Permalink
Commits on Oct 22, 2013
  1. Removed a bad tests: the matcher uses and requires implicit hydrogens…

    johnmay committed Oct 22, 2013
    … explicitly, and the test does not have them; the testFindMatchingAtomType_IAtomContainer_IAtom() does and works find [backport]
Commits on Aug 7, 2013
  1. Also customUnused for the full PMD reports

    egonw committed Aug 7, 2013
    Change-Id: Idf790c9430872554b9d52295c13a8cfab29c35a8
  2. Put the PMD unused/migration reports in a separate folder to not over…

    egonw committed Aug 7, 2013
    …write the full reports
    
    Change-Id: I99677b4a13599dab0f7cea429b6774bbc3a6b0b5
  3. Added missing @cdk.githash tags

    egonw authored and johnmay committed Aug 7, 2013
    Change-Id: I41d229b3a9b5996a0924b34e3e23f1525dafbd21
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  4. Fixed the class JavaDoc syntax, correcting a false fix in commit 4fc4837

    egonw authored and johnmay committed Aug 7, 2013
    
    
    Change-Id: If0eb90c725a97ccfb53dd8c6c34d5de26f7767bb
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  5. Added missing JavaDoc

    egonw authored and johnmay committed Aug 7, 2013
    Change-Id: I75e0bf8f95e85c1023ee2b06ce08f1c5568ee988
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  6. Ignore the UnusedModifier PMD test

    egonw authored and johnmay committed Aug 7, 2013
    Change-Id: I92ca55f26e95f188dfb11adf086b47896630a2fe
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  7. Added Joos Kiener (patch in 1.4.19) as author

    egonw committed Aug 5, 2013
    Change-Id: I9c055d01f0eb1805b71131eac2207794cbbef6a2
  8. Updated PMD from 5.0.1 to 5.0.4

    egonw committed Aug 7, 2013
    Change-Id: I82bc18998f0044fdf478bad90b2529265d3adbf5
Commits on Aug 5, 2013
  1. If the proper behavior is to throw an exception, then the unit test s…

    egonw authored and johnmay committed Aug 5, 2013
    …hould expect it
    
    Change-Id: Ia47ea485b73ecec0d9259272aef0b111e142d022
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  2. Open for more fixing

    egonw committed Aug 5, 2013
    Change-Id: I938046a30cabf1d019c4da75e2d1c3f18f09865a
  3. Release 1.4.19

    egonw committed Aug 5, 2013
    Change-Id: Ib36f4a52e51dc2a64e299140bde4029e113e39fb
  4. Exact mass and natural abundance is not preserved on reading/writing …

    johnmay committed Aug 4, 2013
    …CML. As these attributes are boxed primitives they can be null and throw an exception when unboxed by 'assertEquals'. Before checking the values the attributes are not checked for nullity.
    
    Change-Id: If6b52cf6f22d23405b8f15045d8ca1dccf0bcd74
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
  5. Resolves unit test failure (previous commits). When a double bond is …

    johnmay authored and egonw committed Aug 5, 2013
    …found and there are no 2D coordinates (e.g. unspecified configuration) then return then return '0' for the configuration value.
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
  6. Backport for cdk-1.4.x: use IMolecule in IMoleculeSet

    egonw committed Aug 5, 2013
    Change-Id: I110f4bc5078de535f8840eae811ad69752503b39
  7. When a reaction references a molecule which is unknown - automaticall…

    johnmay authored and egonw committed Aug 5, 2013
    …y create one with that Id. This happens when the set of molecules is defined after the reaction. This commit resolve the test in error 'CML2Test. testBug2697568'
    
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
  8. Resolves two long standing errors in 'cdk-extra'. The method should t…

    johnmay authored and egonw committed Aug 4, 2013
    …hrow an exception when one tries to attach to an invalid atom number (e.g. 7-chlorohexane). The existing error was using the ParseException constructor incorrectly and thus would throw an error. The constructor is for generating error messages to do with syntax. As this is a semantic error the constructor did not function as intended. Simply replacing the use of this constructor with a normal error message resolves the issue.
    
