New version, based on CDK 2.9

egonw · Apr 7, 2024 · f4d2d67 · f4d2d67
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diff --git a/README.md b/README.md
@@ -2,12 +2,12 @@
 
 # Groovy Cheminformatics with the Chemistry Development Kit
 
-[Edition 2.8-1](https://egonw.github.io/cdkbook/)
+[Edition 2.9-0](https://egonw.github.io/cdkbook/)
 
 **Egon L. Willighagen** PhD<br />
 Long time CDK developer
 
-© E.L. Willighagen 2011-2023
+© E.L. Willighagen 2011-2024
 
 License: CC-BY-SA 4.0 International
 
@@ -20,6 +20,6 @@ License: CC-BY-SA 4.0 International
 
 ## About
 
-Further information: [http://chem-bla-ics.blogspot.com/](http://chem-bla-ics.blogspot.com/)
+Further information: [https://chem-bla-ics.linkedchemistry.info/](https://chem-bla-ics.linkedchemistry.info/)
 
 E.L. Willighagen <[email protected]>
diff --git a/code/AdjacencyMatrixCalc.code.md b/code/AdjacencyMatrixCalc.code.md
@@ -1,7 +1,7 @@
 # AdjacencyMatrixCalc.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.*;
 import org.openscience.cdk.config.*;

diff --git a/code/AromaticAtomCountDescriptorParams.code.md b/code/AromaticAtomCountDescriptorParams.code.md
@@ -1,7 +1,7 @@
 # AromaticAtomCountDescriptorParams.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.qsar.descriptors.molecular.*;
 

diff --git a/code/AromaticBond.code.md b/code/AromaticBond.code.md
@@ -1,7 +1,7 @@
 # AromaticBond.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/AromaticBonds.code.md b/code/AromaticBonds.code.md
@@ -1,7 +1,7 @@
 # AromaticBonds.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.smiles.*;

diff --git a/code/AromaticSMILES.code.md b/code/AromaticSMILES.code.md
@@ -1,7 +1,7 @@
 # AromaticSMILES.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.smiles.SmilesGenerator;
 import org.openscience.cdk.interfaces.*;

diff --git a/code/AromaticityDemo.code.md b/code/AromaticityDemo.code.md
@@ -1,7 +1,7 @@
 # AromaticityDemo.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.smiles.*;

diff --git a/code/AtomContainerAddAtomsAndBonds.code.md b/code/AtomContainerAddAtomsAndBonds.code.md
@@ -1,7 +1,7 @@
 # AtomContainerAddAtomsAndBonds.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/AtomContainerAddAtomsAndBonds2.code.md b/code/AtomContainerAddAtomsAndBonds2.code.md
@@ -1,7 +1,7 @@
 # AtomContainerAddAtomsAndBonds2.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/AtomContainersForLoopingInSet.code.md b/code/AtomContainersForLoopingInSet.code.md
@@ -1,7 +1,7 @@
 # AtomContainersForLoopingInSet.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.silent.*;
 import org.openscience.cdk.*;
@@ -20,6 +20,6 @@ for (i=0; i<set.getAtomContainerCount(); i++) {
 **Output:**
 ```plain
 Number of containers: 2
-container 0 has hashcode 632168320
-container 1 has hashcode 1761382759
+container 0 has hashcode 517960153
+container 1 has hashcode 551377008
 ```
diff --git a/code/AtomContainersLoopingInSet.code.md b/code/AtomContainersLoopingInSet.code.md
@@ -1,7 +1,7 @@
 # AtomContainersLoopingInSet.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.silent.*;
 import org.openscience.cdk.*;
@@ -20,6 +20,6 @@ for (atomContainer in set.atomContainers()) {
 **Output:**
 ```plain
 Number of containers: 2
-container's hashcode 1263085541
-container's hashcode 1281205497
+container's hashcode 285831951
+container's hashcode 32777062
 ```
diff --git a/code/AtomCoordinates.code.md b/code/AtomCoordinates.code.md
@@ -1,7 +1,7 @@
 # AtomCoordinates.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/AtomCountDescriptorParams.code.md b/code/AtomCountDescriptorParams.code.md
@@ -1,7 +1,7 @@
 # AtomCountDescriptorParams.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.qsar.descriptors.molecular.*;
 

diff --git a/code/AtomLabels.code.md b/code/AtomLabels.code.md
@@ -1,7 +1,7 @@
 # AtomLabels.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
  import org.openscience.cdk.templates.*;
  import org.openscience.cdk.isomorphism.*;

