egonw/cdkbook

Groovy Cheminformatics with the Chemistry Development Kit

Groovy Cheminformatics with the Chemistry Development Kit

Edition 2.9-1

Egon L. Willighagen PhD
Long time CDK developer

© E.L. Willighagen 2011-2024

License: CC-BY-SA 4.0 International

Dependencies

• Groovy
• nodejs and npm
• citation-js (see doi:10.7717/peerj-cs.214)
• CDK (see doi:10.1186/S13321-017-0220-4)

About

Further information: https://chem-bla-ics.linkedchemistry.info/

E.L. Willighagen [email protected]

cdkbook's Issues

possible CML convention registration issue

Processing  ProteinFromSequence.groovyin
doing ProteinFromSequence.out...
org.openscience.cdk.io.cml.CMLHandler WARN: Detected unknown convention: cdk:substructureList

review IsotopeFactory warnings

Processing  IsotopesDemo.groovyin
doing IsotopesDemo.out...
org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 43
org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 61
org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 84
org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 85
org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 86
org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 87
org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 88
org.openscience.cdk.config.IsotopeFactory ERROR: Could not find major isotope for: 89

Invalid URLs in Markdown files

Errors in introduction.md

• [403] https://doi.org/10.1021/CI025584Y | Cached: Error (cached)

Errors in graph.md

• [403] https://doi.org/10.1021/CI960013P – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/C160017A018 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI960322F – Failed: Network error: Forbidden

Errors in reaction.md

• [403] https://doi.org/10.1021/CI0502698 – Failed: Network error: Forbidden

Errors in atomsbonds.md

• [403] https://doi.org/10.1021/CI025584Y – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI00047A033 – Failed: Network error: Forbidden

Errors in io.md

• [403] https://doi.org/10.1021/CI00057A005 | Cached: Error (cached)
• [403] https://doi.org/10.1021/CI00007A012 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI7004687 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI990052B – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI00034A005 | Cached: Error (cached)

Errors in cheminfo.md

• [403] https://doi.org/10.1021/CI600234Z – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI00034A005 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI025584Y – Failed: Network error: Forbidden
• [403] https://doi.org/10.1002/9783527613106 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1126/SCIENCE.166.3902.178 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/JA00757A020 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1098/RSPA.1929.0094 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI00057A005 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI00027A001 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI049714 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/JA01203A022 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI00025A015 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/AC50055A016 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/A1000016X – Failed: Network error: Forbidden
• [403] https://doi.org/10.1126/SCIENCE.126.3278.814 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/CI9704423 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1126/SCIENCE.1105511 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1021/C160017A018 – Failed: Network error: Forbidden
• [403] https://doi.org/10.1080/10408340600969601 – Failed: Network error: Forbidden

Errors in descriptor.md

• [403] https://doi.org/10.1021/CI050400B – Failed: Network error: Forbidden
• [TIMEOUT] http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/# | Timeout

This content was produced by a GitHub Action.

book as Jupyter notebook(s) with Groovy kernel

• like this simple demo
• notebooks can be linked similar to linked markdown pages
• languages can be mixed in the same notebook

Invalid URLs in Markdown files

Errors in writingApps.i.md

• [404] https://github.com/cdk/cdk/releases/tag/cdk-%3Cversion/%3E – Failed: Network error: Not Found

This content was produced by a GitHub Action.

write up examples of SMIRKS

See cdk/cdk#916 (comment)

Broken figure link

In https://egonw.github.io/cdkbook/graph.html#inchi-atom-numbers:

