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

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Hi,

Attached are the patches for CMLRoundTripTest.java and CMLCoreModule.java, now
fixing both atom and bonds multiple properties issue.

Best regards,
Nina

ant...@ya... wrote:

> Yes, I think the single property handling has been fixed in trunk by Stefan
> somewhere in the end of June
> 
> 
> --- 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..., "Nina Jeliazkova" <ni...@ac...>
> > CC: "cdkdevel" <cdk...@li...>
> > Datum: Montag, 25. August 2008, 15:28
> > 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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