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Commits on Aug 30, 2015

• Bump version for release

  johnmay

  committedAug 30, 2015
  8e11eb3

• Merge pull request #147 from cdk/java3d-dep

  egonw

  committedAug 30, 2015
  e2a307c

• Merge pull request #146 from egonw/fix/pmdWarnings

  johnmay

  committedAug 30, 2015
  2b89dbd

Commits on Aug 29, 2015

• Creates fewer String objects: only concatenate when debugging is turned on

  egonw

  committedAug 29, 2015
  4bd50de

• Fixed a PMD warning: Variables that are final and static should be all capitals

  egonw

  committedAug 29, 2015
  1e6e999

• Close readers when we're done with them

  egonw

  committedAug 29, 2015
  220a863

Commits on Aug 28, 2015

• Removed some unused code

  egonw

  committedAug 28, 2015
  8f54e78

• Fixed the unit tests: fail() causes the method to exit, so that not all tests were run

  egonw

  committedAug 28, 2015
  cec4cb4

• Fixed a few 'unused variable' warnings

  egonw

  committedAug 28, 2015
  857b0c0

• Removed some dead code

  egonw

  committedAug 28, 2015
  c53eac9

• Cooked some lists (no longer 'raw type')

  egonw

  committedAug 28, 2015
  3398981

Commits on Aug 26, 2015

• Upgrade java3d dependency - we previously used 1.5.2 then switch to 1.3.1 but this had an API difference that users depended on.

  johnmay

  committedAug 26, 2015
  40c1007

Commits on Aug 25, 2015

• Disable AuxInfo generation in InChIFactory by default. This can be as much as 20% of the compute time and is largely ignored. If the AuxInfo is wanted it can be generated by explicitly passing in a…

  

  johnmay

  authored and

  egonw

  committedAug 25, 2015
  dfd18ef

Commits on Aug 24, 2015

• Merge pull request #144 from egonw/fix/pmdWarnings

  johnmay

  committedAug 24, 2015
  ace58d2

• Merge pull request #143 from egonw/feature/ignorePMDonSMSD

  johnmay

  committedAug 24, 2015
  ee57194

Commits on Aug 23, 2015

• Removed unused imports

  egonw

  committedAug 23, 2015
  d47a308

• User indexOf(char) instead of indexOf(String).

  egonw

  committedAug 23, 2015
  a05ca52

• Fixed a few variable name warnings

  egonw

  committedAug 23, 2015
  ed84551

• Ignore PMD warnings/errors in the SMSD section

  egonw

  committedAug 23, 2015
  f22bc97

• More efficient use of StringBuilder.append()

  egonw

  committedAug 23, 2015
  d865450

• Don't use String concatenation to deal with null atoms

  egonw

  committedAug 23, 2015
  42ae450

• Don't use String concatenation to deal with null atoms

  egonw

  committedAug 23, 2015
  20c145a

• Use interfaces instead of implementations: IPseudoAtom

  egonw

  committedAug 23, 2015
  cd91c50

• Fixed a PMD warning: use append(char) instead of append(String) for single chars (and a few more append() split ups)

  egonw

  committedAug 23, 2015
  66f8f71

• Don't compare doubles as identical, as there is machine uncertainty in any non-integer value

  egonw

  committedAug 23, 2015
  af852f0

Commits on Aug 19, 2015

• Include copyright statements and some cleanup after review.

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  7acf190

• Deprecate implementations and ignore failing tests of old methods.

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  ef57f35

• Delegate existing MMFF partial charge methods to new implementation.

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  cce1021

• New MMFF partial charges implementation. Relocate tests from descriptor and rebase using SMILES (required due to InChI standardisations).

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  aea097e

• Correct citation id.

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  df40c1c

• Internal class for MMFF Parameter Loading - duplicates/replaces some functionality of the ForceFieldConfigurator/MMFF94BasedParameterSetReader.

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  86fcbe1

• Map symbolic types HOCS and HON down to integer type 21. These appear in the validation suite and labelled as *new* in the parameter files but do not appear in the papers.

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  ac69e27

• Internal API additions allow us to pass back which bonds are aromatic by MMFF's model. Ideally we would seperate out the aromaticity to a optional preprocessing step but at the moment the aromatici…

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  9e6a6e4

• Representation independant type assignment for nitro groups.

  

  johnmay

  authored and

  egonw

  committedAug 19, 2015
  5d825f6

Commits on Aug 7, 2015

• Load prime numbers from an external file.

  johnmay

  committedAug 7, 2015
  dc7f453

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