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Commits on Dec 24, 2014

• Release 1.5.9

  johnmay

  committedDec 24, 2014
  3f41d3b

• Recognition of projection based stereochemistry.

  

  johnmay

  authored and

  egonw

  committedDec 24, 2014
  3c34040

Commits on Dec 21, 2014

• Improved warning message when a compound without a 3D structure is provided.

  

  johnmay

  authored and

  egonw

  committedDec 21, 2014
  0d166ea

Commits on Dec 20, 2014

• Updated JavaDocs for the IMolecule removal

  

  egonw

  authored and

  johnmay

  committedDec 20, 2014
  772d55a

• Updated JavaDocs for the IMolecule removal

  

  egonw

  authored and

  johnmay

  committedDec 20, 2014
  4460b51

Commits on Dec 18, 2014

• Rectify LINGOs regressions.

  

  johnmay

  authored and

  egonw

  committedDec 18, 2014
  b03297f

Commits on Dec 15, 2014

• Adhere to variable name conventions

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  52330f4

• Fixed a PMD warning: fixed variable names (start with lower case char; length)

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  121435f

• Fixed a PMD warning: removed an underscore from a non-final var

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  59460f0

• Fixed a PMD warning: removed an underscore from a non-final var

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  5282618

• Fixed a PMD warning: final static vars should have fully capatalized names

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  ceef23c

• Removed dead code

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  feab2b2

• Fixed a PMD warning: removed an underscore from a non-final var

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  cc1609e

• Removed a private, unused variable

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  e375961

• Fixed a PMD warning: final static vars should have fully capatalized names

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  df75599

• Updated the default value in the unit test

  

  egonw

  authored and

  johnmay

  committedDec 15, 2014
  d12166a

Commits on Dec 14, 2014

• Terminate SMARTS parsing on whitespace or EOF.

  

  johnmay

  authored and

  egonw

  committedDec 14, 2014
  84c89ca

Commits on Dec 11, 2014

• Check the classType is valid.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  d595bea

• Delegate to the constructor of IntArrayCountFingerprint.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  c31bf57

• Ensure first bit is never negative and use a count list for the hash counts.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  5efab8e

• Allow CFP of varied length.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  7e3d267

• Produce bit and count fingerprints in Lingos.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  7ce4e06

• Utils for creating bit and count fingerprints from feature maps.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  c160452

• Ideally aromaticity would be done outside of the fingerprint. Since it is already there we don't want to take it out but we can avoid the need to do atom typing by using a different aromaticity model.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  d9bfba5

• Tidy up Lingos similarity implementation and ensure aromatic SMILES are generated.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  c7896a8

• Make method2 of the continuous tanimoto the default. It provides better discrimination.

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  96d70bf

• Flip around the implementation and the default (we're going to switch them and use method2).

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  3739558

• CFP does not correctly implement count fingerprints. The similarity measures (see Tanimoto class) expect the bits in sorted order. Without this invariant the CFP similarity is way off par. (Spotted…

  

  johnmay

  authored and

  egonw

  committedDec 11, 2014
  e6f9ba7

Commits on Dec 4, 2014

• Avoid NPE due to implicit bond.

  

  johnmay

  authored and

  egonw

  committedDec 4, 2014
  5a8905e

• Update beam to 0.7. Minor fixes to Kekulisation, reset Ring Numbering between components (fragments are now canonical C1CC1.C1CC1 instead of C1CC1.C2CC2).

  

  johnmay

  authored and

  egonw

  committedDec 4, 2014
  adaed1c

• Already okay in the CDK but needed fixing in BEAM.

  

  johnmay

  authored and

  egonw

  committedDec 4, 2014
  d058440

Commits on Dec 2, 2014

• Unit tests for bug reports by Yannick on the cdk-user@ mailing list

  

  egonw

  authored and

  johnmay

  committedDec 2, 2014
  99e38b5

• Merge branch 'master' of github.com:cdk/cdk

  johnmay

  committedDec 2, 2014
  5790920

• Tell eclipse to run JavaCC on import (i.e. before the module is built).

  johnmay

  committedDec 2, 2014
  04b1062

Commits on Nov 28, 2014

• Add info on creating a Jar of sources.

  johnmay

  committedNov 28, 2014
  1161464

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