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Updated to CDK 2.7.1
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egonw committed May 21, 2022
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9 changes: 5 additions & 4 deletions README.md
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# Groovy Cheminformatics with the Chemistry Development Kit

[Edition 2.3-2](https://egonw.github.io/cdkbook/)
[Edition 2.7.1-1](https://egonw.github.io/cdkbook/)

**Egon L. Willighagen** PhD<br />
Long time CDK developer

© E.L. Willighagen 2011-2020
© E.L. Willighagen 2011-2022

License: CC-BY-SA 4.0 International

## Dependencies

* Groovy
* nodejs and citation-js (see [doi:10.7717/peerj-cs.214](https://doi.org/10.7717/peerj-cs.214))
* [CDK](https://cdk.github.io/)
* nodejs and npm
* citation-js (see doi:[10.7717/peerj-cs.214](https://doi.org/10.7717/peerj-cs.214))
* [CDK](https://cdk.github.io/) (see doi:[10.1186/S13321-017-0220-4](https://doi.org/10.1186/S13321-017-0220-4))

## About

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53 changes: 3 additions & 50 deletions classinfo.tsv
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@@ -1,52 +1,27 @@
AcidicGroupCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
AdjacencyMatrix org.openscience.cdk.graph.matrix core
AllRingsFinder org.openscience.cdk.ringsearch standard
ALOGPDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
AminoAcidCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarprotein
APolDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
AromaticAtomsCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
AromaticBondsCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
Aromaticity org.openscience.cdk.aromaticity standard
AtomContainerManipulator org.openscience.cdk.tools.manipulator standard
AtomCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
AtomTypeManipulator org.openscience.cdk.tools.manipulator standard
AutocorrelationDescriptorCharge org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
AutocorrelationDescriptorMass org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
AutocorrelationDescriptorPolarizability org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
BasicGroupCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
BCUTDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
BondCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
BooleanResult org.openscience.cdk.qsar.result standard
BPolDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
CarbonTypesDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
CDKAtomTypeMatcher org.openscience.cdk.atomtype core
CDKConstants org.openscience.cdk core
CDKHydrogenAdder org.openscience.cdk.tools valencycheck
ChiChainDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
ChiClusterDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
ChiPathClusterDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
ChiPathDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
CircularFingerprinter org.openscience.cdk.fingerprint fingerprint
ConnectivityChecker org.openscience.cdk.graph standard
CPSADescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
CycleFinder org.openscience.cdk.graph core
DebugChemObjectBuilder org.openscience.cdk.debug datadebug
DefaultChemObjectBuilder org.openscience.cdk data
DescriptorEngine org.openscience.cdk.qsar qsarmolecular
DescriptorValue org.openscience.cdk.qsar standard
DoubleArrayResult org.openscience.cdk.qsar.result standard
DoubleResult org.openscience.cdk.qsar.result standard
EccentricConnectivityIndexDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
ElectronDonation org.openscience.cdk.aromaticity standard
Elements org.openscience.cdk.config core
Fingerprinter org.openscience.cdk.fingerprint standard
FMFDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
FragmentComplexityDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
GravitationalIndexDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
HBondAcceptorCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
HBondDonorCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
HybridizationFingerprinter org.openscience.cdk.fingerprint standard
HybridizationRatioDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
IAtom org.openscience.cdk.interfaces interfaces
IAtomContainer org.openscience.cdk.interfaces interfaces
IAtomContainerSet org.openscience.cdk.interfaces interfaces
Expand All @@ -60,11 +35,11 @@ IChemObjectBuilder org.openscience.cdk.interfaces interfaces
IChemObjectReader org.openscience.cdk.io interfaces
IChemObjectReaderErrorHandler org.openscience.cdk.io interfaces
ICountFingerprint org.openscience.cdk.fingerprint core
IDescriptor org.openscience.cdk.qsar qsar
IDescriptorResult org.openscience.cdk.qsar.result standard
IDescriptor org.openscience.cdk.qsar interfaces
IDescriptorResult org.openscience.cdk.qsar.result interfaces
IElement org.openscience.cdk.interfaces interfaces
IFingerprinter org.openscience.cdk.fingerprint core
IImplementationSpecification org.openscience.cdk standard
IImplementationSpecification org.openscience.cdk interfaces
ILonePair org.openscience.cdk.interfaces interfaces
IMolecularDescriptor org.openscience.cdk.qsar qsar
IMonomer org.openscience.cdk.interfaces interfaces
Expand All @@ -81,42 +56,20 @@ Isotopes org.openscience.cdk.config core
IStrand org.openscience.cdk.interfaces interfaces
IteratingPCCompoundXMLReader org.openscience.cdk.io.iterator io
IteratingSDFReader org.openscience.cdk.io.iterator ctab
KappaShapeIndicesDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
KierHallSmartsDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
LargestChainDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
LargestPiSystemDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
LengthOverBreadthDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
LongestAliphaticChainDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
MACCSFingerprinter org.openscience.cdk.fingerprint fingerprint
MannholdLogPDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
MDEDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
MDLRXNReader org.openscience.cdk.io ctab
MDLV2000Writer org.openscience.cdk.io ctab
ModelBuilder3D org.openscience.cdk.modeling.builder3d builder3d
Mol2Format org.openscience.cdk.io.formats ioformats
MolecularFormulaManipulator org.openscience.cdk.tools.manipulator formula
MomentOfInertiaDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
PDBReader org.openscience.cdk.io pdb
PetitjeanNumberDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
PetitjeanShapeIndexDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
RebondTool org.openscience.cdk.graph.rebond standard
RotatableBondsCountDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
RuleOfFiveDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
SilentChemObjectBuilder org.openscience.cdk.silent silent
SmilesGenerator org.openscience.cdk.smiles smiles
SmilesParser org.openscience.cdk.smiles smiles
StructureDiagramGenerator org.openscience.cdk.layout sdg
SybylAtomTypeMatcher org.openscience.cdk.atomtype atomtype
TopologicalMatrix org.openscience.cdk.graph.matrix qsarmolecular
TPSADescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
UniversalIsomorphismTester org.openscience.cdk.isomorphism standard
VABCDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
VABCVolume org.openscience.cdk.geometry.volume standard
VAdjMaDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
WeightDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
WeightedPathDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
WHIMDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
WienerNumbersDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
XLogPDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
XMLIsotopeFactory org.openscience.cdk.config extra
ZagrebIndexDescriptor org.openscience.cdk.qsar.descriptors.molecular qsarmolecular
4 changes: 3 additions & 1 deletion createMarkdown.groovy
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// Copyright (c) 2018-2019 Egon Willighagen <[email protected]>
// Copyright (c) 2018-2022 Egon Willighagen <[email protected]>
//
// GPL v3

