#488 Fixed reading of charge info from PDB files

Accepted
closed
nobody
cdk-1.4.x (181)
5
2012-10-28
2012-02-19
No

Discussion

  • John May

    John May - 2012-02-19

    The changes look good but line 673 should be:
    if (lineLength >= 80) and not if(lineLength >= 79)

    otherwise:
    String frag = cLine.substring(78, 80).trim();

    may throw an index out of bounds exception.

    Probably fine though as if I remember correctly the PDB dates back to fortran where everything's always 80 characters.

    Only spotted this from doing the checks on the MDL*Reader's :-).

     
  • Egon Willighagen

    John, how about this updated patch?

    https://github.com/egonw/cdk/commit/41e997b61957ddf1df2d9d0b7f6f1189a0cc6be1

    Do you know how to 'sign off' a patch?

    Just applied it to some new local branch, make sure things compile with 'ant clean dist-all test-dist-all' and then run:

    git commit --amend --signoff

    If you could then place it somewhere online, then Rajarshi or I can push it to the repository, and everyone will see that you reviewed and approved the patch.

     
  • Egon Willighagen

    No, this is exactly what I need :) thanx!

     

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