Re: [Cdk-devel] CML roundtrip issue - patch

[<ant...@ya...>]

No, not really. I only tried the round-tripping with single property per atom/bond/molecule (seeCMLCustomPropertyTest.java) and as soon I saw it does not work, I tried to figure out why. Then I attempted to patch the CMLCoreModule in order to make it parse all custom properties - nearly in the same way you did - but then I decided to not to go in that direction since I was not sure if any custom properties are meant to be handled by the general parser at all. Additionally, the properties I needed to maintain were of rather very specific nature, so I decided to go for the customizer/convention extensions and implemented these.

BTW, Egon, could you put a citation link to the article you mention into the Javadocs of CMLCoreModule?

Regards,

Aleksey
--- Nina Jeliazkova <ni...@ac...> schrieb am Mo, 25.8.2008:

> Von: Nina Jeliazkova <ni...@ac...>
> Betreff: Re: [Cdk-devel] CML roundtrip issue - patch
> An: ant...@ya...
> CC: "Daniel Zaharevitz" <Zah...@ma...>, "cdkdevel" <cdk...@li...>
> Datum: Montag, 25. August 2008, 15:03
> Aleksey,
> 
> I have tested and fixed only atom properties; do you have
> tests for others?
> 
> Regards,
> Nina
> 
> 
> 
> ant...@ya... wrote:
> > Hi all,
> >
> > Probably a bit late question, but - what about custom
> bond properties and custom molecule properties in a molecule
> set or a reaction - are these assigned correctly?
> >
> > Regards
> >
> > Aleksey
> >
> > --- Nina Jeliazkova <ni...@ac...> schrieb am
> Mo, 25.8.2008:
> >
> >   
> >> Von: Nina Jeliazkova <ni...@ac...>
> >> Betreff: Re: [Cdk-devel] CML roundtrip issue -
> patch
> >> An: "Daniel Zaharevitz"
> <Zah...@ma...>, "Nina Jeliazkova"
> <ni...@ac...>
> >> CC: "cdkdevel"
> <cdk...@li...>
> >> Datum: Montag, 25. August 2008, 14:02
> >> Hi All,
> >>
> >> Attached is the patch for the [ 1930029 ] bug.
> Sorry,
> >> didn't manage to upload
> >> it in sourceforge :(
> >>
> >> Best regards,
> >> Nina
> >>
> >> Daniel Zaharevitz <Zah...@ma...>
> wrote:
> >>
> >>     
> >>> On Aug 25, 2008, at 4:19 AM, Nina Jeliazkova
> wrote:
> >>>
> >>>       
> >>>> Hi Aleksey, all,
> >>>>
> >>>> I've added a comment and example to
> the bug
> >>>>         
> >> 1930029 Aleksey had  
> >>     
> >>>> submitted and
> >>>> IMHO it should be reopened.
> >>>>
> >>>> http://sourceforge.net/tracker/index.php? 
> >>>>
> >>>>         
> >>
> func=detail&aid=1930029&group_id=20024&atid=120024
> >>     
> >>>> The test is attached in this email, since
> it
> >>>>         
> >> seems there is no way  
> >>     
> >>>> to attach a
> >>>> file for a closed bug.
> >>>>
> >>>>
> >>>>         
> >>> I have noticed this and also problems with
> atom
> >>>       
> >> labels. I started to  
> >>     
> >>> look into fixes, but the startup costs
> associated with
> >>>       
> >> learning the  
> >>     
> >>> details of the parsing slowed me down and I
> also got
> >>>       
> >> tied up with our  
> >>     
> >>> program's mainframe migration. I do plan
> to work
> >>>       
> >> on this some more,  
> >>     
> >>> so if anyone makes progress, please make sure
> to post
> >>>       
> >> details, leave  
> >>     
> >>> comments, etc. I think ultimately CDK needs a
> richer
> >>>       
> >> model for a  
> >>     
> >>> property, but obviously the first step is to
> get the
> >>>       
> >> simple  
> >>     
> >>> properties working correctly.
> >>>
> >>> DanZ
> >>>
> >>>
> >>>
> >>> /********************************************
> >>>     Daniel Zaharevitz
> >>>     Chief, Information Technology Branch
> >>>     National Cancer Institute
> >>>     Zah...@ma...
> >>> ********************************************/
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>       
> >>
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