import groovy.xml.XmlSlurper

input = args[0]

cdkVersion = "??"
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6 changes: 4 additions & 2 deletions findClasses.groovy
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// Copyright (c) 2019 Egon Willighagen <[email protected]>
// Copyright (c) 2019-2022 Egon Willighagen <[email protected]>
//
// GPL v3

//
// find all classes and makes a data file to be complemented with additional data
//
// it takes one optional argument, which is appended to the output

import groovy.xml.XmlSlurper

if (args.length == 0) {
println "groovy findClasses.groovy <directory>"
System.exit(0)
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4 changes: 3 additions & 1 deletion findFigures.groovy
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// Copyright (c) 2018 Egon Willighagen <[email protected]>
// Copyright (c) 2018-2022 Egon Willighagen <[email protected]>
//
// GPL v3

import groovy.xml.XmlSlurper

chapterCounters = new HashMap<String,String>();
chapterCounter = 0
def chapterLines = new File("order.txt").readLines()
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4 changes: 3 additions & 1 deletion findSections.groovy
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// Copyright (c) 2019 Egon Willighagen <[email protected]>
// Copyright (c) 2019-2022 Egon Willighagen <[email protected]>
//
// GPL v3

// find all topics and makes a data file to be converted into an Index
//
// it takes one optional argument, which is appended to the output

import groovy.xml.XmlSlurper

chapterCounters = new HashMap<String,String>();
chapterCounter = 0
appendixCounter = 0
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4 changes: 3 additions & 1 deletion findTopics.groovy
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@@ -1,11 +1,13 @@
// Copyright (c) 2019 Egon Willighagen <[email protected]>
// Copyright (c) 2019-2022 Egon Willighagen <[email protected]>
//
// GPL v3

// find all topics and makes a data file to be converted into an Index
//
// it takes one optional argument, which is appended to the output

import groovy.xml.XmlSlurper

if (args.length == 0) {
println "groovy findTopics.groovy <directory>"
System.exit(0)
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2 changes: 1 addition & 1 deletion index.i.md
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Expand Up @@ -30,7 +30,7 @@ Edition <version/>-<minor/>
**Egon L. Willighagen** PhD<br />
Long time CDK developer

© E.L. Willighagen 2011-2020
© E.L. Willighagen 2011-2022

License: CC-BY-SA 4.0 International

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4 changes: 3 additions & 1 deletion makeToC.groovy
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@@ -1,11 +1,13 @@
// Copyright (c) 2019 Egon Willighagen <[email protected]>
// Copyright (c) 2019-2022 Egon Willighagen <[email protected]>
//
// GPL v3

// find all topics and makes a data file to be converted into an Index
//
// it takes one optional argument, which is appended to the output

import groovy.xml.XmlSlurper

def chapterCounter = 0

chapters = "order.txt"
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4 changes: 3 additions & 1 deletion numberScripts.groovy
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@@ -1,7 +1,9 @@
// Copyright (c) 2018-2020 Egon Willighagen <[email protected]>
// Copyright (c) 2018-2022 Egon Willighagen <[email protected]>
//
// GPL v3

import groovy.xml.XmlSlurper

chapters = "order.txt"
chapterCounters = new HashMap<String,String>();
chapterCounter = 0
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