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Updated to CDK 2.7.1
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‎README.md‎

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# Groovy Cheminformatics with the Chemistry Development Kit
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[Edition 2.3-2](https://egonw.github.io/cdkbook/)
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[Edition 2.7.1-1](https://egonw.github.io/cdkbook/)
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**Egon L. Willighagen** PhD<br />
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Long time CDK developer
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© E.L. Willighagen 2011-2020
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© E.L. Willighagen 2011-2022
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License: CC-BY-SA 4.0 International
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## Dependencies
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* Groovy
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* nodejs and citation-js (see [doi:10.7717/peerj-cs.214](https://doi.org/10.7717/peerj-cs.214))
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* [CDK](https://cdk.github.io/)
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* nodejs and npm
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* citation-js (see doi:[10.7717/peerj-cs.214](https://doi.org/10.7717/peerj-cs.214))
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* [CDK](https://cdk.github.io/) (see doi:[10.1186/S13321-017-0220-4](https://doi.org/10.1186/S13321-017-0220-4))
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## About
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‎classinfo.tsv‎

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AcidicGroupCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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AdjacencyMatrix org.openscience.cdk.graph.matrix core
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AllRingsFinder org.openscience.cdk.ringsearch standard
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ALOGPDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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AminoAcidCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarprotein
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APolDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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AromaticAtomsCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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AromaticBondsCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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Aromaticity org.openscience.cdk.aromaticity standard
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AtomContainerManipulator org.openscience.cdk.tools.manipulator standard
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AtomCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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AtomTypeManipulator org.openscience.cdk.tools.manipulator standard
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AutocorrelationDescriptorCharge org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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AutocorrelationDescriptorMass org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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AutocorrelationDescriptorPolarizability org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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BasicGroupCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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BCUTDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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BondCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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BooleanResult org.openscience.cdk.qsar.result standard
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BPolDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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CarbonTypesDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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CDKAtomTypeMatcher org.openscience.cdk.atomtype core
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CDKConstants org.openscience.cdk core
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CDKHydrogenAdder org.openscience.cdk.tools valencycheck
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ChiChainDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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ChiClusterDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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ChiPathClusterDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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ChiPathDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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CircularFingerprinter org.openscience.cdk.fingerprint fingerprint
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ConnectivityChecker org.openscience.cdk.graph standard
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CPSADescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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CycleFinder org.openscience.cdk.graph core
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DebugChemObjectBuilder org.openscience.cdk.debug datadebug
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DefaultChemObjectBuilder org.openscience.cdk data
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DescriptorEngine org.openscience.cdk.qsar qsarmolecular
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DescriptorValue org.openscience.cdk.qsar standard
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DoubleArrayResult org.openscience.cdk.qsar.result standard
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DoubleResult org.openscience.cdk.qsar.result standard
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EccentricConnectivityIndexDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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ElectronDonation org.openscience.cdk.aromaticity standard
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Elements org.openscience.cdk.config core
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Fingerprinter org.openscience.cdk.fingerprint standard
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FMFDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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FragmentComplexityDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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GravitationalIndexDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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HBondAcceptorCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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HBondDonorCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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HybridizationFingerprinter org.openscience.cdk.fingerprint standard
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HybridizationRatioDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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IAtom org.openscience.cdk.interfaces interfaces
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IAtomContainer org.openscience.cdk.interfaces interfaces
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IAtomContainerSet org.openscience.cdk.interfaces interfaces
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IChemObjectReader org.openscience.cdk.io interfaces
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IChemObjectReaderErrorHandler org.openscience.cdk.io interfaces
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ICountFingerprint org.openscience.cdk.fingerprint core
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IDescriptor org.openscience.cdk.qsar qsar
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IDescriptorResult org.openscience.cdk.qsar.result standard
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IDescriptor org.openscience.cdk.qsar interfaces
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IDescriptorResult org.openscience.cdk.qsar.result interfaces
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IElement org.openscience.cdk.interfaces interfaces
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IFingerprinter org.openscience.cdk.fingerprint core
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IImplementationSpecification org.openscience.cdk standard
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IImplementationSpecification org.openscience.cdk interfaces
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ILonePair org.openscience.cdk.interfaces interfaces
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IMolecularDescriptor org.openscience.cdk.qsar qsar
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IMonomer org.openscience.cdk.interfaces interfaces
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IStrand org.openscience.cdk.interfaces interfaces
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IteratingPCCompoundXMLReader org.openscience.cdk.io.iterator io
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IteratingSDFReader org.openscience.cdk.io.iterator ctab
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KappaShapeIndicesDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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KierHallSmartsDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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LargestChainDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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LargestPiSystemDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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LengthOverBreadthDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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LongestAliphaticChainDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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MACCSFingerprinter org.openscience.cdk.fingerprint fingerprint
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MannholdLogPDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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MDEDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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MDLRXNReader org.openscience.cdk.io ctab
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MDLV2000Writer org.openscience.cdk.io ctab
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ModelBuilder3D org.openscience.cdk.modeling.builder3d builder3d
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Mol2Format org.openscience.cdk.io.formats ioformats
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MolecularFormulaManipulator org.openscience.cdk.tools.manipulator formula
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MomentOfInertiaDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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PDBReader org.openscience.cdk.io pdb
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PetitjeanNumberDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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PetitjeanShapeIndexDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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RebondTool org.openscience.cdk.graph.rebond standard
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RotatableBondsCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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RuleOfFiveDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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SilentChemObjectBuilder org.openscience.cdk.silent silent
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SmilesGenerator org.openscience.cdk.smiles smiles
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SmilesParser org.openscience.cdk.smiles smiles
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StructureDiagramGenerator org.openscience.cdk.layout sdg
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SybylAtomTypeMatcher org.openscience.cdk.atomtype atomtype
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TopologicalMatrix org.openscience.cdk.graph.matrix qsarmolecular
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TPSADescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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UniversalIsomorphismTester org.openscience.cdk.isomorphism standard
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VABCDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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VABCVolume org.openscience.cdk.geometry.volume standard
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VAdjMaDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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WeightDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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WeightedPathDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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WHIMDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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WienerNumbersDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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XLogPDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
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XMLIsotopeFactory org.openscience.cdk.config extra
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ZagrebIndexDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular

