Utility methods for input/output. More...

Collaboration diagram for denoptim.io.DenoptimIO:

Static Public Member Functions
static Object	readDENOPTIMData (String pathname) throws Exception
	Reads any content of a given pathname and tries to read DENOPTIM data from it. More...

static List< Candidate >	readGenerationFromSummary (File file) throws DENOPTIMException
	Reads a `FileFormat#GENSUMMARY` file and searches all the files defining each member of the population. More...

static List< IAtomContainer >	readAllAtomContainers (File file) throws IOException, CDKException
	Returns a single collection with all atom containers found in a file of any format. More...

static ArrayList< IAtomContainer >	readSDFFile (String fileName) throws DENOPTIMException
	Reads a file containing multiple molecules (multiple SD format)) More...

static File	writeVertexesToFile (File file, FileFormat format, List< Vertex > vertexes) throws DENOPTIMException
	Writes vertexes to file. More...

static File	writeVertexToFile (File file, FileFormat format, Vertex vertex, boolean append) throws DENOPTIMException
	Writes vertexes to file. More...

static File	writeVertexesToFile (File file, FileFormat format, List< Vertex > vertexes, boolean append) throws DENOPTIMException
	Writes vertexes to file. More...

static void	writeVertexesToJSON (File file, List< Vertex > vertexes) throws DENOPTIMException
	Writes vertexes to JSON file. More...

static void	writeVertexesToJSON (File file, List< Vertex > vertexes, boolean append) throws DENOPTIMException
	Writes vertexes to JSON file. More...

static void	writeVertexToSDF (String pathName, Vertex vertex) throws DENOPTIMException
	Writes a vertex to an SDF file. More...

static void	writeVertexesToSDF (File file, List< Vertex > vertexes, boolean append) throws DENOPTIMException
	Write a list of vertexes to file. More...

static void	writeSDFFile (String fileName, IAtomContainer mol) throws DENOPTIMException
	Writes `IAtomContainer` to SDF file. More...

static void	writeSDFFile (String fileName, List< IAtomContainer > mols) throws DENOPTIMException
	Writes `IAtomContainer`s to SDF file. More...

static void	writeSDFFile (String fileName, List< IAtomContainer > mols, boolean append) throws DENOPTIMException
	Writes a set of `IAtomContainer`s to SDF file. More...

static void	writeSDFFile (String fileName, IAtomContainer mol, boolean append) throws DENOPTIMException
	Writes an `IAtomContainer` to SDF file. More...

static void	writeMol2File (String fileName, IAtomContainer mol, boolean append) throws DENOPTIMException

static void	writeXYZFile (String fileName, IAtomContainer mol, boolean append) throws DENOPTIMException

static void	writeSmilesSet (String fileName, String[] smiles, boolean append) throws DENOPTIMException
	Writes multiple smiles string array to the specified file. More...

static void	writeSmiles (String fileName, String smiles, boolean append) throws DENOPTIMException
	Writes a single smiles string to the specified file. More...

static void	writeData (String fileName, String data, boolean append) throws DENOPTIMException
	Write text-like data file. More...

static List< CandidateLW >	readLightWeightCandidate (File file) throws DENOPTIMException
	Read only selected data from a GA produced items. More...

static double[]	readPopulationProps (File file) throws DENOPTIMException
	Read the min, max, mean, and median of a population from `FileFormat#GENSUMMARY` file. More...

static List< String >	readPopulationMemberPathnames (File file) throws DENOPTIMException
	Read the pathnames to the population members from a `FileFormat#GENSUMMARY` file. More...

static List< CandidateLW >	readPopulationMembersTraces (File file) throws DENOPTIMException
	Read the minimal info that can be found in a `FileFormat#GENSUMMARY` file about the members of a population. More...

static ArrayList< String >	readList (String fileName) throws DENOPTIMException
	Read list of data as text. More...

static ArrayList< String >	readList (String fileName, boolean allowEmpty) throws DENOPTIMException
	Read list of data as text. More...

static String	readText (String fileName) throws DENOPTIMException
	Read text from file. More...

static List< Map< String, Object > >	readSDFProperties (String pathName, List< String > propNames) throws DENOPTIMException
	Extract selected properties from SDF files. More...

static String	getChemDoodleString (IAtomContainer mol) throws DENOPTIMException
	Generate the ChemDoodle representation of the molecule. More...

static Set< APClass >	readAllAPClasses (File fragLib)

static void	writeCompatibilityMatrix (String fileName, HashMap< APClass, ArrayList< APClass > > cpMap, HashMap< APClass, APClass > capMap, HashSet< APClass > ends) throws DENOPTIMException
	The class compatibility matrix. More...

static void	readCompatibilityMatrix (String fileName, HashMap< APClass, ArrayList< APClass > > compatMap, HashMap< APClass, APClass > cappingMap, Set< APClass > forbiddenEndList) throws DENOPTIMException
	Read the APclass compatibility matrix data from file. More...

static void	readRCCompatibilityMatrix (String fileName, HashMap< APClass, ArrayList< APClass > > rcCompatMap) throws DENOPTIMException
	Reads the APclass compatibility matrix for ring-closing connections (the RC-CPMap). More...

static ArrayList< Candidate >	readCandidates (File file) throws DENOPTIMException
	Reads SDF files that represent one or more tested candidates. More...

static ArrayList< Candidate >	readCandidates (File file, boolean allowNoUID) throws DENOPTIMException
	Reads SDF files that represent one or more tested or to be tested candidates. More...

static void	writeCandidatesToFile (File file, List< Candidate > popMembers, boolean append) throws DENOPTIMException
	Writes candidate items to file. More...

static void	writeCandidateToFile (File file, Candidate candidate, boolean append) throws DENOPTIMException
	Writes one candidate item to file. More...

static ArrayList< GraphEdit >	readDENOPTIMGraphEditFromFile (String fileName) throws DENOPTIMException
	Reads a list of graph editing tasks from a JSON file. More...

static ArrayList< DGraph >	readDENOPTIMGraphsFromFile (File inFile) throws Exception
	Reads a list of `DGraph`s from file. More...

static ArrayList< DGraph >	readDENOPTIMGraphsFromFile (File inFile, FileFormat format) throws Exception
	Reads a list of `DGraph`s from file. More...

static ArrayList< DGraph >	readDENOPTIMGraphsFromSDFile (String fileName) throws DENOPTIMException
	Reads a list of <`DGraph`s from a SDF file. More...

static DGraph	readGraphFromSDFileIAC (IAtomContainer mol) throws DENOPTIMException
	Converts an atom container read in from an SDF file into a graph, if possible. More...

static DGraph	readGraphFromSDFileIAC (IAtomContainer mol, int molId) throws DENOPTIMException
	Converts an atom container read in from an SDF file into a graph, if possible. More...

static DGraph	readGraphFromSDFileIAC (IAtomContainer mol, int molId, String fileName) throws DENOPTIMException
	Converts an atom container read in from an SDF file into a graph, if possible. More...

static ArrayList< DGraph >	readDENOPTIMGraphsFromTxtFile (String fileName, FragmentSpace fragSpace, Logger logger) throws DENOPTIMException
	Reads a list of <`DGraph`s from a text file. More...

static ArrayList< Vertex >	readDENOPTIMVertexesFromJSONFile (String fileName) throws DENOPTIMException
	Reads a list of `Vertex`es from a JSON file. More...

static ArrayList< DGraph >	readDENOPTIMGraphsFromJSONFile (String fileName) throws DENOPTIMException
	Reads a list of `DGraph`s from a JSON file. More...

static File	writeGraphToFile (File file, FileFormat format, DGraph graph, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Writes the a graph to file. More...

static File	writeGraphsToFile (File file, FileFormat format, List< DGraph > modGraphs, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Writes the graphs to file. More...

static void	writeGraphsToSDF (File file, List< DGraph > graphs, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Writes the graphs to SDF file. More...

static void	writeGraphToSDF (File file, DGraph graph, boolean append, boolean make3D, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Writes the graph to SDF file. More...

static void	writeGraphToSDF (File file, DGraph graph, boolean append, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Writes the graph to SDF file. More...

