBuilderUtils | Utilities for molecular models builder |
| CMultiMolecularModelBuilder | |
| ►CRingClosureTool | Toolkit to perform ring closing conformational search |
| CRingClosedMolComparator | Compares the Molecule3DBuilder afters ring closing-biased conformational adaptation |
| CThreeDimTreeBuilder | Tool to build build three-dimensional (3D) tree-like molecular structures from DGraph |
| CThreeDimTreeBuilderTest | Unit test for TreeBuilder3D |
| ►Nprograms | |
| ►Ncombinatorial | |
| CCEBLParameters | Parameters controlling execution of the combinatorial algorithm for exploration of a fragment space by layer (CEBL) |
| CFragSpaceExplorer | Combinatorial exploration of the fragment space |
| ►Ndenovo | |
| CGAParameters | Parameters for genetic algorithm |
| CGAParametersTest | Unit test |
| CGARunner | Programs that runs de novo design by a genetic algorithm |
| ►Nfitnessevaluator | |
| CFitnessEvaluationTask | Task that calls the fitness provider |
| CFitnessRunner | Stand-alone fitness provider |
| CFPRunner | Runs a fitness provider task as defined in the static parameters |
| CFRParameters | Parameters controlling execution of FitnessRunner |
| ►Nfragmenter | |
| CCuttingRule | A cutting rule with three SMARTS queries (atom 1, bond, atom2) and options |
| CFragmenter | Tool to create fragments by chopping 2D/3D chemical structures |
| CFragmenterParameters | Parameters controlling execution of the fragmenter |
| CMatchedBond | |
| ►Ngenetweeker | |
| CGeneOpsRunner | Tool to run genetic operations in a stand-alone fashion, i.e., outside of a genetic algorithm run |
| ►CGeneOpsRunnerParameters | Parameters controlling execution of TestOperator |
| COperator | Testable Operators |
| ►Ngrapheditor | |
| CGraphEditor | Tool for editing DGraphs |
| CGraphEdParameters | Parameters controlling execution of GraphEditor |
| ►Ngraphlisthandler | |
| CGraphListsHandler | Tool for handling lists of graphs |
| CGraphListsHandlerParameters | Parameters controlling execution of GraphEditor |
| ►Nisomorphism | |
| CIsomorphism | Tool to perform isomorphism analysis on DGraphs |
| CIsomorphismParameters | Parameters controlling execution of Isomorphism main class |
| ►Nmol2graph | |
| CMol2Graph | Tool for creating DGraphs from molecules |
| CMol2GraphParameters | Parameters controlling execution of GraphEditor |
| ►Nmoldecularmodelbuilder | |
| CMMBuilderParameters | Parameters for the conformer generator (3D builder) |
| CMolecularModelBuilder | Builder of molecular models |
| ►CRunTimeParameters | Collection of parameters controlling the behavior of the software |
| CParametersType | Identifier of the type of parameters |
| ►Ntask | |
| CFitnessTask | Task that assesses the fitness of a given graph |
| CParallelAsynchronousTaskExecutor | Runs tasks parallel in asynchronous fashion |
| CProcessHandler | |
| CProgramTask | Task structure for any of the main programs in the denoptim project, such as genetic algorithm and combinatorial exploration of fragment spaces |
| ►CStaticTaskManager | Manager for tasks submitted by the GUI |
| CShutDownHook | Shutdown hook that stops all child tasks upon shutdown of JavaVM |
| CStreamGobbler | See http://www.javaworld.com/jw-12-2000/jw-1229-traps.html?page=4 |
| CTask | A task that can throw exceptions |
| CTasksBatchManager | Class that manages the submission of a batch of tasks |
| ►Nutils | |
| CAtomOrganizer | Tool for re-organizing the list of atoms of an IAtomContainer |
| CCartesianSpaceUtils | Utilities for working in the Cartesian space |
| CConnectedLigand | A ConnectedLigand is just an atom with an explicit field reporting the number of connected atoms |
| CConnectedLigandComparator | Compare two ConnectedLigand according to the number of connected atoms and the mass number |
| CCrossoverType | Types of crossover defined |
| CDummyAtomHandler | Toll to add/remove dummy atoms from linearities or multi-hapto sites |
| CFormulaUtils | Utilities for manipulating molecular formulas |
| CFormulaUtilsTest | Unit test for tools manipulating molecular formulae |
| CGeneralUtils | General utilities |
| CGenUtilsTest | Unit test |
| CGraphConversionTool | Tool to convert string into graphs and into molecular representation |
| CGraphConversionToolTest | Unit test for GraphConversionTool |
| ►CGraphEdit | Definition of a graph editing task |
| CEditTask | Defined the kind of graph editing task |
| CGraphUtils | Utilities for graphs |
| CManySMARTSQuery | Container of lists of atoms matching a list of SMARTS |
| CMathUtils | Some useful math operations |
| CMoleculeUtils | Utilities for molecule conversion |
| CMoleculeUtilsTest | Unit test for DENOPTIMMoleculeUtils |
| CMutationType | 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 |
| CObjectPair | 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 |
| CRandomizer | Tool to generate random numbers and random decisions |
| CRandomizerTest | Unit test |
| CRingClosingUtils | Toolbox useful when dealing with Ring Closing Attractors and ring closures |
| CRotationalSpaceUtils | Tool box for definition and management of the rotational space, which is given by the list of rotatable bonds |
| CRotBndConstraint | The definition of a constraint applying to rotatable bonds |
| CSizeControlledSet | Class meant to collect unique strings without leading to memory overflow |
| CSizeControlledSetTest | Unit test for SizeControlledSet |
| CStatUtils | Utilities for calculating basic statistics |
| CTaskUtils | Utilities for tasks |
1.9.4