[Cdk-devel] [ cdk-Patches-3489419 ] Fixed reading of charge info from PDB files

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Patches item #3489419, was opened at 2012-02-19 09:56
Message generated for change (Settings changed) made by egonw
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https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3489419&group_id=20024

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Category: cdk-1.4.x
Group: Needs Review
>Status: Closed
>Resolution: Fixed
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


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Comment By: Egon Willighagen (egonw)
Date: 2012-02-19 13:23

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

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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

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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.

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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 :-).


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