static void	writeGraphsToSDF (File file, List< DGraph > graphs, boolean append, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Writes the graphs to SDF file. More...

static void	writeGraphsToSDF (File file, List< DGraph > modGraphs, boolean append, boolean make3D, Logger logger, Randomizer randomizer) throws DENOPTIMException
	Writes the graphs to SDF file. More...

static void	writeGraphToJSON (File file, DGraph graph) throws DENOPTIMException
	Writes the graph to JSON file. More...

static void	writeGraphsToJSON (File file, List< DGraph > graphs) throws DENOPTIMException
	Writes the graphs to JSON file. More...

static void	writeGraphsToJSON (File file, List< DGraph > graphs, boolean append) throws DENOPTIMException
	Writes the graphs to JSON file. More...

static void	writeGraphToFile (String fileName, DGraph graph, boolean append) throws DENOPTIMException
	Writes the string representation of a graph to file. More...

static Map< File, FileFormat >	readRecentFilesMap ()
	Reads the file defined in `DENOPTIMConstants#RECENTFILESLIST` and makes a map that contains the pathname and the format of each recent file. More...

static ArrayList< Vertex >	readVertexes (File file, Vertex.BBType bbt) throws UndetectedFileFormatException, IOException, IllegalArgumentException, DENOPTIMException
	Reads `Vertex`es from any file that can contain such items. More...

static ArrayList< Vertex >	readDENOPTIMVertexesFromSDFile (String fileName, Vertex.BBType bbt) throws DENOPTIMException
	Reads a list of `Vertex`es from a SDF file. More...

static LinkedHashMap< String, String >	readCSDFormulae (File file) throws DENOPTIMException
	Read molecular formula from TXT data representation produced by Cambridge Structural Database tools (such as Conquest). More...

static void	readCuttingRules (BufferedReader reader, List< CuttingRule > cutRules, String source) throws DENOPTIMException
	Read cutting rules from a stream. More...

static void	readCuttingRules (File file, List< CuttingRule > cutRules) throws DENOPTIMException
	Read cutting rules from a properly formatted text file. More...

static void	readCuttingRules (ArrayList< String > cutRulLines, List< CuttingRule > cutRules, String source) throws DENOPTIMException
	Read cutting rules from a properly formatted text file. More...

static void	writeCuttingRules (File file, List< CuttingRule > cutRules) throws DENOPTIMException
	Writes a formatted text file that collects cutting rule. More...

static void	appendTxtFiles (File f1, List< File > files) throws IOException
	Appends the second file to the first. More...

static List< BridgeHeadFindingRule >	readBridgeHesFindingRules (String fileName) throws DENOPTIMException
	Reads a list of rules for identifying potential bridge-head sites. More...

static List< BridgeHeadFindingRule >	readBridgeHesFindingRules (BufferedReader br) throws IOException
	Reads a list of rules for identifying potential bridge-head sites. More...

Static Public Attributes
static final String	FS = System.getProperty("file.separator")
	File separator from system. More...

static final String	NL = System.getProperty("line.separator")
	Newline character from system. More...

Static Private Attributes
static final IChemObjectBuilder	builder

Detailed Description

Utility methods for input/output.

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 113 of file DenoptimIO.java.

Member Function Documentation

◆ appendTxtFiles()

static void denoptim.io.DenoptimIO.appendTxtFiles	(	File	f1,
		List< File >	files
	)		throws IOException

static

Appends the second file to the first.

Parameters

f1	file being elongated
list	files providing the content to place in f1.

Exceptions

IOException

Definition at line 2565 of file DenoptimIO.java.

Referenced by denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations().

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◆ getChemDoodleString()

static String denoptim.io.DenoptimIO.getChemDoodleString ( IAtomContainer mol ) throws DENOPTIMException

static

Generate the ChemDoodle representation of the molecule.

Parameters

mol

Returns: molecule as a formatted string

Exceptions

DENOPTIMException

Definition at line 1078 of file DenoptimIO.java.

◆ readAllAPClasses()

static Set< APClass > denoptim.io.DenoptimIO.readAllAPClasses ( File fragLib )

static

Definition at line 1115 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readVertexes(), and denoptim.graph.Vertex.BBType.UNDEFINED.

Referenced by denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCappingGroupLibs(), denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromFragmentLibs(), and denoptim.io.DenoptimIOTest.testReadAllAPClasses().

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◆ readAllAtomContainers()

static List< IAtomContainer > denoptim.io.DenoptimIO.readAllAtomContainers ( File file ) throws IOException, CDKException

static

Returns a single collection with all atom containers found in a file of any format.

CIF files are internally converted to SDF files, causing loss of information beyond molecular structure in Cartesian coordinates. So, if you need more than molecular structure from CIF files, do not use this method.

Parameters

file	the file to read.

Returns: the list of containers found in the file.

Exceptions

IOException	if the file is not found or not readable.
CDKException	if the reading of the file goes wrong.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Definition at line 283 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.FS, denoptim.files.FileUtils.getTempFolder(), and denoptim.io.DenoptimIO.readAllAtomContainers().

Referenced by denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer(), denoptim.gui.GUIVertexInspector.importStructureFromFile(), denoptim.io.IteratingAtomContainerReader.IteratingAtomContainerReader(), denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile(), denoptim.fitness.FitnessExpressionParser.makeIBitFingerprint(), denoptim.programs.mol2graph.Mol2GraphParameters.processParameters(), denoptim.io.DenoptimIO.readAllAtomContainers(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.gui.MoleculeViewPanel.showPopup(), and denoptim.io.DenoptimIOTest.testReadAllAtomContainersFromCIF().

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◆ readBridgeHesFindingRules() [1/2]

static List< BridgeHeadFindingRule > denoptim.io.DenoptimIO.readBridgeHesFindingRules ( BufferedReader br ) throws IOException

static

Reads a list of rules for identifying potential bridge-head sites.

Parameters

reader the source of data.

Returns: the list of rules found in the reader.

Exceptions

IOException
DENOPTIMException	in case we cannot read, find, or understand the data.

Definition at line 2650 of file DenoptimIO.java.

References denoptim.json.DENOPTIMgson.getReader().

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◆ readBridgeHesFindingRules() [2/2]

static List< BridgeHeadFindingRule > denoptim.io.DenoptimIO.readBridgeHesFindingRules ( String fileName ) throws DENOPTIMException

static

Reads a list of rules for identifying potential bridge-head sites.

Parameters

fileName the pathname of the file to read

Returns: the list of rules found in the file.

Exceptions

DENOPTIMException in case we cannot read, find, or understand the data.

Definition at line 2609 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readBridgeHesFindingRules().

Referenced by denoptim.graph.rings.RingClosureParameters.interpretKeyword(), denoptim.io.DenoptimIO.readBridgeHesFindingRules(), and denoptim.graph.rings.RingClosureParameters.RingClosureParameters().

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◆ readCandidates() [1/2]

static ArrayList< Candidate > denoptim.io.DenoptimIO.readCandidates ( File file ) throws DENOPTIMException

static

Reads SDF files that represent one or more tested candidates.

Candidates are provided with a graph representation, a unique identifier, and either a fitness value or a mol_error defining why this candidate could not be evaluated.

Parameters

file	the SDF file to read.

Returns: the list of candidates.

Exceptions

DENOPTIMException is something goes wrong while reading the file or interpreting its content

Definition at line 1379 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readCandidates().

Referenced by denoptim.ga.EAUtils.getPopulationFromFile(), denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile(), denoptim.io.DenoptimIO.readCandidates(), denoptim.io.DenoptimIO.readDENOPTIMData(), denoptim.io.DenoptimIO.readGenerationFromSummary(), and denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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◆ readCandidates() [2/2]

static ArrayList< Candidate > denoptim.io.DenoptimIO.readCandidates	(	File	file,
		boolean	allowNoUID
	)		throws DENOPTIMException

static

Reads SDF files that represent one or more tested or to be tested candidates.

Parameters

file	the SDF file to read.
allowNoUID	use `true` if candidates should be allowed to have no unique identifier.

Returns: the list of candidates.

