Never mind. Figured it out. For future questioners,
StructureDiagramGenerator with a call to "generateCoordinates" works
wonders.
pdanese wrote:
>
>
> Hi,
>
> let's say that I have a smiles string that i'd like to parse and then
> write out as a mol file.
>
> taken from the javadocs I have the following code:
>
> SmilesParser sp = new
> SmilesParser(DefaultChemObjectBuilder.getInstance());
> FileWriter w = new FileWriter("C:\\benz.mol");
> IMolecule m = sp.parseSmiles("c1ccccc1");
>
> MDLWriter mw = new MDLWriter(w);
>
>
> mw.write(m);
> mw.close();
>
> ******************************************************
> this code parses the smiles string properly and generates a molfile that
> is *more or less** correct.
>
> ***HOWEVER***, when viewing the molfile in a 2-D editor (MDL Draw or
> whatever), ALL OF THE ATOMS ARE PILED ON TOP OF EACH OTHER.
>
> Is there a way to 'prettify' the output (or at least make the atoms
> non-overlapping?
>
> TIA!!!!
>
--
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