This is the complete list of members for denoptim.io.DenoptimIO, including all inherited members.

appendTxtFiles(File f1, List< File > files)	denoptim.io.DenoptimIO	static
builder	denoptim.io.DenoptimIO	privatestatic
FS	denoptim.io.DenoptimIO	static
getChemDoodleString(IAtomContainer mol)	denoptim.io.DenoptimIO	static
NL	denoptim.io.DenoptimIO	static
readAllAPClasses(File fragLib)	denoptim.io.DenoptimIO	static
readAllAtomContainers(File file)	denoptim.io.DenoptimIO	static
readBridgeHesFindingRules(String fileName)	denoptim.io.DenoptimIO	static
readBridgeHesFindingRules(BufferedReader br)	denoptim.io.DenoptimIO	static
readCandidates(File file)	denoptim.io.DenoptimIO	static
readCandidates(File file, boolean allowNoUID)	denoptim.io.DenoptimIO	static
readCompatibilityMatrix(String fileName, HashMap< APClass, ArrayList< APClass > > compatMap, HashMap< APClass, APClass > cappingMap, Set< APClass > forbiddenEndList)	denoptim.io.DenoptimIO	static
readCSDFormulae(File file)	denoptim.io.DenoptimIO	static
readCuttingRules(BufferedReader reader, List< CuttingRule > cutRules, String source)	denoptim.io.DenoptimIO	static
readCuttingRules(File file, List< CuttingRule > cutRules)	denoptim.io.DenoptimIO	static
readCuttingRules(ArrayList< String > cutRulLines, List< CuttingRule > cutRules, String source)	denoptim.io.DenoptimIO	static
readDENOPTIMData(String pathname)	denoptim.io.DenoptimIO	static
readDENOPTIMGraphEditFromFile(String fileName)	denoptim.io.DenoptimIO	static
readDENOPTIMGraphsFromFile(File inFile)	denoptim.io.DenoptimIO	static
readDENOPTIMGraphsFromFile(File inFile, FileFormat format)	denoptim.io.DenoptimIO	static
readDENOPTIMGraphsFromJSONFile(String fileName)	denoptim.io.DenoptimIO	static
readDENOPTIMGraphsFromSDFile(String fileName)	denoptim.io.DenoptimIO	static
readDENOPTIMGraphsFromTxtFile(String fileName, FragmentSpace fragSpace, Logger logger)	denoptim.io.DenoptimIO	static
readDENOPTIMVertexesFromJSONFile(String fileName)	denoptim.io.DenoptimIO	static
readDENOPTIMVertexesFromSDFile(String fileName, Vertex.BBType bbt)	denoptim.io.DenoptimIO	static
readGenerationFromSummary(File file)	denoptim.io.DenoptimIO	static
readGraphFromSDFileIAC(IAtomContainer mol)	denoptim.io.DenoptimIO	static
readGraphFromSDFileIAC(IAtomContainer mol, int molId)	denoptim.io.DenoptimIO	static
readGraphFromSDFileIAC(IAtomContainer mol, int molId, String fileName)	denoptim.io.DenoptimIO	static
readLightWeightCandidate(File file)	denoptim.io.DenoptimIO	static
readList(String fileName)	denoptim.io.DenoptimIO	static
readList(String fileName, boolean allowEmpty)	denoptim.io.DenoptimIO	static
readPopulationMemberPathnames(File file)	denoptim.io.DenoptimIO	static
readPopulationMembersTraces(File file)	denoptim.io.DenoptimIO	static
readPopulationProps(File file)	denoptim.io.DenoptimIO	static
readRCCompatibilityMatrix(String fileName, HashMap< APClass, ArrayList< APClass > > rcCompatMap)	denoptim.io.DenoptimIO	static
readRecentFilesMap()	denoptim.io.DenoptimIO	static
readSDFFile(String fileName)	denoptim.io.DenoptimIO	static
readSDFProperties(String pathName, List< String > propNames)	denoptim.io.DenoptimIO	static
readText(String fileName)	denoptim.io.DenoptimIO	static
readVertexes(File file, Vertex.BBType bbt)	denoptim.io.DenoptimIO	static
scanLoggingLevels(Logger logger)	denoptim.io.DenoptimIO	static