Exceptions

DENOPTIMException is something goes wrong while reading the file or interpreting its content

Definition at line 1398 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.GAGENDIRNAMEROOT, denoptim.io.DenoptimIO.readSDFFile(), denoptim.graph.Candidate.setGeneration(), and denoptim.graph.Candidate.setSDFFile().

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◆ readCompatibilityMatrix()

static void denoptim.io.DenoptimIO.readCompatibilityMatrix	(	String	fileName,
		HashMap< APClass, ArrayList< APClass > >	compatMap,
		HashMap< APClass, APClass >	cappingMap,
		Set< APClass >	forbiddenEndList
	)		throws DENOPTIMException

static

Read the APclass compatibility matrix data from file.

Parameters

fileName	the file to be read
compatMap	container for the APClass compatibility rules
cappingMap	container for the capping rules
forbiddenEndList	container for the definition of forbidden ends

Exceptions

DENOPTIMException

Definition at line 1206 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.APCMAPCAPPING, denoptim.constants.DENOPTIMConstants.APCMAPCOMPRULE, denoptim.constants.DENOPTIMConstants.APCMAPFORBIDDENEND, denoptim.constants.DENOPTIMConstants.APCMAPIGNORE, and denoptim.graph.APClass.make().

Referenced by denoptim.fragspace.FragmentSpace.FragmentSpace(), denoptim.fragspace.FragmentSpace.importCompatibilityMatrixFromFile(), and denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile().

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◆ readCSDFormulae()

static LinkedHashMap< String, String > denoptim.io.DenoptimIO.readCSDFormulae ( File file ) throws DENOPTIMException

static

Read molecular formula from TXT data representation produced by Cambridge Structural Database tools (such as Conquest).

Essentially, this method reads a text file expecting to find lines as the following among lines with other kinds of information:

REFCODE: ABEWOT
[...]
Formula:           C36 H44 Cl1 P2 Ru1 1+,F6 P1 1-

Parameters

file	the text file to read

Returns: the mapping of CSD's REFCODE as key to their respective molecular formula as formatted in the input.

Exceptions

DENOPTIMException if any exception occurs during the reading of the file or if the file does not exist.

Definition at line 2342 of file DenoptimIO.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.processParameters(), and denoptim.io.DenoptimIOTest.testReadCSDFormulae().

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◆ readCuttingRules() [1/3]

static void denoptim.io.DenoptimIO.readCuttingRules	(	ArrayList< String >	cutRulLines,
		List< CuttingRule >	cutRules,
		String	source
	)		throws DENOPTIMException

static

Read cutting rules from a properly formatted text file.

Parameters

cutRulLines	text lines containing cutting rules. These are expected to be lines starting with the `DENOPTIMConstants.CUTRULKEYWORD` keyword.
cutRules	the collector of the cutting rules. The collection is already sorted by priority when this method returns.
source	the source of text. This is used only in logging as the source of the text that we are trying to convert into cutting rules. For example, a file name.

Exceptions

DENOPTIMException in case there are errors in the formatting of the text contained in the file.

Definition at line 2469 of file DenoptimIO.java.

References denoptim.programs.fragmenter.CuttingRule.getPriority().

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◆ readCuttingRules() [2/3]

static void denoptim.io.DenoptimIO.readCuttingRules	(	BufferedReader	reader,
		List< CuttingRule >	cutRules,
		String	source
	)		throws DENOPTIMException

static

Read cutting rules from a stream.

Parameters

reader	the stream providing text lines.
cutRules	the collector of the cutting rules. The collection is already sorted by priority when this method returns.
source	the source of text. This is used only in logging as the source of the text that we are trying to convert into cutting rules. For example, a file name.

Exceptions

DENOPTIMException in case there are errors in the formatting of the text contained in the file.

Definition at line 2400 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.CUTRULKEYWORD, and denoptim.io.DenoptimIO.readCuttingRules().

Referenced by denoptim.gui.CuttingRulesSelectionDialog.CuttingRulesSelectionDialog(), denoptim.gui.GUIVertexInspector.dialogToDefineCuttingRules(), denoptim.programs.fragmenter.FragmenterParameters.processParameters(), denoptim.programs.mol2graph.Mol2GraphParameters.processParameters(), denoptim.io.DenoptimIO.readCuttingRules(), denoptim.io.DenoptimIOTest.testIOCuttingRules(), and denoptim.io.DenoptimIOTest.testReadCuttingRulsedDefault().

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◆ readCuttingRules() [3/3]

static void denoptim.io.DenoptimIO.readCuttingRules	(	File	file,
		List< CuttingRule >	cutRules
	)		throws DENOPTIMException

static

Read cutting rules from a properly formatted text file.

Parameters

file	the file to read.
cutRules	the collector of the cutting rules. The collection is already sorted by priority when this method returns.

Exceptions

DENOPTIMException in case there are errors in the formatting of the text contained in the file.

Definition at line 2438 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.CUTRULKEYWORD, denoptim.io.DenoptimIO.readCuttingRules(), and denoptim.io.DenoptimIO.readList().

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◆ readDENOPTIMData()

static Object denoptim.io.DenoptimIO.readDENOPTIMData ( String pathname ) throws Exception

static

Reads any content of a given pathname and tries to read DENOPTIM data from it.

As the type of the returned value if not defined this method is meant of untyped coding context, like the interfacing with Python. Please, avoid to use it in typed code context, like within JAVA code.

Parameters

pathname the pathname to read.

Returns: any DENOPTIM-like data that could be found in the given pathname.

Exceptions

Exception if for any reason no data can be returned.

Definition at line 140 of file DenoptimIO.java.

References denoptim.files.FileUtils.detectFileFormat(), denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.io.DenoptimIO.readCandidates(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.io.DenoptimIO.readGenerationFromSummary(), denoptim.io.DenoptimIO.readVertexes(), and denoptim.files.FileFormat.UNRECOGNIZED.

Referenced by denoptim.integration.python.Py4JGetawayServer.loadData().

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◆ readDENOPTIMGraphEditFromFile()

static ArrayList< GraphEdit > denoptim.io.DenoptimIO.readDENOPTIMGraphEditFromFile ( String fileName ) throws DENOPTIMException

static

Reads a list of graph editing tasks from a JSON file.

Parameters

fileName the pathname of the file to read

Returns: the list of editing tasks

Exceptions

DENOPTIMException

Definition at line 1482 of file DenoptimIO.java.

References denoptim.json.DENOPTIMgson.getReader().

Referenced by denoptim.programs.grapheditor.GraphEdParameters.processParameters().

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◆ readDENOPTIMGraphsFromFile() [1/2]

static ArrayList< DGraph > denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile ( File inFile ) throws Exception

static

Reads a list of DGraphs from file.

Parameters

fileName the pathname of the file to read

Returns: the list of graphs

Exceptions

Exception

Definition at line 1552 of file DenoptimIO.java.

References denoptim.files.FileUtils.detectFileFormat(), and denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile().

Referenced by denoptim.programs.combinatorial.CEBLParameters.processParameters(), denoptim.programs.graphlisthandler.GraphListsHandlerParameters.processParameters(), denoptim.ga.EAUtils.readCandidateFromFile(), denoptim.io.DenoptimIO.readDENOPTIMData(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.gui.GUIGraphHandler.readGraphsFromFile(), denoptim.programs.grapheditor.GraphEdParameters.readInputGraphs(), denoptim.programs.fitnessevaluator.FPRunner.run(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), denoptim.programs.isomorphism.Isomorphism.runProgram(), and denoptim.programs.genetweeker.GeneOpsRunner.runXOver().

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◆ readDENOPTIMGraphsFromFile() [2/2]

static ArrayList< DGraph > denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile	(	File	inFile,
		FileFormat	format
	)		throws Exception

static

Reads a list of DGraphs from file.

Parameters

inFile	the file to read
format	the format of the file to read. We assume this has been detected from previous calls of `FileUtils#detectFileFormat(File)` and that now we want to avoid having to call that method again.

Returns: the list of graphs

Exceptions

Exception

Definition at line 1572 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.GRAPHTAG, denoptim.io.DenoptimIO.readDENOPTIMGraphsFromJSONFile(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromSDFile(), denoptim.io.DenoptimIO.readVertexes(), denoptim.graph.Vertex.BBType.UNDEFINED, and denoptim.files.FileFormat.VRTXSDF.

