On 7 May 2010 17:47, Leonid Chepelev <[email protected]> wrote:
> Hello,
>
> (Sorry I posted this on Nabble OpenBabel forum already, but that seems to be
> simply an archive of this list.)
It should have appeared here - must be some problem.
> I would like to convert SMILES strings to their 3D forms in the SDF format.
> However, the difficulty is that I am now forced to use the Java API of
> OpenBabel to do this.
>
> One approach would be to use the class OBBuilder to build 3D structures.
> However, this class seems to not be present in the Java API of openbabel,
> making it impossible to use.
Yes - it'll be there in the next release though.
In the meanwhile you need to use the Gen3D Operation with code
something similar to the following Python code:
gen3d = openbabel.OBOp.FindType("Gen3D")
gen3d.Do(myOBMol)
> Another approach would be to generate the 3D structure with converter
> options, as is shown in the following code.
>
> import org.openbabel.*;
>
> public class Main {
> public static void main(String[] args) {
> System.loadLibrary("openbabel_java");
> OBConversion conv = new OBConversion();
> OBMol mol = new OBMol();
> conv.SetInFormat("smi");
> conv.ReadString(mol, "C(Cl)(=O)CCC(=O)Cl");
> conv.SetOutFormat("sdf");
> conv.SetOptions("gen3D", OBConversion.Option_type.OUTOPTIONS);
> System.out.print(conv.WriteString(mol));
> }
> }
>
> However, the problem is that the gen3D option does not seem to have any
> effect (with INOPTION and GENOPTION option types), and the result is quite
> unexpected with OUTOPTION, as follows.
>
>
> OpenBabel05071010562D
>
> 0 0 0 0 0 999 V3000
> M V30 BEGIN CTAB
> M V30 COUNTS 8 7 0 0 0
> M V30 BEGIN ATOM
> M V30 1 C 0 0 0 0
> M V30 2 Cl 0 0 0 0
> M V30 3 O 0 0 0 0
> M V30 4 C 0 0 0 0
> M V30 5 C 0 0 0 0
> M V30 6 C 0 0 0 0
> M V30 7 O 0 0 0 0
> M V30 8 Cl 0 0 0 0
> M V30 END ATOM
> M V30 BEGIN BOND
> M V30 1 1 1 2
> M V30 2 2 1 3
> M V30 3 1 1 4
> M V30 4 1 4 5
> M V30 5 1 5 6
> M V30 6 2 6 7
> M V30 7 1 6 8
> M V30 END BOND
> M V30 END CTAB
> M END
> $$$$
>
> Would you happen to know what is going on? Am I doing something wrong? Or
> perhaps the 3D generation capability is not yet available through the
> OpenBabel Java API, in which case I would have to do SYSTEM calls? Perhaps I
> should use the CDK 3D structure generator as an alternative?
>
> Thank you very much for any help.
> ------------------------------------------------------------------------------
>
>
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