So, this new edition is again thicker, summing up to 152 pages now, which is 28 pages more than the 3rd edition . Indeed, the table of contents is more than half a page longer in itself, though, just barely, still fitting on four pages. In fact, I had to remove one (new) subsection title, because it would take otherwise two further pages.

The new content is again a mix of sections and chapters. While writing new chapters, I find myself realizing I need to cover more basics. Those get typically added as new sections. I did not get many feature requests, except for one email pointing me the text promised how to interpret and handle failing atom type perception, which explains one of the new sections. The full list of new content is:

• Section 2.1.4: explaining the three flavors of atomic coordinates
• Extended Section 2.2: added detail about electron counts of bonds (partly in reply to this post by Rich)
• Chapter 5 “Protein and DNA”: four pages, mostly about PDB files, and the matching CDK data structure
• Chapter 6 “IChemObjectBuilders”: four pages explaining the four alternative builders CDK 1.4.7 has
• Section 7.8: a new section with recipes on how to post-process read input, discussing MDL molfiles only now. It talks about what information is present in the file format, and what steps must be untertaken to add missing information
• Section 8.2.4 “No atom type perceived?!”
• Section 11.4: describes how to depict aromatic rings
• Section 11.5: describes how to change the background color of depictions
• Section 13.4: explains how to calculate the Van der Waals volume of molecules
• Section 18.1.3: discussing the API improvement in the iterating readers
• Appendix C: a list of all descriptors provided by the CDK
• Appendix D: a list of file formats known by the CDK, indicating which has readers and writers

On top of that, I improved other bits of the book too, such as the resolution of the depictions of molecules, as well as those of various diagrams. Also the number of scripts has seriously gone up, from 94 to 134!

Appendix C is a prelude to a chapter I am already writing, but did not get finished yet: a chapter about descriptor calculation. But since I just started a new post-doc position, it may take another six months for that chapter to make it into print.

The paperbak is available from Lulu.com, an on-demand publisher, as well as this ebook version.

I am starting to get the hang of this publishing soon, publishing often thing, and just uploaded edition 1.4.1-0 of the Groovy Cheminformatics book. The cover is the same (with one typo fix), and the content is 20 pages thicker. True, six of those pages are isotope masses of all natural isotopes. That leaves 14 pages with this new content:

• Section 2.7 on line notations with 2.7.1 about reading and writing SMILES
• Section 6.3 about Sybyl (mol2) atom types
• Section 7.4 on atom numbering with 7.4.1 on Morgan atom numbers, and 7.4.2 on InChI atom numbers
• Chapter 9 on molecule depiction with the new rendering code, with
  • Section 9.1 on drawing molecules,
  • Section 9.2 on rendering parameters, and
  • Section 9.3 on the generator API and how to add custom content
• Section 11.4 on calculating aromaticity
• Appendix A.2 listing all Sybyl atom types
• Appendix B listing all naturally occurring isotopes

Features requests most welcome.

Some project are never finished. Neither is this one, but it is never too late to change how things work, so, taking advantage of publishing-on-demand, here I introduce the release-soon, release-often equivalent of cheminformatics books, my Groovy Cheminformatics with the Chemistry Development Kit book:

With a serious discount for just being the first edition (1.3.8-0), but still counting at 72 pages with 75 code examples, this edition marks a personal milestone (and probably not much more than that). There remains much to do, but I promised a release by tomorrow, so here it is. Next releases will contain more code examples, more functionality descriptions, and more literature reviewing where such code is used in science. The plan is to make new editions with each new CDK release, as well as new editions when I added a new chapter, section, or just paragraph. But, there will not be a Nightly build service anytime soon.

The current table of content is as follows:

Now, the book content is not open content. However, it contains nothing that is not available in other means. It’s just the compilation that makes this book interesting, as well as that I put effort in ensuring the code examples remain working. For that, I ask a minor financial contribution.

But, it will need to understand things like UK-92,480. This is made possible with the Oscar4 refactorings we are currently working on. You only need to register a dedicated dictionary . Oscar4 has a default dictionary which corresponds to the dictionary used by Oscar3, and a dictionary based on ChEBI (an old version) (see this folder in the source code repository).