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◆ readDENOPTIMGraphsFromJSONFile()

static ArrayList< DGraph > denoptim.io.DenoptimIO.readDENOPTIMGraphsFromJSONFile ( String fileName ) throws DENOPTIMException

static

Reads a list of DGraphs from a JSON file.

Parameters

fileName the pathname of the file to read

Returns: the list of graphs

Exceptions

DENOPTIMException

Definition at line 1876 of file DenoptimIO.java.

References denoptim.graph.DGraph.fromJson(), and denoptim.json.DENOPTIMgson.getReader().

Referenced by denoptim.combinatorial.CombinatorialExplorerByLayer.exploreCombinationsAtGivenLevel(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.gui.GUIGraphHandler.readGraphsFromFile(), denoptim.io.DenoptimIO.readVertexes(), and denoptim.io.DenoptimIOTest.testSerializeDeserializeDENOPTIMGraphs().

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◆ readDENOPTIMGraphsFromSDFile()

static ArrayList< DGraph > denoptim.io.DenoptimIO.readDENOPTIMGraphsFromSDFile ( String fileName ) throws DENOPTIMException

static

Reads a list of <DGraphs from a SDF file.

Parameters

fileName the pathname of the file to read.

Returns: the list of graphs

Exceptions

DENOPTIMException

Definition at line 1627 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readGraphFromSDFileIAC(), and denoptim.io.DenoptimIO.readSDFFile().

Referenced by denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.gui.GUIGraphHandler.readGraphsFromFile(), and denoptim.io.DenoptimIO.readVertexes().

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◆ readDENOPTIMGraphsFromTxtFile()

static ArrayList< DGraph > denoptim.io.DenoptimIO.readDENOPTIMGraphsFromTxtFile	(	String	fileName,
		FragmentSpace	fragSpace,
		Logger	logger
	)		throws DENOPTIMException

static

Reads a list of <DGraphs from a text file.

Parameters

fileName the pathname of the file to read.

Returns: the list of graphs.

Exceptions

DENOPTIMException

Definition at line 1753 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.APCMAPIGNORE, and denoptim.utils.GraphConversionTool.getGraphFromString().

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◆ readDENOPTIMVertexesFromJSONFile()

static ArrayList< Vertex > denoptim.io.DenoptimIO.readDENOPTIMVertexesFromJSONFile ( String fileName ) throws DENOPTIMException

static

Reads a list of Vertexes from a JSON file.

Parameters

fileName the pathname of the file to read.

Returns: the list of vertexes.

Exceptions

DENOPTIMException

Definition at line 1810 of file DenoptimIO.java.

References denoptim.graph.Vertex.fromJson(), and denoptim.json.DENOPTIMgson.getReader().

Referenced by denoptim.io.DenoptimIO.readVertexes(), denoptim.io.DenoptimIOTest.testAppendToJSON(), and denoptim.io.DenoptimIO.writeVertexesToJSON().

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◆ readDENOPTIMVertexesFromSDFile()

static ArrayList< Vertex > denoptim.io.DenoptimIO.readDENOPTIMVertexesFromSDFile	(	String	fileName,
		Vertex.BBType	bbt
	)		throws DENOPTIMException

static

Reads a list of Vertexes from a SDF file.

Parameters

fileName the pathname of the file to read.

Returns: the list of vertexes.

Exceptions

DENOPTIMException

Definition at line 2301 of file DenoptimIO.java.

References denoptim.json.DENOPTIMgson.getReader(), denoptim.graph.Vertex.parseVertexFromSDFFormat(), and denoptim.io.DenoptimIO.readSDFFile().

Referenced by denoptim.io.DenoptimIO.readVertexes().

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◆ readGenerationFromSummary()

static List< Candidate > denoptim.io.DenoptimIO.readGenerationFromSummary ( File file ) throws DENOPTIMException

static

Reads a FileFormat#GENSUMMARY file and searches all the files defining each member of the population.

If the pathnames found in FileFormat#GENSUMMARY do not exist, this method will try to build the candidate's files pathnames relative to the location of the FileFormat#GENSUMMARY. This assumes that the original folder structure of a FileFormat#GA_RUN has been preserved.

Parameters

file	the generation summary file (`FileFormat#GENSUMMARY`) to read

Returns: population members

Exceptions

DENOPTIMException

Definition at line 238 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readCandidates(), and denoptim.io.DenoptimIO.readPopulationMemberPathnames().

Referenced by denoptim.io.DenoptimIO.readDENOPTIMData(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ readGraphFromSDFileIAC() [1/3]

static DGraph denoptim.io.DenoptimIO.readGraphFromSDFileIAC ( IAtomContainer mol ) throws DENOPTIMException

static

Converts an atom container read in from an SDF file into a graph, if possible.

Otherwise, throws an exception.

Parameters

mol	the atom container coming from SDF representation
molId	identified used only for logging purposed

Returns: the corresponding graph or null.

Exceptions

DENOPTIMException is the atom container cannot be converted due to lack of the proper SDF tags, or failure in the conversion.

Definition at line 1653 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readGraphFromSDFileIAC().

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromSDFile(), and denoptim.io.DenoptimIO.readGraphFromSDFileIAC().

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◆ readGraphFromSDFileIAC() [2/3]

static DGraph denoptim.io.DenoptimIO.readGraphFromSDFileIAC	(	IAtomContainer	mol,
		int	molId
	)		throws DENOPTIMException

static

Converts an atom container read in from an SDF file into a graph, if possible.

Otherwise, throws an exception.

Parameters

mol	the atom container coming from SDF representation
molId	identified used only for logging purposed

Returns: the corresponding graph or null.

Exceptions

DENOPTIMException is the atom container cannot be converted due to lack of the proper SDF tags, or failure in the conversion.

Definition at line 1670 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readGraphFromSDFileIAC().

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◆ readGraphFromSDFileIAC() [3/3]

static DGraph denoptim.io.DenoptimIO.readGraphFromSDFileIAC	(	IAtomContainer	mol,
		int	molId,
		String	fileName
	)		throws DENOPTIMException

static

Converts an atom container read in from an SDF file into a graph, if possible.

Otherwise, throws an exception.

Parameters

mol	the atom container coming from SDF representation
molId	identified used only for logging purposes. If negative it is ignored.
fileName	a pathname used only for logging errors. This is usually the pathname to the file from which we took the atom container. If empty it is ignored

Returns: the corresponding graph or null.

Exceptions

DENOPTIMException is the atom container cannot be converted due to lack of the proper SDF tags, or failure in the conversion.

Definition at line 1691 of file DenoptimIO.java.

References denoptim.graph.DGraph.fromJson(), denoptim.constants.DENOPTIMConstants.GRAPHJSONTAG, and denoptim.constants.DENOPTIMConstants.GRAPHTAG.

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◆ readLightWeightCandidate()

static List< CandidateLW > denoptim.io.DenoptimIO.readLightWeightCandidate ( File file ) throws DENOPTIMException

static

Read only selected data from a GA produced items.

This is a light-weight reader of SDF files containing an item, which can be successfully or Unsuccessfully evaluated.

Parameters

fileName the pathname to SDF file

Returns: the light-weight item description.

Exceptions

DENOPTIMException

Definition at line 770 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.constants.DENOPTIMConstants.GRAPHLEVELTAG, denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.constants.DENOPTIMConstants.PROVENANCE, denoptim.io.DenoptimIO.readSDFProperties(), denoptim.graph.CandidateLW.setError(), denoptim.graph.CandidateLW.setFitness(), denoptim.graph.CandidateLW.setGeneratingSource(), denoptim.graph.CandidateLW.setLevel(), and denoptim.constants.DENOPTIMConstants.UNIQUEIDTAG.

Referenced by denoptim.gui.GUIInspectFSERun.importFSERunData(), denoptim.gui.GUIInspectGARun.readOneGeneration(), and denoptim.io.DenoptimIOTest.testReadLightWeightCandidate().