writeCandidatesToFile(File file, List< Candidate > popMembers, boolean append)	denoptim.io.DenoptimIO	static
writeCandidateToFile(File file, Candidate candidate, boolean append)	denoptim.io.DenoptimIO	static
writeCompatibilityMatrix(String fileName, HashMap< APClass, ArrayList< APClass > > cpMap, HashMap< APClass, APClass > capMap, HashSet< APClass > ends)	denoptim.io.DenoptimIO	static
writeCuttingRules(File file, List< CuttingRule > cutRules)	denoptim.io.DenoptimIO	static
writeData(String fileName, String data, boolean append)	denoptim.io.DenoptimIO	static
writeGraphsToFile(File file, FileFormat format, List< DGraph > modGraphs, Logger logger, Randomizer randomizer)	denoptim.io.DenoptimIO	static
writeGraphsToJSON(File file, List< DGraph > graphs)	denoptim.io.DenoptimIO	static
writeGraphsToJSON(File file, List< DGraph > graphs, boolean append)	denoptim.io.DenoptimIO	static
writeGraphsToSDF(File file, List< DGraph > graphs, Logger logger, Randomizer randomizer)	denoptim.io.DenoptimIO	static
writeGraphsToSDF(File file, List< DGraph > graphs, boolean append, Logger logger, Randomizer randomizer)	denoptim.io.DenoptimIO	static
writeGraphsToSDF(File file, List< DGraph > modGraphs, boolean append, boolean make3D, Logger logger, Randomizer randomizer)	denoptim.io.DenoptimIO	static
writeGraphToFile(File file, FileFormat format, DGraph graph, Logger logger, Randomizer randomizer)	denoptim.io.DenoptimIO	static
writeGraphToFile(String fileName, DGraph graph, boolean append)	denoptim.io.DenoptimIO	static
writeGraphToJSON(File file, DGraph graph)	denoptim.io.DenoptimIO	static
writeGraphToSDF(File file, DGraph graph, boolean append, boolean make3D, Logger logger, Randomizer randomizer)	denoptim.io.DenoptimIO	static
writeGraphToSDF(File file, DGraph graph, boolean append, Logger logger, Randomizer randomizer)	denoptim.io.DenoptimIO	static
writeMol2File(String fileName, IAtomContainer mol, boolean append)	denoptim.io.DenoptimIO	static
writeSDFFile(String fileName, IAtomContainer mol)	denoptim.io.DenoptimIO	static
writeSDFFile(String fileName, List< IAtomContainer > mols)	denoptim.io.DenoptimIO	static
writeSDFFile(String fileName, List< IAtomContainer > mols, boolean append)	denoptim.io.DenoptimIO	static
writeSDFFile(String fileName, IAtomContainer mol, boolean append)	denoptim.io.DenoptimIO	static
writeSmiles(String fileName, String smiles, boolean append)	denoptim.io.DenoptimIO	static
writeSmilesSet(String fileName, String[] smiles, boolean append)	denoptim.io.DenoptimIO	static
writeVertexesToFile(File file, FileFormat format, List< Vertex > vertexes)	denoptim.io.DenoptimIO	static
writeVertexesToFile(File file, FileFormat format, List< Vertex > vertexes, boolean append)	denoptim.io.DenoptimIO	static
writeVertexesToJSON(File file, List< Vertex > vertexes)	denoptim.io.DenoptimIO	static
writeVertexesToJSON(File file, List< Vertex > vertexes, boolean append)	denoptim.io.DenoptimIO	static
writeVertexesToSDF(File file, List< Vertex > vertexes, boolean append)	denoptim.io.DenoptimIO	static
writeVertexToFile(File file, FileFormat format, Vertex vertex, boolean append)	denoptim.io.DenoptimIO	static
writeVertexToSDF(String pathName, Vertex vertex)	denoptim.io.DenoptimIO	static
writeXYZFile(String fileName, IAtomContainer mol, boolean append)	denoptim.io.DenoptimIO	static