Hi,
I have an exception while parsing a SMART string using a SMARTQueryTool:
csp[i] = new SMARTSQueryTool("O=C1NCCSc2ccccc12");
The exception message is the following:
org.openscience.cdk.exception.CDKException: The string
O=C1NCCSc2ccccc12 is not a valid SMARTS string: Encountered "Sc" at
line 1, column 8.
Was expecting one of:
<EOF>
"!" ...
"-" ...
I dont know very well the SMART syntax, but building a molecule in MOE
using this string makes no problem, and JOELib does not complain
either about it when building a JOESmartsPattern. Besides, building a
molecule using this query in the pubchem molecule builder
(http://pubchem.ncbi.nlm.nih.gov/edit/index.html) can be done without
any error message too.
So is it a CDK issue ?
Quoting Egon Willighagen <[email protected]>:
> On Thu, Apr 23, 2009 at 10:12 AM, Vincent Le Guilloux
> <[email protected]> wrote:
>> Quoting Rajarshi Guha <[email protected]>:
>>> More practically, the CDK did not recognize the atom type of the
>>> oxygen... this can, for example, be the results of it being negative
>>> and have three neighbors...
>>
>> The weired thing here is that the CDK does not recognizes the atom type
>> while it still display the right element symbol...
>
> That is what I have been trying to explain:
>
> element type != atom type
>
>> The thing is that i've tested here my code on a dataset of 3000 molecules,
>> and I had at least a hundred of compounds for which the CDK complains with
>> this same error.
>
> Feel free to email me structures that fail...
>
>> I guess the structures may be corrupted in most cases, but still.
>
> Possibly...
>
> Egon
>
> --
> Post-doc @ Uppsala University
> http://chem-bla-ics.blogspot.com/
>
>
--
Vincent Le Guilloux
Phd Student - ICOA - UMR CNRS 6005
Div. of chemoinformatic and molecular modeling.
University of Orléans
Phone: ++33 2 38 49 45 77
Fax : ++33 2 38 41 72 81
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