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◆ readList() [1/2]

static ArrayList< String > denoptim.io.DenoptimIO.readList ( String fileName ) throws DENOPTIMException

static

Read list of data as text.

Parameters

fileName the pathname to the file to read.

Returns: list of data

Exceptions

DENOPTIMException

Definition at line 961 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readList().

Referenced by denoptim.gui.GUIInspectGARun.buildAndFillMonitorPlot(), denoptim.files.FileUtils.canWriteAndReadTo(), denoptim.integration.tinker.ConformationalSearchPSSROT.fixLongeLinesInXYZ(), denoptim.fitness.FitnessExpressionParser.makeStringArray(), denoptim.ga.ExternalCmdsListener.processExternalCmdFile(), denoptim.io.DenoptimIO.readCuttingRules(), denoptim.io.DenoptimIO.readList(), denoptim.io.DenoptimIO.readPopulationMemberPathnames(), denoptim.io.DenoptimIO.readPopulationMembersTraces(), denoptim.io.DenoptimIO.readPopulationProps(), denoptim.io.DenoptimIO.readRecentFilesMap(), denoptim.ga.EAUtils.readUID(), denoptim.utils.SizeControlledSetTest.test(), denoptim.programs.denovo.GAParametersTest.testLogging(), and denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ readList() [2/2]

static ArrayList< String > denoptim.io.DenoptimIO.readList	(	String	fileName,
		boolean	allowEmpty
	)		throws DENOPTIMException

static

Read list of data as text.

Parameters

fileName	the pathname to the file to read.
allowEmpty	if `true` the method is allowed to return an empty list if the file exists and is empty

Returns: list of data

Exceptions

DENOPTIMException

Definition at line 977 of file DenoptimIO.java.

◆ readPopulationMemberPathnames()

static List< String > denoptim.io.DenoptimIO.readPopulationMemberPathnames ( File file ) throws DENOPTIMException

static

Read the pathnames to the population members from a FileFormat#GENSUMMARY file.

Parameters

fileName the pathname to the file to read.

Returns: list of data

Exceptions

DENOPTIMException

Definition at line 886 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.FS, and denoptim.io.DenoptimIO.readList().

Referenced by denoptim.io.DenoptimIO.readGenerationFromSummary(), and denoptim.gui.GUIInspectGARun.readOneGeneration().

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◆ readPopulationMembersTraces()

static List< CandidateLW > denoptim.io.DenoptimIO.readPopulationMembersTraces ( File file ) throws DENOPTIMException

static

Read the minimal info that can be found in a FileFormat#GENSUMMARY file about the members of a population.

Parameters

fileName the pathname to the FileFormat#GENSUMMARY file to read.

Returns: list of population members defined to the extent that information is available in the FileFormat#GENSUMMARY file.

Exceptions

DENOPTIMException if the file cannot be read.

Definition at line 919 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readList(), and denoptim.graph.CandidateLW.setFitness().

Referenced by denoptim.gui.GUIInspectGARun.readOneGeneration().

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◆ readPopulationProps()

static double[] denoptim.io.DenoptimIO.readPopulationProps ( File file ) throws DENOPTIMException

static

Read the min, max, mean, and median of a population from FileFormat#GENSUMMARY file.

Parameters

fileName the pathname to the file to read.

Returns: list of data

Exceptions

DENOPTIMException

Definition at line 845 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readList().

Referenced by denoptim.gui.GUIInspectGARun.readOneGeneration().

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◆ readRCCompatibilityMatrix()

static void denoptim.io.DenoptimIO.readRCCompatibilityMatrix	(	String	fileName,
		HashMap< APClass, ArrayList< APClass > >	rcCompatMap
	)		throws DENOPTIMException

static

Reads the APclass compatibility matrix for ring-closing connections (the RC-CPMap).

Note that RC-CPMap is by definition symmetric. Though, true entries can be defined either from X:Y or Y:X, and we make sure such entries are stored in the map. This method assumes that the APclasses reported in the RC-CPMap are defined, w.r.t bond order, in the regular compatibility matrix as we wont check it this condition is satisfied.

Parameters

fileName
rcCompatMap

Exceptions

DENOPTIMException

Definition at line 1300 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.APCMAPCOMPRULE, denoptim.constants.DENOPTIMConstants.APCMAPIGNORE, and denoptim.graph.APClass.make().

Referenced by denoptim.fragspace.FragmentSpace.FragmentSpace(), and denoptim.fragspace.FragmentSpace.importRCCompatibilityMatrixFromFile().

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◆ readRecentFilesMap()

static Map< File, FileFormat > denoptim.io.DenoptimIO.readRecentFilesMap ( )

static

Reads the file defined in DENOPTIMConstants#RECENTFILESLIST and makes a map that contains the pathname and the format of each recent file.

Ignores any entry that is present in the file but cannot be found in the system.

Returns: the recent files map

Definition at line 2190 of file DenoptimIO.java.

References denoptim.logging.StaticLogger.appLogger, denoptim.files.FileUtils.checkExists(), denoptim.io.DenoptimIO.readList(), and denoptim.constants.DENOPTIMConstants.RECENTFILESLIST.

Referenced by denoptim.files.FileUtils.addToRecentFiles(), and denoptim.gui.MainToolBar.updateOpenRecentMenu().

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◆ readSDFFile()

static ArrayList< IAtomContainer > denoptim.io.DenoptimIO.readSDFFile ( String fileName ) throws DENOPTIMException

static

Reads a file containing multiple molecules (multiple SD format))

Parameters

fileName the file containing the molecules

Returns: IAtomContainer[] an array of molecules

Exceptions

DENOPTIMException

Definition at line 348 of file DenoptimIO.java.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromFile(), denoptim.gui.GUIGraphHandler.importGraphsFromFile(), denoptim.io.DenoptimIO.readCandidates(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromSDFile(), denoptim.io.DenoptimIO.readDENOPTIMVertexesFromSDFile(), denoptim.io.DenoptimIO.readSDFProperties(), denoptim.programs.fitnessevaluator.FPRunner.run(), denoptim.graph.TemplateTest.testGetIAtomContainer(), denoptim.graph.TemplateTest.testGetIAtomContainer_DeepVertex(), and denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol().

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◆ readSDFProperties()

static List< Map< String, Object > > denoptim.io.DenoptimIO.readSDFProperties	(	String	pathName,
		List< String >	propNames
	)		throws DENOPTIMException

static

Extract selected properties from SDF files.

Parameters

pathName	to the file to read
propNames	the list of property names to extract. All the rest will be ignored.

Returns: a corresponding map of results.

Exceptions

DENOPTIMException if the file cannot be read.

Definition at line 1052 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.readSDFFile().

Referenced by denoptim.io.DenoptimIO.readLightWeightCandidate().

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◆ readText()

static String denoptim.io.DenoptimIO.readText ( String fileName ) throws DENOPTIMException

static

Read text from file.

Parameters

fileName the pathname to the file to read.

Returns: the text.

Exceptions

DENOPTIMException

Definition at line 1018 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.NL.

Referenced by denoptim.combinatorial.CEBLUtils.deserializeCheckpoint(), denoptim.gui.GUITextReader.displayContent(), and denoptim.programs.fitnessevaluator.FPRunner.run().

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◆ readVertexes()

static ArrayList< Vertex > denoptim.io.DenoptimIO.readVertexes	(	File	file,
		Vertex.BBType	bbt
	)		throws UndetectedFileFormatException, IOException, IllegalArgumentException, DENOPTIMException

static

Reads Vertexes from any file that can contain such items.

Parameters

file	the file we want to read.
bbt	the type of building blocks assigned to each new vertex, if not already specified by the content of the file, i.e., this method does not overwrite the `Vertex.BBType` defined in the file.

Exceptions

IOException
UndetectedFileFormatException
DENOPTIMException
IllegalArgumentException
Exception

Definition at line 2244 of file DenoptimIO.java.

References denoptim.files.FileUtils.detectFileFormat(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromJSONFile(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromSDFile(), denoptim.io.DenoptimIO.readDENOPTIMVertexesFromJSONFile(), denoptim.io.DenoptimIO.readDENOPTIMVertexesFromSDFile(), and denoptim.graph.Template.setInnerGraph().