Adding a new dictionary is very straightforward: you just implement the IChemNameDict interface. This is, for example, what the OPSIN dictionary looks like:

public class OpsinDictionary
implements IChemNameDict, IInChIProvider {

  private URI uri;

  public OpsinDictionary() throws URISyntaxException {
    this.uri = new URI(
      "http://wwmm.cam.ac.uk/oscar/dictionariy/opsin/"
    );
  }

  // the URI is somewhat like a namespace
  public URI getURI() {
    return uri;
  }

  // there are no stop words defined in this
  // dictionary
  public boolean hasStopWord(String queryWord) {
    return false;
  }

  // see hasStopWord()
  public Set getStopWords() {
    return Collections.emptySet();
  }

  // it has the name in the dictionary if the name
  // can be converted into an InChI
  public boolean hasName(String queryName) {
    return getInChI(queryName).size() != 0;
  }

  // this dictionary can return InChIs for names
  // so, it implements the IInChIProvider interface
  public Set getInChI(String queryName) {
    try {
      NameToStructure nameToStructure =
        NameToStructure.getInstance();
      OpsinResult result = nameToStructure
        .parseChemicalName(
          queryName, false
        );
      if (result.getStatus()
          == OPSIN_RESULT_STATUS.SUCCESS) {
        Set inchis = new HashSet();
        String inchi = NameToInchi
          .convertResultToInChI(
            result, false
          );
        inchis.add(inchi);
        return inchis;
      }
    } catch (NameToStructureException e) {
      e.printStackTrace();   
    }
    return Collections.emptySet();
  }

  public String getInChIforShortestSMILES(
    String queryName)
  {
    Set inchis = getInChI(queryName);
    if (inchis.size() == 0) return null;
    return inchis.iterator().next();
  }

  // since names are converted on the fly, we do
  // not enumerate them
  public Set getNames(String inchi) {
    return Collections.emptySet();
  }
  public Set getNames() {
    return Collections.emptySet();
  }
  public Set getOrphanNames() {
    return Collections.emptySet();
  }
  public Set getChemRecords() {
    return Collections.emptySet();
  }
  public boolean hasOntologyIdentifier(
    String identifier)
  {
    // this ontology does not use ontology
    // identifiers
    return false;
  }
}

Now, you can implement the interface in various ways. You can even have the implementation hook into a SQL database with JDBC, or use something else fancy. The dictionary will be used at various steps of the Oscar4 text analysis workflow.

Mind you, the refactoring is not over yet, and the details may change here and there.

Your comments are most welcome!

So, what are the API requirements set out? These include (but are not limited to):

• have reasonable defaults
• being able to add custom dictionaries
• easily change the chemical entity recogniser
• plugin text normalization (see Peter’s post on UNICODE )

This week I worked on the dictionary refactoring, and talked with Lezan about the ChemicalTagger and trying to get this based on the newer Oscar code (I think we’ll be able to finish that today). So, I cleaned up some code I did in the first week, and introduced a Oscar class providing a Java API to the Oscar functionality.

So, to get started with Oscar in your application, you only need to do:

Oscar oscar = new Oscar(
  this.getClass().getClassLoader()
);
oscar.loadDefaultDictionaries();
Map<NamedEntity,String> structures =
  oscar.getNamedEntities(
    "Ingredients: acetic acid, water."
  );

The ClassLoader is needed because the Oscar class will not generally know how to load custom classes.

You can add additional dictionaries, by implementing the IChemNameDict interface and one or more of IInChIProvider, ISMILESProvider, and ICMLProvider. For example, adding the OPSIN dictionary would extend the above code to:

Oscar oscar = new Oscar(
  this.getClass().getClassLoader()
);
oscar.loadDefaultDictionaries();
oscar.getChemNameDict().register(
  new OpsinDictionary()
);
Map<NamedEntity,String> structures =
  oscar.getNamedEntities(
    "Ingredients: acetic acid, water."
  );

And, I think the oscar.getChemNameDict() method will be renamed to something like oscar.getDictionaryRegistry() really soon.

CDK 1.2 code

IChemObjectBuilder builder =
  DefaultChemObjectBuilder.getInstance();
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("C"));

CDK 1.4 code

IChemObjectBuilder builder =
  DefaultChemObjectBuilder.getInstance();
IMolecule molecule = builder.newInstance(
  IMolecule.class
);
molecule.addAtom(
  builder.newInstance(IAtom.class, "C")
);

Now, please note that the builder.newInstance() method may actually return null. This is not the case for the DefaultChemObjectBuilder , or the NoNotifiationChemObjectBuilder , but future releases may have dedicated builders that do have such functionality. However, these builder would not supposed to be used for building molecules anyway.

