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

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Hi,

Actually, single atom/bond property works fine with current trunk code;
multiple atom and bond properties did not (same issue for bonds, will try to
fix it shortly); for the rest I have still to find out.

ant...@ya... wrote:

> 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. 

Well, it does handle properties written in <scalar> tag, so it is better to
get them handled right :)

Regards,
Nina

> 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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> > >>     
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