Referenced by denoptim.fragmenter.ParallelConformerExtractionAlgorithm.createAndSubmitTasks(), denoptim.fragspace.FragmentSpace.FragmentSpace(), denoptim.gui.GUIVertexInspector.importVerticesFromFile(), denoptim.gui.GUIVertexInspector.initialize(), denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), denoptim.programs.fragmenter.FragmenterParameters.processParameters(), denoptim.io.DenoptimIO.readAllAPClasses(), denoptim.io.DenoptimIO.readDENOPTIMData(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.programs.fragmenter.Fragmenter.runProgram(), denoptim.io.DenoptimIOTest.testIOEmptyVertex(), denoptim.io.DenoptimIOTest.testIOMolFragment(), and denoptim.io.DenoptimIOTest.testIOTemplate().

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◆ writeCandidatesToFile()

static void denoptim.io.DenoptimIO.writeCandidatesToFile	(	File	file,
		List< Candidate >	popMembers,
		boolean	append
	)		throws DENOPTIMException

static

Writes candidate items to file.

Always overwrites.

Parameters

file	the file where to print.
popMembers	the list of candidates to print to file.
append	use `true` to append if the file exist

Exceptions

DENOPTIMException

Definition at line 1434 of file DenoptimIO.java.

References denoptim.files.FileFormat.CANDIDATESDF, and denoptim.io.DenoptimIO.writeSDFFile().

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

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◆ writeCandidateToFile()

static void denoptim.io.DenoptimIO.writeCandidateToFile	(	File	file,
		Candidate	candidate,
		boolean	append
	)		throws DENOPTIMException

static

Writes one candidate item to file.

Always overwrites.

Parameters

file	the file where to print.
candidate	the candidate to print to file.
append	use `true` to append if the file exist

Exceptions

DENOPTIMException

Definition at line 1460 of file DenoptimIO.java.

References denoptim.files.FileFormat.CANDIDATESDF, and denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.ga.EAUtils.getPopulationFromFile(), denoptim.ga.EAUtils.outputFinalResults(), denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ writeCompatibilityMatrix()

static void denoptim.io.DenoptimIO.writeCompatibilityMatrix	(	String	fileName,
		HashMap< APClass, ArrayList< APClass > >	cpMap,
		HashMap< APClass, APClass >	capMap,
		HashSet< APClass >	ends
	)		throws DENOPTIMException

static

The class compatibility matrix.

Parameters

fileName	the file to be read
cpMap	container for the APClass compatibility rules
capMap	container for the capping rules
ends	container for the definition of forbidden ends

Definition at line 1143 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.APCMAPCAPPING, denoptim.constants.DENOPTIMConstants.APCMAPCOMPRULE, denoptim.constants.DENOPTIMConstants.APCMAPFORBIDDENEND, denoptim.constants.DENOPTIMConstants.APCMAPIGNORE, denoptim.io.DenoptimIO.NL, and denoptim.io.DenoptimIO.writeData().

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), and denoptim.gui.CompatibilityMatrixForm.writeCopatibilityMatrixFile().

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◆ writeCuttingRules()

static void denoptim.io.DenoptimIO.writeCuttingRules	(	File	file,
		List< CuttingRule >	cutRules
	)		throws DENOPTIMException

static

Writes a formatted text file that collects cutting rule.

Parameters

file	the file where to write.
cutRules	the cutting rules to write.

Exceptions

DENOPTIMException

Definition at line 2535 of file DenoptimIO.java.

References denoptim.constants.DENOPTIMConstants.CUTRULKEYWORD, denoptim.io.DenoptimIO.NL, and denoptim.io.DenoptimIO.writeData().

Referenced by denoptim.gui.CuttingRulesSelectionDialog.CuttingRulesSelectionDialog(), and denoptim.io.DenoptimIOTest.testIOCuttingRules().

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◆ writeData()

static void denoptim.io.DenoptimIO.writeData	(	String	fileName,
		String	data,
		boolean	append
	)		throws DENOPTIMException

static

Write text-like data file.

Parameters

fileName
data
append

Exceptions

DENOPTIMException

Definition at line 739 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.NL.

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◆ writeGraphsToFile()

static File denoptim.io.DenoptimIO.writeGraphsToFile	(	File	file,
		FileFormat	format,
		List< DGraph >	modGraphs,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

static

Writes the graphs to file.

Always overwrites.

Parameters

file	the file where to print
format	how to print graphs on file
modGraphs	the list of graphs to print

Returns: the reference to the file written.

Exceptions

DENOPTIMException

Definition at line 1980 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeGraphsToJSON(), and denoptim.io.DenoptimIO.writeGraphsToSDF().

Referenced by denoptim.gui.GUIGraphHandler.initialize(), denoptim.programs.grapheditor.GraphEditor.runProgram(), and denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ writeGraphsToJSON() [1/2]

static void denoptim.io.DenoptimIO.writeGraphsToJSON	(	File	file,
		List< DGraph >	graphs
	)		throws DENOPTIMException

static

Writes the graphs to JSON file.

Parameters

file	the file where to print
graphs	the list of graphs to print

Exceptions

DENOPTIMException

Definition at line 2141 of file DenoptimIO.java.

References denoptim.json.DENOPTIMgson.getWriter(), and denoptim.io.DenoptimIO.writeData().

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.io.DenoptimIO.writeGraphsToFile(), and denoptim.io.DenoptimIO.writeGraphToJSON().

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◆ writeGraphsToJSON() [2/2]

static void denoptim.io.DenoptimIO.writeGraphsToJSON	(	File	file,
		List< DGraph >	graphs,
		boolean	append
	)		throws DENOPTIMException

static

Writes the graphs to JSON file.

Parameters

file	the file where to print
graphs	the list of graphs to print
append	use `true` to append

Exceptions

DENOPTIMException

Definition at line 2158 of file DenoptimIO.java.

References denoptim.json.DENOPTIMgson.getWriter(), and denoptim.io.DenoptimIO.writeData().

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◆ writeGraphsToSDF() [1/3]

static void denoptim.io.DenoptimIO.writeGraphsToSDF	(	File	file,
		List< DGraph >	graphs,
		boolean	append,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

static

Writes the graphs to SDF file.

Parameters

file	the file where to print
graphs	the list of graphs to print
append	use `true` to append to the file

Exceptions

DENOPTIMException

Definition at line 2070 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeGraphsToSDF().

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◆ writeGraphsToSDF() [2/3]

static void denoptim.io.DenoptimIO.writeGraphsToSDF	(	File	file,
		List< DGraph >	graphs,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

static

Writes the graphs to SDF file.

Parameters

file	the file where to print
graphs	the list of graphs to print

Exceptions

DENOPTIMException

Definition at line 2014 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeGraphsToSDF().

Referenced by denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.io.DenoptimIO.writeGraphsToFile(), denoptim.io.DenoptimIO.writeGraphsToSDF(), and denoptim.io.DenoptimIO.writeGraphToSDF().

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◆ writeGraphsToSDF() [3/3]

static void denoptim.io.DenoptimIO.writeGraphsToSDF	(	File	file,
		List< DGraph >	modGraphs,
		boolean	append,
		boolean	make3D,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

static

Writes the graphs to SDF file.

Parameters

file	the file where to print
modGraphs	the list of graphs to print
append	use `true` to append to the file
make3D	use `true` to convert graph to 3d. If false an empty molecule will be used.

Exceptions

DENOPTIMException

Definition at line 2089 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.builder, denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.utils.GraphUtils.writeSDFFields(), and denoptim.io.DenoptimIO.writeSDFFile().

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◆ writeGraphToFile() [1/2]

static File denoptim.io.DenoptimIO.writeGraphToFile	(	File	file,
		FileFormat	format,
		DGraph	graph,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

static

Writes the a graph to file.

Always overwrites.

Parameters

file	the file where to print.
format	how to print graphs on file.
graph	the graph to print.

Exceptions

DENOPTIMException

Definition at line 1944 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeGraphToJSON(), and denoptim.io.DenoptimIO.writeGraphToSDF().