The general patterns of newInstance() calls is that the first argument is the interface for which you want an instance. All further parameters are passed as parameters for the object’s constructor. The builder maps the input to appropriate class constructors. To know what parameters you can pass when instantiating an IAtom with the DefaultChemObjectBuilder, you would look at the constructor of Atom . Therefore, we can also call:

IAtom atom = builder.newInstance(
  IAtom.class, "C", new Point2d(0,0)
);

CDK 1.2 code

carbon.setHydrogenCount(4);

CDK 1.4 code

carbon.setImplicitHydrogenCount(4);

Yeah, that’s a simple one. Just to make clear, in both versions the count reflected the number of implicit hydrogens. The getHydrogenCount() suggested, however, to return the number of all hydrogens attached to that atom, that is, the sum of implicit and explicit hydrogens.

@Test public Oscar testConstructor()
throws URISyntaxException
{
  Oscar oscar = new Oscar();
  Assert.assertNotNull(oscar);
  return oscar;
}

@Given("#testConstructor")
public String testNormalize(Oscar oscar)
throws URISyntaxException
{
  String input = oscar.normalize(
    "This is a simple input string with benzene."
  );
  Assert.assertNotNull(input);
  return input;
}

@Given("#testConstructor,#testNormalize")
public List testTokenize(
  Oscar oscar, String input) throws Exception
{
  List tokens = oscar.tokenize(input);
  Assert.assertNotNull(tokens);
  Assert.assertNotSame(0, tokens.size());
  return tokens;
}

@Given("#testConstructor,#testTokenize")
public List testRecognizeNamedEntities(
  Oscar oscar, List tokens)
throws Exception
{
  List entities =
    oscar.recognizeNamedEntities(tokens);
  Assert.assertNotNull(entities);
  Assert.assertEquals(1, entities.size());
  return entities;
}

The pattern here is that each test method returns one variable, so that any method depending on two other unit test will have two parameters. The order is defined by the order in which they are given by the @Given clause.

The authors
I am mildly impressed by this release’s list of authors… it is certainly not the usual suspects anymore, and I would like to thank all contributors very much. Interestingly, we also see the number of places where contributions increase, and see patches from 7 different institutes (6 if you count the current ones)!

87  Egon Willighagen
42  Gilleain Torrance
17  Syed Asad Rahman
 9  Rajarshi Guha
 3  Jules Kerssemakers
 4  Mark Rijnbeek
 2  Andreas Truszkowski
 2  Saravanaraj
 1  Jonathan Alversson

The reviewers
The below list has also slight gained size, and I welcome Gilliean and Syed as active reviewers.

56  Rajarshi  Guha 
18  Egon Willighagen 
12  Syed Asad Rahman 
 4  Gilleain Torrance

The changes
The changes include bug fixes (see also the 1.2.6 and 1.2.7 release notes ), but also an updated SMSD engine, a rename of the IAtomType method getHydrogenCount() into getImplicitHydrogenCount() and of MDLWriter into MDLV2000Writer, and the addition of the signature code by Gilleain, and many, many small fixes.