NPE while listing all atom types

Processing  ListAllCDKAtomTypes.groovyin
doing ListAllCDKAtomTypes.out...
Caught: java.lang.NullPointerException: Cannot invoke method compareTo() on null object
java.lang.NullPointerException: Cannot invoke method compareTo() on null object
        at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:47)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:34)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at java_lang_String$compareTo$1.call(Unknown Source)
        at ListAllCDKAtomTypes$1.compare(ListAllCDKAtomTypes.groovy:17)
        at ListAllCDKAtomTypes$1.compare(ListAllCDKAtomTypes.groovy)
        at java.util.TimSort.binarySort(TimSort.java:296)
        at java.util.TimSort.sort(TimSort.java:239)
        at java.util.Arrays.sort(Arrays.java:1438)
        at java_util_Arrays$sort.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
        at ListAllCDKAtomTypes.run(ListAllCDKAtomTypes.groovy:15)
        at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
        at groovy.lang.GroovyShell.run(GroovyShell.java:507)
        at groovy.lang.GroovyShell.run(GroovyShell.java:496)
        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:597)
        at groovy.ui.GroovyMain.run(GroovyMain.java:329)
        at groovy.ui.GroovyMain.process(GroovyMain.java:315)
        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
        at groovy.ui.GroovyMain.main(GroovyMain.java:114)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)
Processing  ListAllSybylAtomTypes.groovyin
doing ListAllSybylAtomTypes.out...
Caught: java.lang.NullPointerException
java.lang.NullPointerException
        at java.lang.String.compareTo(String.java:1155)
        at java.lang.String.compareTo(String.java:111)
        at java_lang_Comparable$compareTo.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at ListAllSybylAtomTypes$1.compare(ListAllSybylAtomTypes.groovy:17)
        at ListAllSybylAtomTypes$1.compare(ListAllSybylAtomTypes.groovy)
        at java.util.TimSort.countRunAndMakeAscending(TimSort.java:355)
        at java.util.TimSort.sort(TimSort.java:234)
        at java.util.Arrays.sort(Arrays.java:1438)
        at java_util_Arrays$sort.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
        at ListAllSybylAtomTypes.run(ListAllSybylAtomTypes.groovy:15)
        at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
        at groovy.lang.GroovyShell.run(GroovyShell.java:507)
        at groovy.lang.GroovyShell.run(GroovyShell.java:496)
        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:597)
        at groovy.ui.GroovyMain.run(GroovyMain.java:329)
        at groovy.ui.GroovyMain.process(GroovyMain.java:315)
        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
        at groovy.ui.GroovyMain.main(GroovyMain.java:114)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)

update the Scholia URL

duplicate Grab output

For example in code/CTR2.code.md:

 ```groovy
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='%CDKVERSION%')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.3')
+

automate creation of the ToC

Which is now manually added to the index.i.md... that should be scripted.

review AtomTypeFactory warnings

Processing  CovalentRadii.groovyin
doing CovalentRadii.out...
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
Processing  RebondToolDemo.groovyin
doing RebondToolDemo.out...
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist
org.openscience.cdk.config.AtomTypeFactory WARN: Taking first atom type, but other may exist

clean up missing references

The current list:

builders.md:1. <a name="citeref1"></a>Missing
builders.md:2. <a name="citeref2"></a>Missing
cheminfo.md:4. <a name="citeref4"></a>Missing
cheminfo.md:8. <a name="citeref8"></a>Missing
cheminfo.md:10. <a name="citeref10"></a>Missing
cheminfo.md:13. <a name="citeref13"></a>Missing
cheminfo.md:14. <a name="citeref14"></a>Missing
cheminfo.md:15. <a name="citeref15"></a>Missing
cheminfo.md:16. <a name="citeref16"></a>Missing
cheminfo.md:17. <a name="citeref17"></a>Missing
cheminfo.md:18. <a name="citeref18"></a>Missing
graph.md:1. <a name="citeref1"></a>Missing
graph.md:2. <a name="citeref2"></a>Missing
graph.md:3. <a name="citeref3"></a>Missing
graph.md:4. <a name="citeref4"></a>Missing
graph.md:5. <a name="citeref5"></a>Missing
graph.md:6. <a name="citeref6"></a>Missing
properties.md:1. <a name="citeref1"></a>Missing
properties.md:2. <a name="citeref2"></a>Missing
protein.md:1. <a name="citeref1"></a>Missing
protein.md:2. <a name="citeref2"></a>Missing

DebugBuilder no longer gives output

Change in the live book:

 ### The Debug Builder
@@ -135,21 +135,6 @@ IChemObjectBuilder builder =
 ... we get this debug information for the data classes:
 