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ writeGraphToFile() [2/2]

static void denoptim.io.DenoptimIO.writeGraphToFile	(	String	fileName,
		DGraph	graph,
		boolean	append
	)		throws DENOPTIMException

static

Writes the string representation of a graph to file.

Parameters

fileName	the file where to print
graph	the graph to print
append	use `true` to append

Exceptions

DENOPTIMException

Definition at line 2175 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeData().

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◆ writeGraphToJSON()

static void denoptim.io.DenoptimIO.writeGraphToJSON	(	File	file,
		DGraph	graph
	)		throws DENOPTIMException

static

Writes the graph to JSON file.

Parameters

file	the file where to print
graph	the graphs to print

Exceptions

DENOPTIMException

Definition at line 2124 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeGraphsToJSON().

Referenced by denoptim.graph.DGraph.appendVertexOnAP(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.graph.DGraph.removeChainUpToBranching(), and denoptim.io.DenoptimIO.writeGraphToFile().

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◆ writeGraphToSDF() [1/2]

static void denoptim.io.DenoptimIO.writeGraphToSDF	(	File	file,
		DGraph	graph,
		boolean	append,
		boolean	make3D,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

static

Writes the graph to SDF file.

Parameters

file	the file where to print.
graph	the of graph to print.
append	use `true` to append to the file.
make3D	use `true` to convert graph to 3d.

Exceptions

DENOPTIMException

Definition at line 2032 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeGraphsToSDF().

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.utils.MoleculeUtils.extractIACForSubgraph(), denoptim.ga.GraphOperations.performMutation(), and denoptim.io.DenoptimIO.writeGraphToFile().

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◆ writeGraphToSDF() [2/2]

static void denoptim.io.DenoptimIO.writeGraphToSDF	(	File	file,
		DGraph	graph,
		boolean	append,
		Logger	logger,
		Randomizer	randomizer
	)		throws DENOPTIMException

static

Writes the graph to SDF file.

Parameters

file	the file where to print
graph	the of graph to print
append	use `true` to append to the file

Exceptions

DENOPTIMException

Definition at line 2051 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeGraphsToSDF().

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◆ writeMol2File()

static void denoptim.io.DenoptimIO.writeMol2File	(	String	fileName,
		IAtomContainer	mol,
		boolean	append
	)		throws DENOPTIMException

static

Definition at line 621 of file DenoptimIO.java.

◆ writeSDFFile() [1/4]

static void denoptim.io.DenoptimIO.writeSDFFile	(	String	fileName,
		IAtomContainer	mol
	)		throws DENOPTIMException

static

Writes IAtomContainer to SDF file.

Parameters

fileName	The file to be write to.
mol	The molecules to be written.

Exceptions

DENOPTIMException

Definition at line 535 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), denoptim.fragmenter.FragmenterTools.checkElementalAnalysisAgainstFormula(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.fragmenter.FragmenterTools.filterStrucutresBySMARTS(), denoptim.utils.MoleculeUtils.getSMILESForMolecule(), denoptim.gui.MoleculeViewPanel.loadChemicalStructure(), denoptim.gui.FragmentViewPanel.loadStructure(), denoptim.graph.rings.PathSubGraph.makeMolecularRepresentation(), denoptim.utils.DummyAtomHandler.removeDummyInHapto(), denoptim.graph.rings.RingClosureFinder.reportForDebug(), denoptim.task.FitnessTask.runFitnessProvider(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram(), denoptim.programs.genetweeker.GeneOpsRunner.runXOver(), denoptim.fragmenter.ParallelFragmentationAlgorithm.splitInputForThreads(), denoptim.fragmenter.FragmentClustererTest.testCluster(), denoptim.fitness.FitnessProviderTest.testGetFitnessWithParametrizedDescriptors(), denoptim.fitness.FitnessExpressionParserTest.testProcessExpressions(), denoptim.io.DenoptimIOTest.testReadLightWeightCandidate(), denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads(), denoptim.io.DenoptimIO.writeCandidatesToFile(), denoptim.io.DenoptimIO.writeCandidateToFile(), denoptim.io.DenoptimIO.writeGraphsToSDF(), denoptim.io.DenoptimIO.writeSDFFile(), and denoptim.io.DenoptimIO.writeVertexesToSDF().

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◆ writeSDFFile() [2/4]

static void denoptim.io.DenoptimIO.writeSDFFile	(	String	fileName,
		IAtomContainer	mol,
		boolean	append
	)		throws DENOPTIMException

static

Writes an IAtomContainer to SDF file.

Parameters

fileName	The file to be written to
mol	The molecule to be written
append

Exceptions

DENOPTIMException

Definition at line 600 of file DenoptimIO.java.

◆ writeSDFFile() [3/4]

static void denoptim.io.DenoptimIO.writeSDFFile	(	String	fileName,
		List< IAtomContainer >	mols
	)		throws DENOPTIMException

static

Writes IAtomContainers to SDF file.

Parameters

fileName	The file to be write to.
mols	The molecules to be written.

Exceptions

DENOPTIMException

Definition at line 551 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeSDFFile().

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◆ writeSDFFile() [4/4]

static void denoptim.io.DenoptimIO.writeSDFFile	(	String	fileName,
		List< IAtomContainer >	mols,
		boolean	append
	)		throws DENOPTIMException

static

Writes a set of IAtomContainers to SDF file.

Parameters

fileName	The file to be written to
mols	The molecules to be written
append	use `true` to append to the file

Exceptions

DENOPTIMException

Definition at line 566 of file DenoptimIO.java.

◆ writeSmiles()

static void denoptim.io.DenoptimIO.writeSmiles	(	String	fileName,
		String	smiles,
		boolean	append
	)		throws DENOPTIMException

static

Writes a single smiles string to the specified file.

Parameters

fileName	The file to be written to
smiles
append	if `true` append to the file

Exceptions

DENOPTIMException

Definition at line 709 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.NL.

◆ writeSmilesSet()

static void denoptim.io.DenoptimIO.writeSmilesSet	(	String	fileName,
		String[]	smiles,
		boolean	append
	)		throws DENOPTIMException

static

Writes multiple smiles string array to the specified file.

Parameters

fileName	The file to be written to
smiles	array of smiles strings to be written
append	if `true` append to the file

Exceptions

DENOPTIMException

Definition at line 676 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.NL.

◆ writeVertexesToFile() [1/2]

static File denoptim.io.DenoptimIO.writeVertexesToFile	(	File	file,
		FileFormat	format,
		List< Vertex >	vertexes
	)		throws DENOPTIMException

static

Writes vertexes to file.

Always overwrites.

Parameters

file	the file where to print
format	how to print vertexes on file
vertexes	the list of vertexes to print

Exceptions

DENOPTIMException

Definition at line 387 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeVertexesToFile().

Referenced by denoptim.fragmenter.ConformerExtractorTask.call(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.gui.GUIGraphHandler.initialize(), denoptim.gui.GUIVertexInspector.initialize(), denoptim.fragmenter.FragmenterTools.manageFragmentCollection(), denoptim.io.DenoptimIOTest.testAppendToJSON(), denoptim.fragmenter.FragmentClustererTest.testCluster(), denoptim.io.DenoptimIOTest.testIOEmptyVertex(), denoptim.io.DenoptimIOTest.testIOMolFragment(), denoptim.io.DenoptimIOTest.testIOTemplate(), denoptim.io.DenoptimIO.writeVertexesToFile(), and denoptim.io.DenoptimIO.writeVertexToFile().

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◆ writeVertexesToFile() [2/2]

static File denoptim.io.DenoptimIO.writeVertexesToFile	(	File	file,
		FileFormat	format,
		List< Vertex >	vertexes,
		boolean	append
	)		throws DENOPTIMException

static

Writes vertexes to file.

Always overwrites.

Parameters

file	the file where to print
format	how to print vertexes on file
vertexes	the list of vertexes to print

Exceptions

DENOPTIMException

Definition at line 421 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeVertexesToJSON(), and denoptim.io.DenoptimIO.writeVertexesToSDF().