• Compare values not objects (fixes #3061263) 1e4adac
• Unit test to reproduce failing atom type perception with one of the options to create a -1 Integer object 87f8bfe
• Smiles parser setting to preserve aromaticity as provided in the Smiles String itself. ae21ee2
• Added two further unit tests: one to see if the descriptor properly ‘ignores’ hydrogens; a second to reproduce the numbers in the original Wiener paper from 1947 91c58dd
• Renabled test which was (accidentally?) outcommented when switching to JUnit4 in commit 06a1a3dd ac82b12
• Added a reference to the original Wiener paper 0c5187e
• No need to declare throws for other Exception’s if the superclass is already declared thrown itself (also, no need to define java.lang explicitly) e73a291
• Minor cleanup: corrected copyright statement; simplified JavaDoc by removing empty parameter table 6292875
• Replaced inline citation by reference to the main bibliography 8ddbb1b
• Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms 6a6db0b
• Updated javadocs and added extra unit test ac211ce
• Implementation of a descriptor to measure molecular complexity in terms of sp3 to sp2 ratio of carbon atoms bd9fb4f
• Removed output to STDOUT 18f7d52
• Fix for branching bracket issue when generating SMILES for BrC1C(Br)C(Br)C(Br)C(Br)C1Br 526362e
• Unit test for bug #3040273. 3bf8397
• Fixed hybridization information: these are sp3 hybridized systems e8cec0f
• More missing elements for SMILES parsing problems reported in bug #3048501 bcb8432
• Unit tests for SMILES parsing bugs reported in #3048501 bb5ffe1
• Upper case the first character to also properly recognize lower cased ‘aromatic’ two-character element symbols (fixes SMILES parsign of things like c1[se]ccccc1 3f6056b
• JavaDoc fixes: correct @cdk.cite use, and small typo d097acf
• Updated the JavaDoc for an API changed a while ago: the getInChIToStructure() method now takes an IChemObjectBuilder as second argument (fixes #3035890) 3e1aba0
• Updated the JavaDoc for the atoms() Iterable API change (fixes #3034824) 2a5bb6b
• Added the maven build file (closes #3042475) 6209a48
• a)removed blank/unused methods and fixed imports Signed-off-by: Syed Asad Rahman 911af3f
• a)IMatch to Match and constructor call for state used TargetProperties for faster processing Signed-off-by: Syed Asad Rahman 4a2f9c1
• a)Assert cleaned and fixed b)Correct ASSERT imports used a420b61
• Removed unused code cb4048e
• Updated checking of indices which now are -1 if unset, instead of null cd8ccee
• a) Default constructor supported as per changes in the CDK b) VFMCS index error should point to -1 not null Signed-off-by: Syed Asad Rahman 9c6c830
• a)Refactored matchers, atom matcher and bond matcher b)getTanimoto score fixed for single atoms 1dae4f2
• Updates for the getImplicitHydrogenCount() renaming 0f64e4d
• The smsd module now depends on the signature module 7d5fc9d
• Latest SMSD code 1.2.0: Major changes are: 7217e82
• Use the factory to not depend on an implementation e2c8329
• Renamed get/setHydrogenCount() to get/setImplicitHydrogenCount(), per report #3020065 8ec9ad4
• Introduced a helper class with info about the CDK library: the version number, which is read from the build.props which is now included in the cdk-core.jar 5a2bc65
• Also take into account super classes 0de5777
• Renamed MDLWriter into MDLV2000Writer (implements #3029447) f0256d0
• Assert pattern has the expected value as first argument d4045cc
• Use the builder pattern to instantiate an IIsotope 6760330
• MDLV2000 reader interprets D and T without M ISO line mandatory f6fd82b
• Use the PT class to see if something can be an element and removing the redundant element symbol info 937c4c7
• Fixed annotation with TestMethod, not TestClass (fixes #3016632) 9eb04e5
• Skip inner classes for @cdk.module and @cdk.githash JavaDoc tests (fixes #3043084) d070396
• Throw a CDKException when a QUADRUPLE bond order is in the input, which is not supported by the MDL/Symyx molfile format (fixes #3029352) 32cdc48
• Deal with a special situation: pyridine N-oxide in the non-charge-separated representation, with a N.sp2.3 nitrogen, with two double bonds. Previously, any ring-outward double bond would disqualify the ring as aromatic. This compound is now an exception. c66039d
• Assert the compound is aromatic (fixes false negative) d1da527
• Exporting the signatures jar 7959947
• Removed the OpenJavaDocCheck Jazzy extension which was not supposed to go in; it’s not ready for prime time 9364179
• Added missing dependencies (fixes failing unit tests) e582852
• Added missing dependencies (fixes failing unit tests) ef14ef0
• Added missing dependency a0f22f6
• Copy the 2D templates into the source distribution 5bcd111
• Added finally blocks to MolHandler to close its input streams, with proper logging calls if it fails Fixes bug #3032568 1201e01
• UIT timeout fix 5a329d4
• Cleaned up exception handling in TemplateHandler.loadTemplates() to be more specific and less pessimistic. e1df763
• QSAR descriptor values made serializeable 2ef459c
• Fixed assertion to compare two Vector3d’s c133da5
• Added test to assert that two Vector3d’s are identical 6651956
• All methods now tested 004770a
• Hooking up test machinery 32155b0
• Altered the getTetrahedralDescription to be get stereo and return ITetrahedralChirality.Stereo f61266c
• Moved Stereotool to stereo package a99c918
• Convenience method that returns chirality descriptor (R/S) given four atoms in priority order 7abbdcc
• Missing docs 9a55100
• Copyright statements d96f596
• Just to be paranoid, test +/- tetrahedra above and below the XY plane e32f334
• Tests for square planar shapes, trig bipyr, and oct 8b49490
• Cleanup and fixing (I think) of the trigonal bipyramidal method 1b01c84
• Test for 3 colinear points 01ae3fc
• Better docs bb38d10
• Tests for tetrahedral sign, some basic defined vectors 897b6ee
• Test class, and name change of distanceToPlane to show that it returns signed (+/-) distance 1735551
• Initial go at the StereoTool - functions taken from Jmol’s smiles package for 3D stereo checking c25591f
