[Cdk-commits] [cdk/cdk] c51dab: Compact representation of logical predicates over ...

[GitHub <no...@gi...>]

  Branch: refs/heads/master
  Home:   https://github.com/cdk/cdk
  Commit: c51dab80c1d23a6eeba52a75f31bd414b3b5991b
      https://github.com/cdk/cdk/commit/c51dab80c1d23a6eeba52a75f31bd414b3b5991b
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-03 (Sat, 03 Mar 2018)

  Changed paths:
    A base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.java
    A base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ExprTest.java

  Log Message:
  -----------
  Compact representation of logical predicates over atoms/bonds.


  Commit: 5b898d6c3782c30a34210792f85aec3a0e900e38
      https://github.com/cdk/cdk/commit/5b898d6c3782c30a34210792f85aec3a0e900e38
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-03 (Sat, 03 Mar 2018)

  Changed paths:
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.java
    M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ExprTest.java

  Log Message:
  -----------
  Can't test the recursive expressions yet....


  Commit: b2c49fb292511d9284173dd5b5e5b6be30ccdffd
      https://github.com/cdk/cdk/commit/b2c49fb292511d9284173dd5b5e5b6be30ccdffd
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-03 (Sat, 03 Mar 2018)

  Changed paths:
    M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ExprTest.java

  Log Message:
  -----------
  Ignore not enough...


  Commit: dc4cc12f165553c4d5649a8fc3a14e60407e73bf
      https://github.com/cdk/cdk/commit/dc4cc12f165553c4d5649a8fc3a14e60407e73bf
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-16 (Fri, 16 Mar 2018)

  Changed paths:
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.java

  Log Message:
  -----------
  Provide access to subquery from Expr


  Commit: 89583af4ddbadb535b3a50c4c509416698b7b97e
      https://github.com/cdk/cdk/commit/89583af4ddbadb535b3a50c4c509416698b7b97e
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-16 (Fri, 16 Mar 2018)

  Changed paths:
    M base/interfaces/src/main/java/org/openscience/cdk/isomorphism/matchers/IQueryAtom.java
    M base/interfaces/src/main/java/org/openscience/cdk/isomorphism/matchers/IQueryBond.java

  Log Message:
  -----------
  Update documentation


  Commit: 81a5c891a2849defc3ae0609c2270cb740de774d
      https://github.com/cdk/cdk/commit/81a5c891a2849defc3ae0609c2270cb740de774d
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-16 (Fri, 16 Mar 2018)

  Changed paths:
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryBond.java

  Log Message:
  -----------
  Make QueryAtom and QueryBond non-abstract, add an Expr field.


  Commit: f7e8a3b25a68e7a0e44811da807cd59d3a76fa70
      https://github.com/cdk/cdk/commit/f7e8a3b25a68e7a0e44811da807cd59d3a76fa70
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-16 (Fri, 16 Mar 2018)

  Changed paths:
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/ComponentGrouping.java

  Log Message:
  -----------
  Update component grouping to also use the component id's from the query getProperty(). Previously queries/targets were handled differently incoming patches allow us to treat this more the same leading cleaner code - notice both the query and target now go into 'determineComponents' in the constructor.


  Commit: a6d7f8284247b2a2d5159ddec8cfb144c84f00f2
      https://github.com/cdk/cdk/commit/a6d7f8284247b2a2d5159ddec8cfb144c84f00f2
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-18 (Sun, 18 Mar 2018)

  Changed paths:
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.java
    M base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ExprTest.java

  Log Message:
  -----------
  Slight improvement on ordering of expression trees when using 'AND', without this '[C@H]' in SMARTS comes out as '[HC@]' valid but ugly.


  Commit: 7f6d0ca5881bcbbcc72a3eb08e53ddb3ebd03468
      https://github.com/cdk/cdk/commit/7f6d0ca5881bcbbcc72a3eb08e53ddb3ebd03468
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-18 (Sun, 18 Mar 2018)

  Changed paths:
    A tool/smarts/src/main/java/org/openscience/cdk/isomorphism/Smarts.java
    A tool/smarts/src/test/java/org/openscience/cdk/isomorphism/SmartsExprReadTest.java
    A tool/smarts/src/test/java/org/openscience/cdk/isomorphism/SmartsExprWriteTest.java

  Log Message:
  -----------
  New SMARTS parser and generator.


  Commit: d2e1aaae2635fe9026e8c6a14f4438ddd6148087
      https://github.com/cdk/cdk/commit/d2e1aaae2635fe9026e8c6a14f4438ddd6148087
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-18 (Sun, 18 Mar 2018)

  Changed paths:
    A tool/smarts/src/test/java/org/openscience/cdk/isomorphism/ParserTest.java

  Log Message:
  -----------
  Duplicate existing parser tests from the JAVACC parse showing everything is passed okay.


  Commit: e0139ba60b2de6650486044d88e8af7acac11243
      https://github.com/cdk/cdk/commit/e0139ba60b2de6650486044d88e8af7acac11243
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-25 (Sun, 25 Mar 2018)

  Changed paths:
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/Smarts.java

  Log Message:
  -----------
  Documentation new Smarts documentation.


  Commit: fc3793f34811e841f5bb465e528146c08fc6c045
      https://github.com/cdk/cdk/commit/fc3793f34811e841f5bb465e528146c08fc6c045
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-25 (Sun, 25 Mar 2018)

  Changed paths:
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/Smarts.java

  Log Message:
  -----------
  a and A don't need square brackets.


  Commit: 157575a7c097f269af746daad5abeeeab8300722
      https://github.com/cdk/cdk/commit/157575a7c097f269af746daad5abeeeab8300722
  Author: John Mayfield <jo...@ne...>
  Date:   2018-03-25 (Sun, 25 Mar 2018)

  Changed paths:
    M tool/smarts/src/main/java/org/openscience/cdk/isomorphism/Smarts.java

  Log Message:
  -----------
  affect not effect


  Commit: 9fbfb4210af8a13812da07f0ee66a2a65fb930d5
      https://github.com/cdk/cdk/commit/9fbfb4210af8a13812da07f0ee66a2a65fb930d5
  Author: Egon Willighagen <ego...@gm...>
  Date:   2018-04-03 (Tue, 03 Apr 2018)

  Changed paths:
    M base/interfaces/src/main/java/org/openscience/cdk/isomorphism/matchers/IQueryAtom.java
    M base/interfaces/src/main/java/org/openscience/cdk/isomorphism/matchers/IQueryBond.java
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/ComponentGrouping.java
    A base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.java
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java
    M base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryBond.java
    A base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ExprTest.java
    A tool/smarts/src/main/java/org/openscience/cdk/isomorphism/Smarts.java
    A tool/smarts/src/test/java/org/openscience/cdk/isomorphism/ParserTest.java
    A tool/smarts/src/test/java/org/openscience/cdk/isomorphism/SmartsExprReadTest.java
    A tool/smarts/src/test/java/org/openscience/cdk/isomorphism/SmartsExprWriteTest.java

  Log Message:
  -----------
  Merge pull request #429 from cdk/patch/exprs

All OK now. (@johnmay, I was waiting for your last green light: https://github.com/cdk/cdk/pull/429#discussion_r176358010 )


Compare: https://github.com/cdk/cdk/compare/0d06182f95c4...9fbfb4210af8