Key Changes

• JDK Versions:
  • JDK 8 (minimum)
  • JDK 11 (minimum if not using cdk-iordf)
  • JDK 17 (recommended)
• The project is now built with Java 11+ but compiled to target Java 8. If you have any issues please let us know.
• The master branch has been renamed to main.
• logj4-core is no longer a dependency of cdk-log4j, you should include these separately if you intend to use Log4j
• A new cdk-slf4j module allows connecting logging to SLF4J
• MayGen structure generator, provides the ability to generate millions and millions of structures that have a given formulae.

Maygen maygen = new Maygen(SilentChemObjectBuilder.getInstance());
maygen.setFormula("C3Cl2H4");
maygen.setConsumer(new SmiOutputConsumer(new OutputStreamWriter(System.out)));
maygen.run();

Maygen is pure Java, if you need more speed consider Surge by the same author.

• New Smallest Ring utilities for single atom/bond

if (Cycles.smallRingSize(atom, 7) != 0) {
 // atom is in a ring 7 or smaller
}
if (Cycles.smallRingSize(bond, 7) != 0) {
  // bond is in a ring 7 or smaller
}

• RAW/Count Path Fingerprints

IFingerprinter fpr = new Fingerprinter();
Map<String, Integer> feats = fpr.getRawFingerprint(mol);

• Where possible "Re-inflate" convex rings on cyclcophanes:
  Before: now:

• New substructure/copy utility that allows a whole or part of a structure to be copied. Atoms are bonds are selected by providing a predicate:

IAtomContainer dst = builder.newAtomContainer();
AtomContainerManipulator.copy(dst, src, a -> a.isInRing(), b -> b.isInRing()); //  select the cyclic part of a molecule

// select atoms in a set, the bonds will also be selected
Set<IAtom> subset = ...
AtomContainerManipulator.copy(dst, src, a -> subset.contains(a)); 

• New exclusive atoms filter that provides non-overlapping substructure matches, note the input order can determine which matches are selected.

for (int[] mapping : Pattern.findSubstructure(query).matchAll(mol).exclusiveAtoms()) {
   // ...
}

• Stereo perception corner-cases. Reject:
  ,
  , ok:

Summary

• Merged all PRs and resolved all open issues related to bugs
• InChINumbersTools: Use JNA InChI options by @johnmay in #799
• Avoid integer overflow in MF by @johnmay in #808, #810
• Ensure correct stereo consistency (Fix #812) by @johnmay in #813
• SMILES: Fix an issue with stereochemistry being lost on generic atoms - @johnmay in #814, #866
• Maygen structure generator by @MehmetAzizYirik in #811
• Weighted path descriptor performance improvements by @johnmay in #817
• Depiction: Fix missing bond annotations by @johnmay in #819
• Utility functions for determining the smallest ring size of an atom/b… by @johnmay in #820
• Better consistentcy in Stereochemistry and Sgroups when removing atoms by @johnmay in #821
• Unify MOLfile V2000/V3000 options by @johnmay in #824, #852
• Improved stereochemistry perception by @johnmay in #826, #839
• Replace Atom symbol (String) comparison with atomic number (integer) by @johnmay in #827
• Improved/fix bugs with XLogP, PiContact, and BCUT, HuLuIndex descriptors by @johnmay in #833, #656, #822, #832
• Additional Raw and count path fingerprints by @johnmay in #834
• "Re-inflate" convex rings in macrocycles. The macrocycle layout can en… by @johnmay in #836
• Fix a corner case in repeat crossing bonds when we have variable atta… by @johnmay in #835
• Restore space as delimiter for string-based definition of InChI options by @marco-foscato in #846
• Update to Apache Jena 4.2 (requires JDK 11) by @egonw in #748
• Fix localisation of alpha channel floats in SVG by @egonw in #868
• Check string bounds on PDB COMPND line. Fixes #870 by @johnmay in #871
• Methods to manipulate atom types in ReactionManipulator by @uli-f in #883, #879
• Added ChemObjectBuilder.newReaction() by @uli-f in #888
• Utilities for selecting a substructure of a molecule. by @johnmay in #889
• Improved CDK Log4J/SLF4J interactions by @johnmay in #878, #876
• Additional SMARTS/matching utilities by @johnmay in #896, #900
• Use Junit5 by @johnmay in #901
• Fix issue with hose code nesting by @johnmay in #828

Authors

 278 John Mayfield
  13 Egon Willighagen
  11 Uli Fechner
   5 Mark Williamson
   3 Valentyn Kolesnikov
   2 MehmetAzizYirik
   2 Marco Foscato
   1 dependabot[bot]
   1 Tim Dudgeon
   1 Otto Brinkhaus
   1 Christoph Steinbeck
   1 Alex

New Contributors

• @marco-foscato made their first contribution in #846
• @tdudgeon made their first contribution in #847
• @OBrink made their first contribution in #851
• @sashashura made their first contribution in #885

Full Changelog: cdk-2.7.1...cdk-2.8