hi,
thanks for your quick reply.
After looking at JUnit test here
org.openscience.cdk.test.io.MDLV2000ReaderTest
i found that reader is expecting 2 <EOF> (end of line)
after the heading so i modified the file and now i am getting a meaningful
error
that: molecule does not have a 2d coordinate. (that is fine) . Thank you
well here is the smile string for the molecule:
O=[N+]([O-])C=1C=C(C(O)=C(C=1)Cl)[N+](=O)[O-]
> Mmm.. that's a file created by the CDK...
>
actually i was testing a sdffile with the rajarshi's fragmenter
link :
http://cheminfo.informatics.indiana.edu/~rguha/code/java/Fragmenter.java
i found that for one of the molecule in the file the fragmenter is taking
too much time..
(1 hour after that i stop the build.)
then i took the file and cut paste the molecule data into the new mol file
and incorporate the error in the file.
that is how the file was created.
Dear Rajarshi,
please take a look at this molecule :
O=[N+]([O-])C=1C=C(C(O)=C(C=1)Cl)[N+](=O)[O-]
fragmenter is unable to fragment it,please tell me what is the problem.
On 8/27/07, Egon Willighagen <[EMAIL PROTECTED]> wrote:
>
> Hi Sushil,
>
> On 8/27/07, sushil ronghe <[EMAIL PROTECTED]> wrote:
> > JChemPaint is giving this error message
> > Error while parsing line 5:-> string index out of range:10
>
> <snip>
>
> > What is wrong?
>
> Mmm.. that's a file created by the CDK...
>
> OK, please create a JUnit file for it, and file a bug report. I will
> look at it then... Example JUnit tests are found in the class
> org.openscience.cdk.test.io.MDLV2000ReaderTest; the failing MDL
> molfile can go into (LGPL implied) src/data/mdl.
>
> Egon
>
> --
> ----
> http://chem-bla-ics.blogspot.com/
>
--
********************************
sushil ronghe
*********************************
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