how to convert smiles to structure

hi Group,

 

can any one help me in how to convert smiles to structure, while converting getting an exception "The type initializer for 'com.jnbridge.jnbcore.ObjectWrapper' threw an exception." at MolHandler mh = new MolHandler(smiles);

can any one help please

 

Thanks in advance.

Kolan

Hi,

 

Here is an example code to read a molecule from String:

// Read molecule from given string
Molecule m = MolImporter.importMol("CC=CC", "smiles");

And an other to read from file:

InputStream is = new BufferedInputStream( new FileInputStream( "filename.smi" ) );
MolImporter molimp = new MolImporter( new MolInputStream( is ) );

Molecule m = new Molecule();
while(molimp.read(m)){
// put your code here

}

If you can attach your code I could help more deeply.

 

Andras

hi  Andras,

Thanks for your kind reply..

 

please find my code as listed below ...

 

MolHandler mh = new MolHandler(smiles);

mh.aromatize();

Molecule mol = new Molecule();

mol=mh.getMolecule();

mol.clean(2, null);

sbyte[] s1 = mol.toBinFormat("png:w300, 4300,b32");

 

but in the first line itself i am getting metioned exception ..

pls help

Thanks & Regards

Raveendar Reddy Kolan

 

 

 

 

Hi Kolan,

Could you send the whole error message (that contains class names, line numbers, ...)?

Regards,
Tamás