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Wednesday, September 15, 2010

CDK 1.3.6: the changes, authors, and reviewers

The list of changes is particularly long for this development release. Therefore, I will list the authors and reviewers first. Note that this release also includes the changes of the 1.2.6 and CDK 1.2.7 release.

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