‎createMarkdown.groovy‎

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// Copyright (c) 2018-2019 Egon Willighagen <egon.willighagen@gmail.com>
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// Copyright (c) 2018-2022 Egon Willighagen <egon.willighagen@gmail.com>
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//
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// GPL v3
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import groovy.xml.XmlSlurper
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input = args[0]
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cdkVersion = "??"

‎findClasses.groovy‎

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// Copyright (c) 2019 Egon Willighagen <egon.willighagen@gmail.com>
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// Copyright (c) 2019-2022 Egon Willighagen <egon.willighagen@gmail.com>
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//
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// GPL v3
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//
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// find all classes and makes a data file to be complemented with additional data
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//
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// it takes one optional argument, which is appended to the output
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import groovy.xml.XmlSlurper
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if (args.length == 0) {
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println "groovy findClasses.groovy <directory>"
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System.exit(0)

‎findFigures.groovy‎

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// Copyright (c) 2018 Egon Willighagen <egon.willighagen@gmail.com>
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// Copyright (c) 2018-2022 Egon Willighagen <egon.willighagen@gmail.com>
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//
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// GPL v3
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import groovy.xml.XmlSlurper
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chapterCounters = new HashMap<String,String>();
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chapterCounter = 0
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def chapterLines = new File("order.txt").readLines()

‎findSections.groovy‎

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// Copyright (c) 2019 Egon Willighagen <egon.willighagen@gmail.com>
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// Copyright (c) 2019-2022 Egon Willighagen <egon.willighagen@gmail.com>
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//
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// GPL v3
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// find all topics and makes a data file to be converted into an Index
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//
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// it takes one optional argument, which is appended to the output
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import groovy.xml.XmlSlurper
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chapterCounters = new HashMap<String,String>();
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chapterCounter = 0
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appendixCounter = 0

‎findTopics.groovy‎

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// Copyright (c) 2019 Egon Willighagen <egon.willighagen@gmail.com>
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// Copyright (c) 2019-2022 Egon Willighagen <egon.willighagen@gmail.com>
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//
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// GPL v3
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// find all topics and makes a data file to be converted into an Index
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//
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// it takes one optional argument, which is appended to the output
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import groovy.xml.XmlSlurper
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if (args.length == 0) {
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println "groovy findTopics.groovy <directory>"
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System.exit(0)

‎index.i.md‎

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**Egon L. Willighagen** PhD<br />
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Long time CDK developer
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© E.L. Willighagen 2011-2020
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© E.L. Willighagen 2011-2022
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License: CC-BY-SA 4.0 International
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‎makeToC.groovy‎

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// Copyright (c) 2019 Egon Willighagen <egon.willighagen@gmail.com>
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// Copyright (c) 2019-2022 Egon Willighagen <egon.willighagen@gmail.com>
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//
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// GPL v3
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// find all topics and makes a data file to be converted into an Index
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// it takes one optional argument, which is appended to the output
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import groovy.xml.XmlSlurper
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chapters = "order.txt"

‎numberScripts.groovy‎

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// Copyright (c) 2018-2020 Egon Willighagen <egon.willighagen@gmail.com>
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// Copyright (c) 2018-2022 Egon Willighagen <egon.willighagen@gmail.com>
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//
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// GPL v3
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import groovy.xml.XmlSlurper
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chapters = "order.txt"
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chapterCounters = new HashMap<String,String>();
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chapterCounter = 0

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