diff --git a/code/AtomTypePerception.code.md b/code/AtomTypePerception.code.md
@@ -1,7 +1,7 @@
 # AtomTypePerception.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/AtomTypePerceptionMolecule.code.md b/code/AtomTypePerceptionMolecule.code.md
@@ -1,7 +1,7 @@
 # AtomTypePerceptionMolecule.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/AtomTypeProperties.code.md b/code/AtomTypeProperties.code.md
@@ -1,7 +1,7 @@
 # AtomTypeProperties.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/AtomTypeUnitTest.code.md b/code/AtomTypeUnitTest.code.md
@@ -1,7 +1,7 @@
 # AtomTypeUnitTest.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import java.net.UnknownHostException;
 import org.openscience.cdk.silent.*;

diff --git a/code/AtomTypeX.code.md b/code/AtomTypeX.code.md
@@ -1,7 +1,7 @@
 # AtomTypeX.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/BioNameType.code.md b/code/BioNameType.code.md
@@ -1,7 +1,7 @@
 # BioNameType.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.io.*;

diff --git a/code/BitSetDemo.code.md b/code/BitSetDemo.code.md
@@ -1,7 +1,7 @@
 # BitSetDemo.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import java.util.BitSet;
 bitset = new BitSet(10);

diff --git a/code/BondOrders.code.md b/code/BondOrders.code.md
@@ -1,7 +1,7 @@
 # BondOrders.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 

diff --git a/code/BondStereos.code.md b/code/BondStereos.code.md
@@ -1,7 +1,7 @@
 # BondStereos.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 

diff --git a/code/Builders.code.md b/code/Builders.code.md
@@ -1,7 +1,7 @@
 # Builders.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/BuildersOldFashion.code.md b/code/BuildersOldFashion.code.md
@@ -1,7 +1,7 @@
 # BuildersOldFashion.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.*;

diff --git a/code/CDKAtomTypeProperties.code.md b/code/CDKAtomTypeProperties.code.md
@@ -1,7 +1,7 @@
 # CDKAtomTypeProperties.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.config.*;

diff --git a/code/CDKConstantsProperties.code.md b/code/CDKConstantsProperties.code.md
@@ -1,7 +1,7 @@
 # CDKConstantsProperties.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
  import org.openscience.cdk.*;
 

diff --git a/code/CTR1.code.md b/code/CTR1.code.md
@@ -1,7 +1,7 @@
 # CTR1.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.io.*;

diff --git a/code/CTR2.code.md b/code/CTR2.code.md
@@ -1,7 +1,7 @@
 # CTR2.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import java.util.List;
 import java.awt.*;

diff --git a/code/CTR4.code.md b/code/CTR4.code.md
@@ -1,7 +1,7 @@
 # CTR4.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.io.*;
 import org.openscience.cdk.io.iterator.*;

diff --git a/code/CalculateMolecularWeight.code.md b/code/CalculateMolecularWeight.code.md
@@ -1,7 +1,7 @@
 # CalculateMolecularWeight.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;

diff --git a/code/CalculateMolecularWeightImplicitHydrogens.code.md b/code/CalculateMolecularWeightImplicitHydrogens.code.md
@@ -1,7 +1,7 @@
 # CalculateMolecularWeightImplicitHydrogens.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.*;
 import org.openscience.cdk.interfaces.*;

diff --git a/code/CalculateMolecularWeightShort.code.md b/code/CalculateMolecularWeightShort.code.md
@@ -1,7 +1,7 @@
 # CalculateMolecularWeightShort.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;

diff --git a/code/CalculateTotalCharge.code.md b/code/CalculateTotalCharge.code.md
@@ -1,7 +1,7 @@
 # CalculateTotalCharge.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;

diff --git a/code/ChemFileForLooping.code.md b/code/ChemFileForLooping.code.md
@@ -1,7 +1,7 @@
 # ChemFileForLooping.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.*;
 file = new ChemFile()

diff --git a/code/ChemFileLooping.code.md b/code/ChemFileLooping.code.md
@@ -1,7 +1,7 @@
 # ChemFileLooping.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.*;
 file = new ChemFile()

diff --git a/code/ChemObjectIdentifiers.code.md b/code/ChemObjectIdentifiers.code.md
@@ -1,7 +1,7 @@
 # ChemObjectIdentifiers.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
  import org.openscience.cdk.*;
 

diff --git a/code/ChemObjectProperties.code.md b/code/ChemObjectProperties.code.md
@@ -1,7 +1,7 @@
 # ChemObjectProperties.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
  import org.openscience.cdk.*;
 

diff --git a/code/ChemSequenceForLooping.code.md b/code/ChemSequenceForLooping.code.md
@@ -1,7 +1,7 @@
 # ChemSequenceForLooping.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.*;
 sequence = new ChemSequence()

diff --git a/code/ChemSequenceLooping.code.md b/code/ChemSequenceLooping.code.md
@@ -1,7 +1,7 @@
 # ChemSequenceLooping.groovy
 **Source code:**
 ```groovy
-@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')
+@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
 
 import org.openscience.cdk.*;
 sequence = new ChemSequence()