[Cdk-commits] [cdk/cdk] 091a7b: Updated murcko fragmenter to speed up preprocessin...

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

  Branch: refs/heads/master
  Home:   https://github.com/cdk/cdk
  Commit: 091a7b22187be83f7e15a72f6a86f762a4f81fcb
      https://github.com/cdk/cdk/commit/091a7b22187be83f7e15a72f6a86f762a4f81fcb
  Author: Rajarshi Guha <raj...@gm...>
  Date:   2013-06-26 (Wed, 26 Jun 2013)

  Changed paths:
    M src/main/org/openscience/cdk/fragment/MurckoFragmenter.java
    M src/test/org/openscience/cdk/fragment/MurckoFragmenterTest.java

  Log Message:
  -----------
  Updated murcko fragmenter to speed up preprocessing and avoid processing duplicate fragments in recursive calls.

Signed-off-by: Rajarshi Guha <raj...@gm...>
Signed-off-by: John May <joh...@gm...>


  Commit: 376177a7640ee387aaa5888771d62ab0c29984bc
      https://github.com/cdk/cdk/commit/376177a7640ee387aaa5888771d62ab0c29984bc
  Author: Rajarshi Guha <raj...@gm...>
  Date:   2013-06-26 (Wed, 26 Jun 2013)

  Changed paths:
    M src/main/org/openscience/cdk/fragment/MurckoFragmenter.java

  Log Message:
  -----------
  Updated to allow user specified molecule hash generator and included the orbital information in default molecular hash generator Removed reset method, no need for it Ensured that we output SMILES rather than fragment hashes Updated check for zero atom linkers to avoid redoing cycle detection. 5x speedup for large symmetric/branched structures Keep molecule hash as Long rather than String

Signed-off-by: Rajarshi Guha <raj...@gm...>
Signed-off-by: John May <joh...@gm...>


  Commit: 65a1c128c493f41c07663657c28e44b778b98e69
      https://github.com/cdk/cdk/commit/65a1c128c493f41c07663657c28e44b778b98e69
  Author: Rajarshi Guha <raj...@gm...>
  Date:   2013-06-26 (Wed, 26 Jun 2013)

  Changed paths:
    M build.xml
    M src/META-INF/fragment.cdkdepends
    M src/META-INF/test-fragment.cdkdepends

  Log Message:
  -----------
  Added dependency of frag module on hash module

Signed-off-by: Rajarshi Guha <raj...@gm...>
Signed-off-by: John May <joh...@gm...>


  Commit: f47e5c035ed05e4d88a3684380568e2f1aa83662
      https://github.com/cdk/cdk/commit/f47e5c035ed05e4d88a3684380568e2f1aa83662
  Author: Rajarshi Guha <raj...@gm...>
  Date:   2013-06-26 (Wed, 26 Jun 2013)

  Changed paths:
    M src/main/org/openscience/cdk/fragment/MurckoFragmenter.java
    M src/test/org/openscience/cdk/fragment/MurckoFragmenterTest.java

  Log Message:
  -----------
  Added inchi for macrocycle test case
Went back to use of spanning tree in check for zero atom linker
Added Javadoc annotation to indicate the class is not threadsafe

Signed-off-by: John May <joh...@gm...>


  Commit: 67ad0b779142700bdc9a554fb35cafbe8b60086d
      https://github.com/cdk/cdk/commit/67ad0b779142700bdc9a554fb35cafbe8b60086d
  Author: Rajarshi Guha <raj...@gm...>
  Date:   2013-06-26 (Wed, 26 Jun 2013)

  Changed paths:
    M src/main/org/openscience/cdk/fragment/MurckoFragmenter.java

  Log Message:
  -----------
  Made the method threadsafe by removing static field

Signed-off-by: John May <joh...@gm...>


  Commit: 1fdbe383129a85f976f379d11d88a89a32674db8
      https://github.com/cdk/cdk/commit/1fdbe383129a85f976f379d11d88a89a32674db8
  Author: Rajarshi Guha <raj...@gm...>
  Date:   2013-06-26 (Wed, 26 Jun 2013)

  Changed paths:
    M src/main/org/openscience/cdk/fragment/MurckoFragmenter.java

  Log Message:
  -----------
  Made the method threadsafe by removing static field
Avoided repeated calls to spanning tree by manually flagging ring bonds before starting search

Signed-off-by: John May <joh...@gm...>


Compare: https://github.com/cdk/cdk/compare/e23923170165...1fdbe383129a