 ```plain
-org.openscience.cdk.debug.DebugAtom DEBUG: Getti...
-  ng max bond order: null
-org.openscience.cdk.debug.DebugAtom DEBUG: Getti...
-  ng bond order sum: null
-org.openscience.cdk.debug.DebugAtom DEBUG: Getti...
-  ng formal charge: 0
-org.openscience.cdk.debug.DebugAtom DEBUG: Getti...
-  ng formal charge: 0
-org.openscience.cdk.debug.DebugAtom DEBUG: Getti...
-  ng hybridization: null
-org.openscience.cdk.debug.DebugAtom DEBUG: Getti...
-  ng formal neighbour count: null
-org.openscience.cdk.debug.DebugAtom DEBUG: Getti...
-  ng covalent radius: null
-org.openscience.cdk.debug.DebugAtom DEBUG: Getti...

figure out how to link between sections and chapters

check possible API change org.openscience.cdk.Atom

Processing  MACCSFingerprint.groovyin
doing MACCSFingerprint.out...
Caught: java.lang.UnsupportedOperationException
java.lang.UnsupportedOperationException
        at org.openscience.cdk.Atom.bonds(Atom.java:260)
        at org.openscience.cdk.isomorphism.matchers.Expr.getTotalHCount(Expr.java:431)
        at org.openscience.cdk.isomorphism.matchers.Expr.matches(Expr.java:278)
        at org.openscience.cdk.isomorphism.matchers.Expr.matches(Expr.java:359)
        at org.openscience.cdk.isomorphism.matchers.Expr.matches(Expr.java:444)
        at org.openscience.cdk.isomorphism.matchers.QueryAtom.matches(QueryAtom.java:763)
        at org.openscience.cdk.isomorphism.AtomMatcher$QueryMatcher.matches(AtomMatcher.java:95)
        at org.openscience.cdk.isomorphism.VFSubState.feasible(VFSubState.java:115)
        at org.openscience.cdk.isomorphism.AbstractVFState.add(AbstractVFState.java:129)
        at org.openscience.cdk.isomorphism.StateStream.map(StateStream.java:108)
        at org.openscience.cdk.isomorphism.StateStream.findNext(StateStream.java:90)
        at org.openscience.cdk.isomorphism.StateStream.<init>(StateStream.java:61)
        at org.openscience.cdk.isomorphism.VentoFoggia$VFIterable.iterator(VentoFoggia.java:252)
        at com.google.common.collect.Iterables.getFirst(Iterables.java:775)
        at org.openscience.cdk.isomorphism.Mappings.first(Mappings.java:508)
        at org.openscience.cdk.smarts.SmartsPattern.match(SmartsPattern.java:136)
        at org.openscience.cdk.isomorphism.Pattern.matches(Pattern.java:117)
        at org.openscience.cdk.fingerprint.MACCSFingerprinter.getBitFingerprint(MACCSFingerprinter.java:145)
        at org.openscience.cdk.fingerprint.IFingerprinter$getBitFingerprint.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:128)
        at MACCSFingerprint.run(MACCSFingerprint.groovy:27)
        at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:263)
        at groovy.lang.GroovyShell.run(GroovyShell.java:507)
        at groovy.lang.GroovyShell.run(GroovyShell.java:496)
        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:597)
        at groovy.ui.GroovyMain.run(GroovyMain.java:329)
        at groovy.ui.GroovyMain.process(GroovyMain.java:315)
        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
        at groovy.ui.GroovyMain.main(GroovyMain.java:114)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)

Invalid URLs in Markdown files

This content was produced by a GitHub Action.

add option to label scripts again

now used in atomsbonds:

automagically number figures and links between text and figure

There currently is no linking:

