#248 Read the MDL/Symyx atom stereo property into a IChemObject p

Accepted
closed
nobody
master (162)
5
2012-10-28
2010-08-12
Egon Willighagen
No

Patch against master, reading an additional atom block field. I am not sure how to map it to the CDK stereo parity information, and should perhaps be mapped to ITetrahedralChirality which is much more difficult.

Until then, please accept this solution. With unit test.

Discussion

  • Seems ok as an initial attempt. What do the numbers (1,2,...) mean, though?

     
  • Asad
    Asad
    2010-08-30

    I tried this patch on the latest master and i got this error

    git am 0001-Read-the-MDL-Symyx-atom-stereo-property-into-a-IChem.patch

    Applying: Read the MDL/Symyx atom stereo property into a IChemObject property
    error: patch failed: src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java:806
    error: src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java: patch does not apply
    Patch failed at 0001 Read the MDL/Symyx atom stereo property into a IChemObject property
    When you have resolved this problem run "git am --resolved".
    If you would prefer to skip this patch, instead run "git am --skip".
    To restore the original branch and stop patching run "git am --abort".

     
  • Gilleain, the numbers indicate the MDL molfile types for clockwise and counter-clockwise stereochemistry.

     
  • Asad, indeed. There was a conflict with a recently applied patch. I'll upload a newly rebase version now.

     
  • Superceded by John May's patches.