• Updated OB note and robustified unit tests 2b96512
• Added support for multi-molecule mol2 files. Updated source and added unit test and test file dbd6df4
• Updated cdk-1.2.x patches for master API e383f4b
• Updated the DebugBond unit test too now: new DebugBond() has zero atoms 6ef1fb1
• Backport patch, to make the patches compile with cdk-1.2.x ce9b1bd
• Additional patch to reduce atom count on setAtom(null, int) and unit tests for the setAtom(IAtom, int) behavior. 6cf95db
• Also fix the new NNBond() == 0 atoms for the nonotify module 23d9685
• Fixed Bond() constructor to create a bond with zero atoms. Also fixed setAtom(IAtom, int) to increase the atom count if a null entry is filled with a non-null IAtom. 916ab96
• Updated test to assume new Bond() creates a bond with zero atoms 4ac7111
• Added two unit tests for aromatic N-oxides that are the basis for failures in SMARTS matching 12fb96b
• added javadoc to IChemObjectReader explaining the split between ISimple and IIterating ChemObjectReaders 1574e42
• Exceptions when clone atomless ISingleElectron and ILonePair too c5d4cd3
• Unit test for ArrayIndexOutOfBoundsException occuring when trying to clone an IAtomContainer with an IBond with no IAtoms d71c31c
• Added unit tests for SMILES with failing atom typing, from email on the cdk-devel mailing list June 11 2010 890d0f5
• Added the N.oxide atom type, for structures like (CH3)N=O bb431e3
• Fixed reading of SD properties: keep the first line too 3133a18
• Added missing dependency 14003dc
• Fixed unit test: surely there is no atom with symbol 0… how long has this been failing?? c888e4f
• Updated fingerprinter javadoc e6fecf2
• Added a test class to aromaticity of three compounds: the last incorrectly fails a454ab8
• Also except N.amide as part of an aromatic ring 3357113
• Added a test class to repeat atom type perception and test consistency 0bd5b42
• Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes a big goof up cd83236
• Replace special chars where spaces are supposed to occur, fixing the fail of the unit tests every now and then 483c856
• Merge branch ‘master’ of ssh://cdk.git.sourceforge.net/gitroot/cdk/cdk eb6defd
• BooleanIOSetting to let MDLWriter output bond type 4 (aromatic) a586d6a
• Reorderd imports 2896226
• Added test cases to check that the code runs when faced with covalently bonded metals. Currenly on failure is due to the presence of Pt, for which we do not have a valency in AtomValence f32e9a2
• chemfilter improvised Signed-off-by: Syed Asad Rahman 2a7ee54
• SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman 8f3c70a
• SMSD Test cases updated as per new code Signed-off-by: Syed Asad Rahman 3266460
• added ExtAtomContainerManipulator Signed-off-by: Syed Asad Rahman d4d8339
• deleted ext Signed-off-by: Syed Asad Rahman b44c82b
• updated SMSD code Signed-off-by: Syed Asad Rahman eccc70d
• updated SMSD code Signed-off-by: Syed Asad Rahman 370a926
• Convenience constructors for AtomSignature that take IAtoms rather than atom indices 935b5f6
• Added missing jar meta file for the Signatures library 805103a
• Updated to reflect the upstream jar name d33a71a
• Abstract methods not part of API are now protected, to discourage thier use 7a92d42
• Various fixes to tests 592b920
• Added the missing assert: runCoverageTest() returns a boolean stating the success 850fd1a
• cdk.cite references for two Faulon papers e7ccc4e
• More missing javadocs - notably the class documentation for AtomSignature and MoleculeSignature 8bd664f
• Mising constructor javadoc, and inheritdoc annotation on AtomSignature 88ffdd6
• Final missing test cf148dd
• Atom signature test methods 888bf60
• Molecule signature tests b64c4e5
• Signature quotient graph test method 0d0a95e
• Missing test for Orbit::iterator 2609f1b
• Removed unused import 020fb92
• Molecule From Signature Builder tests 9d2a0c0
• All orbit methods tested 7c46a7c
• Finally correct junit annotations, and sort test fba5ff5
• BeforeClass method must be static; better clone test 7e370a2
• Fixes some problems flagged by PMD cd3a866
• Use junit’s BeforeClass instead of Before annotation 2566b87
• Added missing githash tags, to add links in the JavaDoc to the source code repository fc0a9f9
• Inherit JavaDoc where methods overwrite a super method d4a9436
• Fixed PMD warnings: more descriptive field names; use of Integer.valueOf() 02020d6
• Added test method annotation for the clone() method cabd95f
• Removed some unnecessary imports 19b21a3
• Test orbit cloning 3c85ab2
• Improved canonical label method in graph signature 0bca11f
• Integer invariants, and updated signatures jarfile 5c838b6
• Added JavaDoc HTML generation for the signature module 7617074
• Hooked in PMD testing for the signature module 7384bc3
• Defined dependencies for the test module 132badc
• Hooked the signature module into the CDK build system 4ea7d48
• Removed the dependency on the nonotify module 93e0a22
• Created a CDK style module test suite a9a4aa8
• MoleculeFromSignatureBuilder tests d7bb6f6
• Extend from CDKTestCase and use the slow running test check 6969629
• Fixed and cleaned up molecule signature tests 3998ed7
• Initial commit of signature package ff2bdeb
• Added OpenJavaDocCheck 0.5 - the Jazzy spell checking extension 57e7eea
• specify fail behavior (returns null) in javadoc bfd06db
• Added PMD tests for detecting misuse of TestClass and TestMethod, e.g. TestClass on a method. (fixes #3014808) c94ebcf
• Removed two lines added in master to the removed doccheck target 9d679fe
• Merge branch ‘cdk-1.2.x’ 055f702
• Improved javadoc generation using a link tag, so that references to java library classes are resolved properly 1f8bb2d
• Update OpenJavaDocCheck to 0.5: fixing a few false positives f0c7d0c
• Removed use of the proprietary DocCheck utility 1523f66
• OpenJavaDocCheck errors are fixed for SMSD related modules Signed-off-by: Syed Asad Rahman ac9384a
• solved cdk-Bugs-3006773 : small JavaDoc errors in the smsd module f66a779
• Fix for character spacing for “APO” line in RGFile output ed510bf
• Branch open for commits for the future 1.3.6 1ab64ff
• Use the new tests in more situations e8b13b2