autogenerated images from R code again

autogenerated dependency diagrams again from the graphviz code

error in the build system

Processing  SimpleFingerprintDemo.groovyin
doing SimpleFingerprintDemo.out...
Caught: java.lang.NoClassDefFoundError: org/openscience/cdk/fingerprint/IFingerprinter
java.lang.NoClassDefFoundError: org/openscience/cdk/fingerprint/IFingerprinter
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:468)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
        at org.codehaus.groovy.tools.RootLoader.oldFindClass(RootLoader.java:175)
        at org.codehaus.groovy.tools.RootLoader.loadClass(RootLoader.java:147)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:411)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:702)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:570)
        at org.codehaus.groovy.control.ClassNodeResolver.tryAsLoaderClassOrScript(ClassNodeResolver.java:184)
        at org.codehaus.groovy.control.ClassNodeResolver.findClassNode(ClassNodeResolver.java:169)
        at org.codehaus.groovy.control.ClassNodeResolver.resolveName(ClassNodeResolver.java:125)
        at org.codehaus.groovy.control.ResolveVisitor.resolveToOuter(ResolveVisitor.java:740)
        at org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:377)
        at org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:340)
        at org.codehaus.groovy.control.ResolveVisitor.resolveOrFail(ResolveVisitor.java:324)
        at org.codehaus.groovy.control.ResolveVisitor.resolveOrFail(ResolveVisitor.java:336)
        at org.codehaus.groovy.control.ResolveVisitor.transformConstructorCallExpression(ResolveVisitor.java:1131)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:770)
        at org.codehaus.groovy.control.ResolveVisitor.transformBinaryExpression(ResolveVisitor.java:1099)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:764)
        at org.codehaus.groovy.ast.ClassCodeExpressionTransformer.visitExpressionStatement(ClassCodeExpressionTransformer.java:144)
        at org.codehaus.groovy.ast.stmt.ExpressionStatement.visit(ExpressionStatement.java:42)
        at org.codehaus.groovy.ast.CodeVisitorSupport.visitBlockStatement(CodeVisitorSupport.java:88)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitBlockStatement(ClassCodeVisitorSupport.java:166)
        at org.codehaus.groovy.control.ResolveVisitor.visitBlockStatement(ResolveVisitor.java:1402)
        at org.codehaus.groovy.ast.stmt.BlockStatement.visit(BlockStatement.java:71)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClassCodeContainer(ClassCodeVisitorSupport.java:104)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitConstructorOrMethod(ClassCodeVisitorSupport.java:115)
        at org.codehaus.groovy.ast.ClassCodeExpressionTransformer.visitConstructorOrMethod(ClassCodeExpressionTransformer.java:55)
        at org.codehaus.groovy.control.ResolveVisitor.visitConstructorOrMethod(ResolveVisitor.java:239)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitMethod(ClassCodeVisitorSupport.java:126)
        at org.codehaus.groovy.ast.ClassNode.visitContents(ClassNode.java:1081)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClass(ClassCodeVisitorSupport.java:53)
        at org.codehaus.groovy.control.ResolveVisitor.visitClass(ResolveVisitor.java:1345)
        at org.codehaus.groovy.control.ResolveVisitor.startResolving(ResolveVisitor.java:214)
        at org.codehaus.groovy.control.CompilationUnit$12.call(CompilationUnit.java:684)
        at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:966)
        at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:626)
        at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:575)
        at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:323)
        at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:293)
        at groovy.lang.GroovyShell.parseClass(GroovyShell.java:677)
        at groovy.lang.GroovyShell.run(GroovyShell.java:506)
        at groovy.lang.GroovyShell.run(GroovyShell.java:496)
        at groovy.ui.GroovyMain.processOnce(GroovyMain.java:597)
        at groovy.ui.GroovyMain.run(GroovyMain.java:329)
        at groovy.ui.GroovyMain.process(GroovyMain.java:315)
        at groovy.ui.GroovyMain.processArgs(GroovyMain.java:134)
        at groovy.ui.GroovyMain.main(GroovyMain.java:114)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:116)
        at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:138)
Caused by: java.lang.ClassNotFoundException: org.openscience.cdk.fingerprint.IFingerprinter
        at org.codehaus.groovy.tools.RootLoader.findClass(RootLoader.java:179)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at org.codehaus.groovy.tools.RootLoader.loadClass(RootLoader.java:151)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 61 more

update the FindAllRingsInLimitedTime example (possible API change)

Processing  FindAllRingsInLimitedTime.groovyin
doing FindAllRingsInLimitedTime.out...
AllRingsFinder.setTimeout() is not used, please use the new threshold values

Insert a "Getting started" chapter after the intro"

First of all: Great Book! The structure is a bit over-systematic or academic. I suggest following the practical approach of the rdkit book and pick the people up where they usually stand, i.e. wanting to read some structures from file and do something with it. So, after the introduction and before getting into the "atom=news atom()" stuff, insert a getting-started section. See https://www.rdkit.org/docs/GettingStartedInPython.html

Make classes clickable and link to the API documentation