    Change-Id: I896e3a3d07322e0a98f317cb331f4ebfe66f8e15
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Commits on Aug 2, 2013
  1. Two convenience methods to make dealing with BODR data a lot easier

    egonw authored and johnmay committed Aug 2, 2013
    Change-Id: I1c29e2d1b412a898bf01ecc2a4d0bb3a145249cd
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  2. Added Lv and Fl names and two missing elements (Uup and Uut) used in …

    egonw authored and johnmay committed Aug 2, 2013
    …Elements.java
    
    Change-Id: I16cfb6e31a5eead58cef870ac5a4d25416870c59
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  3. Fixed the import, matching the cdkdeps

    egonw committed Aug 2, 2013
    Change-Id: Ia1de7eea08c8b4ce0fb4b3e131d482634b14635f
  4. Any bond order is fine, but the IBond must exist (fixes #1305)

    egonw authored and johnmay committed Aug 2, 2013
    Change-Id: Ida9971b5326c4e33e2c1513419b7ad8cb6ac9861
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  5. Added a positive unit test too

    egonw authored and johnmay committed Aug 2, 2013
    Change-Id: Ica5ed8c3f3ab944da83e3c3bdfbd05fcc13e2826
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  6. Basic unit test for bug 1305: null should not match AnyOrderQueryBond

    egonw authored and johnmay committed Aug 2, 2013
    Change-Id: Ia5f6b0e297d6ba571af690b534dc5fb3f2d1a5c0
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  7. Fixed the group for Ds (fixes #1282)

    egonw authored and johnmay committed Aug 2, 2013
    Change-Id: I8fdbb50f171697371090bc8c4615a1af4aa6d8e3
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  8. Removing output from unit tests.

    johnmay authored and egonw committed Aug 2, 2013
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
  9. Unit tests for optional property writing.

    johnmay authored and egonw committed Aug 2, 2013
    Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
  10. white-listing for export properties

    Joos Kiener authored and johnmay committed Aug 1, 2013
    Only properties explicitly inputed into SdfWriter should be
    exported. This new behavior could be added with an extra constructor
    that takes a Set of properties. Using existing constructors keeps
    the old behavior.
    
    Change-Id: I04d42b0d245f5b7479436396efecbcb6daf13669
Commits on Jun 24, 2013
  1. Do not output isotope info in PDB-CML files (fixing the last roundtri…

    egonw authored and johnmay committed Jun 23, 2013
    …pping inconsistency
    
    Change-Id: I9166f590d91867f3fd35a319a8ca667b4ff15f62
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  2. Output the monomers in a sorted manner, to make the CML output more r…

    egonw authored and johnmay committed Jun 23, 2013
    …eproducible
    
    Change-Id: Ice68427060f642d9adec3754e8e068b893ffd697
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  3. Do not output empty properties

    egonw authored and johnmay committed Jun 23, 2013
    Change-Id: I771bab0938c950635f236df229d9309d9fe3d0b1
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  4. Factored out the test for PDB atom customization; also fixed the test…

    egonw authored and johnmay committed Jun 23, 2013
    … to register the customizer (but there is more wrong)
    
    Change-Id: I02ada008ab0736a0137544266566ef96c21d4c56
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  5. Use interfaces instead of implementations

    egonw authored and johnmay committed Jun 23, 2013
    Change-Id: I9d6c1764ea7c3ec6c9b58e2fd4408576b25e2467
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  6. Links from the JavaDoc

    egonw authored and johnmay committed Jun 23, 2013
    Change-Id: I246f4b809f964ef0533412e12c67754bad51e931
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
  7. Test if the monomer ID is read

    egonw authored and johnmay committed Jun 23, 2013
    Change-Id: Id5f8e7fd168a8b170cb1fb7f31943e3c5247a24c
    Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Commits on Jun 11, 2013
  1. Invert test assertion - the molecule is now automatically configured …

    johnmay committed Jun 11, 2013
    …and the structures are the same.