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1.5.13 Release Notes

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John May edited this page Apr 25, 2016 · 7 revisions

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Summary

This release includes some tidy up and bug fixes. Major feature changes are summarised below:

  • Extended 2D color pallet for depictions, we now use the colors used by Jmol.
  • Improved generic label distinction in depiction. It's now possible to tell the differences between a pseudo atom labelled 'Y' (not in italics) and Yttrium. Sub labels (e.g. numbers in 'R1') are superscripted.
  • Resolved issue with isotope calculation failing for large formulae.
  • Improved hybridisation depiction in layout, e.g. azides are now co-linear.
  • Abbreviations are now assigned through cuts rather than sub-structure searching, this allows much better scaling allowing large abbreviation libraries.
  • Correctly read and write tetrahedral parity column in Molfiles.
  • Read support for CXSMILES (ChemAxon Extended SMILES). Allows coordinates, radicals, atom labels/values, brackets, positional variation, etc. to annotated on a SMILES. Write support will be added in future.

Authors

51  John May
27  Egon Willighagen
 5  Tomas Pluskal
 1  Rajarshi Guha

Full Change Log

  • Release 1.5.13. 0b6b19d
  • Correct scaling of reaction conditions. 61389d5
  • Merge pull request #201 from cdk/testFixes_20160418 a54f853
  • Merge pull request #200 from cdk/patch/cxsmiles-read 18639d9
  • Resolving failing unit test, hidx needs to check i,j (local index) nor a,b (labels). ceaa623
  • Additional centering of agents when arrow is small and has conditions. 937f107
  • Unescape Data Sgroup field and allow early termination. 99f911f
  • Make it possible to draw reaction conditions bellow the arrow of a reaction. We use a new property which is picked up during the depiction generation. Some minor tweaks were made to sizing calculations in particular ensuring -1 is not used which was accidentally making some spacing smaller then needed. 7b456eb
  • Read Data Sgroups. e66110e
  • Minor tweak, when checking minimum arrow length account the the size of the arrow head. 42c229e
  • Handling highlighting with contracted abbreviations. 611e055
  • Handling marshalling from CXSMILES state to the CDK data-structures. 7b05e55
  • Preliminary parsing and representation of CXSMILES. fb8d137
  • Safe null unbox. 4ac88d4
  • Merge pull request #199 from cdk/legacy/deprecate-mdlreader a07f829
  • Deprecate MDLReader to avoid confusion. 88f576b
  • When selecting rotation, check if the molecule has an attachment point. 6507edf
  • Shuffle around where stereo assignment is done so it doesn't consider any ionic bonds we temporarily add in.. 9e40edd
  • Slightly better check for laying out co-linear chains. Useful for cumulenes and azides. e79cc4f
  • Improved cumulated bond depiction by restricting when we offset double bonds. 7190b0d
  • Merge pull request #198 from cdk/patch/mdlpartiy 0f8d3cb
  • Use atom index instead of linear scan. d5a6914
  • Write 0D tetrahedral stereochemistry. 5b1ab1a
  • Deprecate stereo parity property on atom. Existing code can continue to use it but it is not the prefered method. 312e836
  • Don't ever show 'ht' superscript. fa571c3
  • Improved single atom bracket aesthetics. 97597e9
  • Abbreviation generate through fragmentation (cuts) rather than SMARTS patterns. ec56b9c
  • New separate API for pseudo atoms vs abbreviations. 250e70b
  • Line of the arrow should be the foreground color. 4b5c439
  • Merge pull request #196 from tomas-pluskal/master 30e8d67
  • Removed the nonsense isNotZero() method 80ba80c
  • Patched a bug in IsotopePatternGenerator df1c2f7
  • Improve arrow aesthetics and avoid making tiny arrows. eb79e25
  • Improved generic label formatting, superscript numbers/primes and make labels italic. This allows clear distinction between the substituent list 'W' and 'Tungsten'. 177e84c
  • Sulphur is a little too bright. 23041fc
  • Additional corner case, when only one bond and other disconnected atoms. d427157
  • Don't bond the same two atoms more than once. 1923e49
  • Merge pull request #192 from cdk/01feb16_2 51f0ffc
  • Merge pull request #191 from cdk/01feb16 a838988
  • Merge pull request #189 from cdk/patch/deprecatemolfactory 84ebe07
  • Update documentation. ef8f4f6
  • Correct erroneous test value. c86a01d
  • Faster an simpler LargestChainDescriptor. 6daeadd
  • Merge pull request #194 from rajarshi/master 7bcbe4f
  • Ensure that we reset visited flag each time we start path search from new atom Added test cases bc35c05
  • Modify default rendering parameters, raster images are slightly smaller. a19eabd
  • Better labelling of unspecified double bond stereo. Previously we took the liberal approach of marking anything unspecified which we couldn't prove might have stereo. Now we do some simple checks for linear chains. 25f1bc3
  • Merge pull request #190 from tomas-pluskal/master 35e874e
  • Prioritise non-pseudo atoms for wedge labelled bonds. 38abffc
  • Account for stereochemistry when replacing atoms. 66f406e
  • Improved the efficiency of isotope sorting 8325aca
  • Fixed failing test: testCalculateIsotopesC10000 6f05bae
  • Added a test for isotope pattern generation for C10000. fed836f
  • Deprecate MoleculeFactory and replace all test usage with TestMoleculeFactory. The only non-test usage was in the legacy module where the required methods were lifted out. a6195f1
  • Merge pull request #188 from egonw/patch/dataFeaturesInIOFormats fcac95e
  • Restored the pom file for annotation 2c4b04e
  • Removed deps on cdk-annotation that no longer exists be91727
  • Merged the last bits of cdk-annotation into cdk-ioformats d430e75
  • Merge pull request #186 from egonw/patch/removeOldConstants 591b21d
  • Merge pull request #185 from egonw/fix/missingJavadoc 0826645
  • Use IBond.Order enums directly (removing the CDKConstants) c14aa1e
  • A bit of missing JavaDocs 896a9dc
  • The dependency on cdk-silent is only in the test scope 70e2a47
  • Removed another redundant dependency 9b21ea6
  • Removed a redundant dependency a188d49
  • Removed a redundant dependency 60004c0
  • Stricter JavaDoc checking (more like DocCheck) 4e3bbf3
  • Do not require docs for private things right now b0cac3c
  • Added missing JavaDoc 9b8b6a2
  • Removed two needless dependencies 6b093ff
  • Revert "Upgrade PMD via Maven plugin 3.6" 4f2237a
  • Do JavaDoc checking with the checkstyle plugin 0c24263
  • Upgrade PMD via Maven plugin 3.6 2f55e56
  • Added instructions on how to list the dependencies c188df0
  • Merge pull request #184 from cdk/patch-12Dec15 3d06f20
  • Colors have changed - update test. 5e10262
  • Don't return null when line intersection fails. e3406c2
  • Merge pull request #183 from cdk/svg-locale 6514cd8
  • SVG output should not be internationalised. 02d01a6
  • Merge pull request #182 from cdk/patch/depict-colors 7905735
  • Correct casing of Jmol. a3d95af
  • Include cdk-depict in the bundle dependency. 6fed885
  • More comprehensive 2d color pallet from JMol. 2a82cec
  • Bumping version - open for changes. cc52feb
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