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Commits on Dec 14, 2016

• Merge pull request #255 from cdk/patch/newelements

  Show description for 26dde5a
  egonw

  authored
  26dde5a

• Merge pull request #256 from cdk/patch/xml-dep-cleanup

  Show description for ff5c506
  egonw

  authored
  ff5c506

• Remove xpp3 dependency only used by PubChem readers.

  johnmay

  committed
  170b6c9

• Merge pull request #254 from cdk/patch/renderingbug

  Show description for dcfa4d1
  egonw

  authored
  dcfa4d1

Commits on Dec 13, 2016

• Proposed element names for 2016.

  johnmay

  committed
  93a8b46

• Update EBI maven repo.

  johnmay

  committed
  20125cd

• Correct atom placer, for co-linear chains just place the atoms as they are.

  johnmay

  committed
  93af028

• Watch out for shallow (and now sharp) bond angles when slanting wedges.

  johnmay

  committed
  5111604

Commits on Dec 10, 2016

• Test for bug report 1384.

  johnmay

  committed
  4c2e39f

Commits on Nov 30, 2016

• Merge pull request #252 from cdk/patch/testfix

  Show description for 4f3a2fa
  egonw

  authored
  4f3a2fa

Commits on Nov 28, 2016

• Auxiliary test.

  johnmay

  committed
  3691b26

• Utility to adjust formula protonation.

  johnmay

  committed
  a878ad5

• Update MF documentation on charge.

  johnmay

  committed
  4803746

• Formulas don't adjust hydrogens based on charge.

  johnmay

  committed
  e60c7aa

• Remove state from IsotopePatternGenerator.

  johnmay

  committed
  b5aea03

• New invariants in SmilesGenerator guard against unsafe aromaticity - update tests.

  johnmay

  committed
  17fae8b

• Merge pull request #251 from rajarshi/master

  Show description for 616be43
  egonw

  authored
  616be43

• Added two test cases for bugs in IsotopePatternGenerator. First bug indicates generator is saving state where it shouldn't. Second bug indicates generator is not considering charge properly

  rajarshi

  committed
  fc58909

Commits on Nov 26, 2016

• More efficient merging of two atom containers.

  johnmay

  committed
  1d1f3e0

• Ensure double bonds are laid out correctly.

  johnmay

  committed
  d03343d

Commits on Nov 9, 2016

• Merge pull request #249 from cdk/patch/layout_091116

  Show description for a46646d
  egonw

  authored
  a46646d

• Merge pull request #248 from cdk/patch/safetychecks

  Show description for 1ec0d36
  egonw

  authored
  1ec0d36

• Use SSSR to decide which side to put double bond.

  johnmay

  committed
  15e2c81

• Ensure all macrocycles go through the macrocycle code.

  johnmay

  committed
  9b27c41

• Test invalid flags.

  johnmay

  committed
  46ba16c

• Additional guard against trying to write molecules in an inconsistent state.

  johnmay

  committed
  974b385

• Stop misuse of the API and ensure only one flag is set at once. This is less powerful but stops users setting custom flags (e.g. 999 in Asad's ReactionDecoder) which has undefined behaviour.

  johnmay

  committed
  b5ff6c4

Commits on Oct 28, 2016

• Merge pull request #247 from cdk/patch/render/prefixcoef

  Show description for 7897397
  egonw

  authored
  7897397

• Merge pull request #246 from cdk/patch/atom-creation

  Show description for ddbc988
  egonw

  authored
  ddbc988

Commits on Oct 19, 2016

• Move coefficient to front if possible.

  johnmay

  committed
  a409100

• Much more robust PDB atom symbol parsing.

  johnmay

  committed
  f3c112b

• Parse hydrogen isotopes.

  johnmay

  committed
  6c8f009

• More robust parsing of atom symbols.

  johnmay

  committed
  f65dcc9

Commits on Oct 16, 2016

• Correct more test with bad atom symbols and symbol visibility due to hcount.

  johnmay

  committed
  c887ff3

• Hydrogen count semantics change - defaults to zero with provided symbol.

  johnmay

  committed
  3c5d224

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