From: SourceForge.net <no...@so...> - 2012-02-19 21:23:18
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Patches item #3489419, was opened at 2012-02-19 09:56 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3489419&group_id=20024 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: cdk-1.4.x Group: Needs Review Status: Open Resolution: None Priority: 5 Private: No Submitted By: Egon Willighagen (egonw) Assigned to: Nobody/Anonymous (nobody) Summary: Fixed reading of charge info from PDB files Initial Comment: Patch for bug https://sourceforge.net/tracker/?func=detail&aid=3474522&group_id=20024&atid=120024: https://github.com/egonw/cdk/commits/362-14x-pdbChargedAtoms ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2012-02-19 13:23 Message: No, this is exactly what I need :) thanx! ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-02-19 13:20 Message: Looks good, have signed off. What do I need to place online? If it's just the patch file for the sign off, here it is: http://www.ebi.ac.uk/~johnmay/git/cdk/patches/0001-Fix-for-charge-parsing-in-PDB-files-based-on-the-pat.patch If not let me know. Cheers, J ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2012-02-19 12:44 Message: 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. ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-02-19 10:27 Message: 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 :-). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3489419&group_id=20024 |