Hello to everybody,
i want to do an chemical structure search in databases. For my project i test
my search which i should develop with an database from pubchem.
For the search i will use CDKPSearch.jar. But this is not my real problem.
The databases that i could download from the pubchem ftp for the substances
havnt any 3D informations. So the following code (which i test for iterating
through all informations) will fail:
MDLReader reader = new MDLReader(new FileReader(new File(filename)));
ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
List<IAtomContainer> containersList =
ChemFileManipulator.getAllAtomContainers(chemFile);
int i=0;
for(IAtomContainer a : containersList){
System.out.println(a.toString() + "; " + i + "/" +
containersList.size());
i++;
}
The Exception causes because 3D informations are not stored.
Now i have tried to download an specific substance with 3D structure. Then the
second Line of the code will throw an exception.
I really don't know if this is the right way and the right usage.
Here is my goal:
1. Converting structure files into sdf (with babel)
2. CDK for creating the query.xml for CDKPSearch
3. CDKPSearch for searching structures in the database (pubchem)
4. CDK for analyse the results (output the results etc.)
Is this the right way?
Best regards,
Jochen Schreiber
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