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◆ writeVertexesToJSON() [1/2]

static void denoptim.io.DenoptimIO.writeVertexesToJSON	(	File	file,
		List< Vertex >	vertexes
	)		throws DENOPTIMException

static

Writes vertexes to JSON file.

Always overwrites.

Parameters

file	the file where to print.
vertexes	the list of vertexes to print.

Exceptions

DENOPTIMException

Definition at line 454 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeVertexesToJSON().

Referenced by denoptim.io.DenoptimIO.writeVertexesToFile(), and denoptim.io.DenoptimIO.writeVertexesToJSON().

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◆ writeVertexesToJSON() [2/2]

static void denoptim.io.DenoptimIO.writeVertexesToJSON	(	File	file,
		List< Vertex >	vertexes,
		boolean	append
	)		throws DENOPTIMException

static

Writes vertexes to JSON file.

Always overwrites.

Parameters

file	the file where to print.
vertexes	the list of vertexes to print.
append	use `true` to append to the existing list of vertexes found in the file.

Exceptions

DENOPTIMException

Definition at line 471 of file DenoptimIO.java.

References denoptim.json.DENOPTIMgson.getWriter(), denoptim.io.DenoptimIO.readDENOPTIMVertexesFromJSONFile(), and denoptim.io.DenoptimIO.writeData().

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◆ writeVertexesToSDF()

static void denoptim.io.DenoptimIO.writeVertexesToSDF	(	File	file,
		List< Vertex >	vertexes,
		boolean	append
	)		throws DENOPTIMException

static

Write a list of vertexes to file.

Parameters

file	the file to write to.
vertexes	the vertexes to be written.
append	use `true` to append instead of overwriting.

Exceptions

DENOPTIMException

Definition at line 514 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.fragspace.FragmentSpaceTest.buildFragmentSpace(), denoptim.graph.FragmentIsomorphismInspector.getMappings(), denoptim.graph.FragmentIsomorphismInspector.isomorphismExists(), denoptim.io.DenoptimIOTest.testReadAllAPClasses(), denoptim.io.DenoptimIO.writeVertexesToFile(), and denoptim.io.DenoptimIO.writeVertexToSDF().

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◆ writeVertexToFile()

static File denoptim.io.DenoptimIO.writeVertexToFile	(	File	file,
		FileFormat	format,
		Vertex	vertex,
		boolean	append
	)		throws DENOPTIMException

static

Writes vertexes to file.

Always overwrites.

Parameters

file	the file where to print
format	how to print vertexes on file
vertex	the vertex to print

Exceptions

DENOPTIMException

Definition at line 403 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeVertexesToFile().

Referenced by denoptim.fragmenter.FragmenterTools.manageFragmentCollection().

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◆ writeVertexToSDF()

static void denoptim.io.DenoptimIO.writeVertexToSDF	(	String	pathName,
		Vertex	vertex
	)		throws DENOPTIMException

static

Writes a vertex to an SDF file.

Parameters

pathName	pathname where to write.
vertices	list of vertices to write.

Exceptions

DENOPTIMException

Definition at line 496 of file DenoptimIO.java.

References denoptim.io.DenoptimIO.writeVertexesToSDF().

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◆ writeXYZFile()

static void denoptim.io.DenoptimIO.writeXYZFile	(	String	fileName,
		IAtomContainer	mol,
		boolean	append
	)		throws DENOPTIMException

static

Definition at line 644 of file DenoptimIO.java.

Member Data Documentation

◆ builder

final IChemObjectBuilder denoptim.io.DenoptimIO.builder

staticprivate

Initial value:

=

SilentChemObjectBuilder.getInstance()

Definition at line 126 of file DenoptimIO.java.

Referenced by denoptim.io.DenoptimIO.writeGraphsToSDF().

◆ FS

final String denoptim.io.DenoptimIO.FS = System.getProperty("file.separator")

static

File separator from system.

Definition at line 119 of file DenoptimIO.java.

Referenced by denoptim.files.FileUtils.getAvailableFileName(), denoptim.programs.fragmenter.FragmenterParameters.getMWSlotFileNameAllFrags(), denoptim.programs.fragmenter.FragmenterParameters.getMWSlotFileNameUnqFrags(), denoptim.io.DenoptimIO.readAllAtomContainers(), and denoptim.io.DenoptimIO.readPopulationMemberPathnames().

◆ NL

final String denoptim.io.DenoptimIO.NL = System.getProperty("line.separator")

static

Newline character from system.

Definition at line 124 of file DenoptimIO.java.

Referenced by denoptim.utils.FormulaUtils.compareFormulaAndElementalAnalysis(), denoptim.files.FileUtils.isLineInTxtFile(), denoptim.io.DenoptimIO.readText(), denoptim.utils.DummyAtomHandler.removeDummy(), denoptim.utils.DummyAtomHandler.removeDummyInHapto(), denoptim.io.DenoptimIO.writeCompatibilityMatrix(), denoptim.io.DenoptimIO.writeCuttingRules(), denoptim.io.DenoptimIO.writeData(), denoptim.io.DenoptimIO.writeSmiles(), and denoptim.io.DenoptimIO.writeSmilesSet().

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

/github/workspace/src/main/java/denoptim/io/DenoptimIO.java

Static Public Member Functions

Static Public Attributes

Static Private Attributes

Detailed Description

Member Function Documentation

◆ appendTxtFiles()

◆ getChemDoodleString()

◆ readAllAPClasses()

◆ readAllAtomContainers()

◆ readBridgeHesFindingRules() [1/2]

◆ readBridgeHesFindingRules() [2/2]

◆ readCandidates() [1/2]

◆ readCandidates() [2/2]

◆ readCompatibilityMatrix()

◆ readCSDFormulae()

◆ readCuttingRules() [1/3]

◆ readCuttingRules() [2/3]

◆ readCuttingRules() [3/3]

◆ readDENOPTIMData()

◆ readDENOPTIMGraphEditFromFile()

◆ readDENOPTIMGraphsFromFile() [1/2]

◆ readDENOPTIMGraphsFromFile() [2/2]

◆ readDENOPTIMGraphsFromJSONFile()

◆ readDENOPTIMGraphsFromSDFile()

◆ readDENOPTIMGraphsFromTxtFile()

◆ readDENOPTIMVertexesFromJSONFile()

◆ readDENOPTIMVertexesFromSDFile()

◆ readGenerationFromSummary()

◆ readGraphFromSDFileIAC() [1/3]

◆ readGraphFromSDFileIAC() [2/3]

◆ readGraphFromSDFileIAC() [3/3]

◆ readLightWeightCandidate()

◆ readList() [1/2]

◆ readList() [2/2]

◆ readPopulationMemberPathnames()

◆ readPopulationMembersTraces()

◆ readPopulationProps()

◆ readRCCompatibilityMatrix()

◆ readRecentFilesMap()

◆ readSDFFile()

◆ readSDFProperties()

◆ readText()

◆ readVertexes()

◆ writeCandidatesToFile()

◆ writeCandidateToFile()

◆ writeCompatibilityMatrix()

◆ writeCuttingRules()

◆ writeData()

◆ writeGraphsToFile()

◆ writeGraphsToJSON() [1/2]

◆ writeGraphsToJSON() [2/2]

◆ writeGraphsToSDF() [1/3]

◆ writeGraphsToSDF() [2/3]

◆ writeGraphsToSDF() [3/3]

◆ writeGraphToFile() [1/2]

◆ writeGraphToFile() [2/2]

◆ writeGraphToJSON()

◆ writeGraphToSDF() [1/2]

◆ writeGraphToSDF() [2/2]

◆ writeMol2File()

◆ writeSDFFile() [1/4]

◆ writeSDFFile() [2/4]

◆ writeSDFFile() [3/4]

◆ writeSDFFile() [4/4]

◆ writeSmiles()

◆ writeSmilesSet()

◆ writeVertexesToFile() [1/2]

◆ writeVertexesToFile() [2/2]

◆ writeVertexesToJSON() [1/2]

◆ writeVertexesToJSON() [2/2]

◆ writeVertexesToSDF()

◆ writeVertexToFile()

◆ writeVertexToSDF()

◆ writeXYZFile()

Member Data Documentation

◆ builder

◆ FS

◆ NL