The changes

• Compare values not objects (fixes #3061263) 324f7f5
• Unit test to reproduce failing atom type perception with one of the options to create a -1 Integer object 9c1b95a
• Removed output to STDOUT 223fc9a
• Fix for branching bracket issue when generating SMILES for BrC1C(Br)C(Br)C(Br)C(Br)C1Br b9b2272
• Unit test for bug #3040273. 6d9b3d2
• Fixed hybridization information: these are sp3 hybridized systems a01de91
• More missing elements for SMILES parsing problems reported in bug #3048501 31f7462
• Unit tests for SMILES parsing bugs reported in #3048501 bf8defd
• A few more missing elements in the SMILES two-character element symbol parsing 5cf9334
• Added missing elements, fixing several problems reported in bug #3048501 6ab74bc
• Upper case the first character to also properly recognize lower cased ‘aromatic’ two-character element symbols (fixes SMILES parsign of things like c1[se]ccccc1 3ec1480
• JavaDoc fixes: correct @cdk.cite use, and small typo 394f9ed
• Updated the JavaDoc for an API changed a while ago: the getInChIToStructure() method now takes an IChemObjectBuilder as second argument (fixes #3035890) be56aac
• Updated the JavaDoc for the atoms() Iterable API change (fixes #3034824) 38873dc

The authors The below numbers are based on the number of commits, but keep in mind that some developers, like myself, need more commits for the same number of changed lines.

13  Egon Willighagen
 2  Saravanaraj

The reviewers The below list is based on who signed off the patches. Anyone who reviews patches in the patch tracker can basically do this. Ask on cdk-devel on how to do this.

 8  Rajarshi Guha
 4  Gilleain Torrance
 2  Egon Willighagen