Hi Christoph,
and thank you for the answer. happy to hear that you would like to help us out. My idea actually was to reuse some code from NMRshiftdb
Here is the story:
Today we receive the user input structure as a molfile from Marvin. We then parse that on to a JChemSearch object. This object (together with an updatehandler) pretty much takes care of everything related to substructure searching, dublicate check etc.
JChem therefore of cause has requirements to the structure table.
We would now like to try to port to first CDK and then JChemPaint to make the chemicalinventory true opensource.
I read the journals about the design of CDK as well as NMRshiftdb and my plan was to get inspiration for the structure tables as well as code for searching and storing.
I have found the sql statements for the tables but I really do have a hard time finding the code. So if you could point me in the right di rection that would be a great help.
I do understand that there is going to be more coding from our hands in order to perform searches and inserts using CDK.
All we basically want to do is do a dublicate check during insert of new structures (to keep the structure table unique (in 2D)) and be able to perform exact match, similarity and substructure searches depending on user choices.
Also I think I now (after reading through most of the API yestersday) understand the concept of ChemObjects, AtomContainer, Bond and Atoms. But I still don't see how I then break up a drawn molecule (molfile) in order to store the fingerprints, smiles, bonds and atoms etc.
Again If you are able to point me to the code so I can see examples in order to fully understand I think we can handle the hard work.
Another option is of cause if any of you would like to join us. I have made a new CVS module (chemicalinventory-cdk), where I will start to edit the current c ode to use CDK. Just let me know and I will register you.
Thank you
claus
Christoph Steinbeck <[EMAIL PROTECTED]> skrev:
and thank you for the answer. happy to hear that you would like to help us out. My idea actually was to reuse some code from NMRshiftdb
Here is the story:
Today we receive the user input structure as a molfile from Marvin. We then parse that on to a JChemSearch object. This object (together with an updatehandler) pretty much takes care of everything related to substructure searching, dublicate check etc.
JChem therefore of cause has requirements to the structure table.
We would now like to try to port to first CDK and then JChemPaint to make the chemicalinventory true opensource.
I read the journals about the design of CDK as well as NMRshiftdb and my plan was to get inspiration for the structure tables as well as code for searching and storing.
I have found the sql statements for the tables but I really do have a hard time finding the code. So if you could point me in the right di rection that would be a great help.
I do understand that there is going to be more coding from our hands in order to perform searches and inserts using CDK.
All we basically want to do is do a dublicate check during insert of new structures (to keep the structure table unique (in 2D)) and be able to perform exact match, similarity and substructure searches depending on user choices.
Also I think I now (after reading through most of the API yestersday) understand the concept of ChemObjects, AtomContainer, Bond and Atoms. But I still don't see how I then break up a drawn molecule (molfile) in order to store the fingerprints, smiles, bonds and atoms etc.
Again If you are able to point me to the code so I can see examples in order to fully understand I think we can handle the hard work.
Another option is of cause if any of you would like to join us. I have made a new CVS module (chemicalinventory-cdk), where I will start to edit the current c ode to use CDK. Just let me know and I will register you.
Thank you
claus
Christoph Steinbeck <[EMAIL PROTECTED]> skrev:
Those classes are indeed "prehistoric material" by CDK means.
I guess they have not been used or maintained for years.
Claus, if you are interested in writing structures to and from databases, we
should discuss the issues.
As you will know, we have written quite some code for doing this within the
NMRShiftDB project. The code is part of the NMRShiftDB code base, which uses a
lot of CDK code.
Cheers,
Chris
Egon Willighagen wrote:
> On Wednesday 28 December 2005 16:22, Claus Stie Kallesøe wrote:
>
>> I have been reading through the cdk library here:
>>http://cdk.sourceforge.net/api/
>>
>> in order to find ou t how I can use the library.
>>
>> As we use a MySql database to store the structures I wanted to use the
>>DBReader.class as the describtion tells me: " Reader that can read from a
>>relational database that can be accessed through JDBC."
>>
>> But I can't fint the class in the cdk-20050826.jar file I have?
>
>
> The DBReader, DBWriter and DBAdmin classes are in the CDK module 'orphaned',
> meaning that no one was maintaining them, and they did not seemed to be used.
>
> The sources, however, can be found in CVS at:
>
> http://cvs.sourceforge.net/viewcvs.py/cdk/cdk/src/org/openscience/cdk/database/
>
>
>> Under org.openscience.cdk.database I only see the XindiceReader.
>>
>> Can you tell me where I can find the DBReader?
>
>
> Note, that the DBReader and DBWriter is closely tied together, and store the
> mole cules CML string in the 'molecules' table:
>
> ps = con.prepareStatement("INSERT INTO molecules VALUES('', ?)");
>
> This does likely not match the setup you are working with.
>
> Nevertheless, the source should give you some insight in how I used MySQL in
> the past.
>
> Egon
>
--
Priv. Doz. Dr. Christoph Steinbeck ([EMAIL PROTECTED])
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
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