[Cdk-devel] IBond.Order patch; decision needed (was: [ cdk-Patches-1837713 ] Preliminary patch to introduce IBond.Order)

[Egon W. <ego...@gm...>]

Hi all,

a quick reminder, as not everyone seemed to have picked this up:

there is the IBond.Order patch waiting in my branch... there are some
regressions in the reaction module, but working on that with Miguel.

Please check the patch, and give your comments, e.g. as explained here:

https://sourceforge.net/tracker/?func=detail&atid=320024&aid=1837713&group_id=20024

Egon

On Nov 26, 2007 11:10 AM, Egon Willighagen <ego...@gm...> wrote:
> Hi all,
>
> my second patch using the new branch-based development model.
>
> Please read and reply by:
>
> 1. commenting to this list
> 2. putting comments in the branch source code using the syntax
> described below (preferred)
>
> Egon
>
>
>
> ---------- Forwarded message ----------
> From: SourceForge.net <no...@so...>
> Date: Nov 24, 2007 7:35 PM
> Subject: [ cdk-Patches-1837713 ] Preliminary patch to introduce IBond.Order
> To: no...@so...
>
>
> Patches item #1837713, was opened at 2007-11-24 19:35
> Message generated for change (Tracker Item Submitted) made by Item Submitter
> You can respond by visiting:
> https://sourceforge.net/tracker/?func=detail&atid=320024&aid=1837713&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: None
> Group: None
> Status: Open
> Priority: 5
> Private: No
> Submitted By: Egon Willighagen (egonw)
> Assigned to: Nobody/Anonymous (nobody)
> Summary: Preliminary patch to introduce IBond.Order
>
> Initial Comment:
> I have been working on a patch the change the API of IBond, and to
> change the IBond method:
>
> public Double getOrder()
>
> into
>
> public IBond.Order getOrder()
>
> The result is available from cdk/branches/egonw/ibondorder
>
> but contains a few regressions, particularly in the cdk.reaction module:
>
> Summary:
> Fixed:
> 2
> New fails:
> 13
> +Testcase: testResonancePositiveCharge_1(org.openscience.cdk.test.qsar.descriptors.bond.ResonancePositiveChargeDescriptorTest)
> +Testcase: testResonancePositiveCharge_2(org.openscience.cdk.test.qsar.descriptors.bond.ResonancePositiveChargeDescriptorTest)
> +Testcase: testResonancePositiveCharge_3(org.openscience.cdk.test.qsar.descriptors.bond.ResonancePositiveChargeDescriptorTest)
> +Testcase: testResonancePositiveCharge_4(org.openscience.cdk.test.qsar.descriptors.bond.ResonancePositiveChargeDescriptorTest)
> +Testcase: testResonancePositiveCharge_5(org.openscience.cdk.test.qsar.descriptors.bond.ResonancePositiveChargeDescriptorTest)
> +Testcase: testResonancePositiveCharge_6(org.openscience.cdk.test.qsar.descriptors.bond.ResonancePositiveChargeDescriptorTest)
> +Testcase: testResonancePositiveCharge_7(org.openscience.cdk.test.qsar.descriptors.bond.ResonancePositiveChargeDescriptorTest)
> +Testcase: testBB_1(org.openscience.cdk.test.reaction.type.BreakingBondReactionTest)
> +Testcase: testAutomaticSearchCentreActiveExample1(org.openscience.cdk.test.reaction.type.RearrangementRadical2ReactionTest)
> +Testcase: testManuallyPutCentreActiveExample1(org.openscience.cdk.test.reaction.type.RearrangementRadical2ReactionTest)
> +Testcase: testAutomaticSearchCentreActiveExample1(org.openscience.cdk.test.reaction.type.RearrangementRadical3ReactionTest)
> +Testcase: testManuallyPutCentreActiveExample1(org.openscience.cdk.test.reaction.type.RearrangementRadical3ReactionTest)
> +Testcase: testSmiles9(org.openscience.cdk.test.smiles.SmilesParserTest)
>
> The testSmiles9 is a time out, but works when run from within Eclipse.
> I guess the tests still leak a lot of memory.
>
> I will consult with Miguel to get these regressions fixed, as there is
> no principle test failing, indicating that our lower level IBond unit
> tests are not complete.
>
> Additionally, I'll started branch to have the LonePairChecker utility
> the reaction module relies on, based on the new CDK atom types. Again,
> together with Miguel.
>
> The branches/egonw/ibondorder/ branch is open for suggestions. You can
> add FIXMEs and TODOs, by adding comment lines like (but please do not
> commit anything else than such lines, most certainly not source code
> style changes):
>
> // FIXME: ibondorder: your comment on what I should fix
> // TODO: ibondorder: your comment on what I might add
>
> The extra "ibondorder:" provide me a filter so that I can quickly see
> in the Eclipse Tasks view what should clean up.
>
> Thanx.
>
> ----------------------------------------------------------------------
>
> You can respond by visiting:
> https://sourceforge.net/tracker/?func=detail&atid=320024&aid=1837713&group_id=20024
>
>
>
> --
> ----
> http://chem-bla-ics.blogspot.com/
>



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