On 9 May 2010 20:08, Leonid Chepelev <leonid.chepe...@gmail.com> wrote:
>>
>> 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)
>>
>
> Hello Noel, and thank you very much for the advice! It sort of works now.
> The following code in Java produces some sort of 3D coordinates, with errors
> that the parameter files for the MM geometry optimization cannot be found (I
> am guessing that's because I've copied the openbabel jar into my project's
> lib folder).
> import org.openbabel.*;
> public class Main {
> public static void main(String[] args) throws Exception {
> 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");
> OBOp gen3d = OBOp.FindType("Gen3D");
> gen3d.Do(mol);
> System.out.print(conv.WriteString(mol));
> }
> }
>
> The output produced is as follows.
>
> OpenBabel05091014533D
> 12 11 0 0 0 0 0 0 0 0999 V2000
> 1.0000 0.0000 0.0000 C 0 0 0 0 0
> 0.1290 1.5086 0.0000 Cl 0 0 0 0 0
> 0.3862 -1.0631 0.0000 O 0 0 0 0 0
> 2.4820 0.0000 0.0000 C 0 0 0 0 0
> 2.9894 1.4328 0.0000 C 0 0 0 0 0
> 4.4714 1.4328 0.0000 C 0 0 0 0 0
> 5.0852 0.3697 0.0000 O 0 0 0 0 0
> 5.3424 2.9414 0.0000 Cl 0 0 0 0 0
> 2.8524 -0.5242 -0.8561 H 0 0 0 0 0
> 2.8337 -0.4977 0.8795 H 0 0 0 0 0
> 2.6189 1.9570 0.8561 H 0 0 0 0 0
> 2.6377 1.9305 -0.8795 H 0 0 0 0 0
> 1 4 1 0 0 0
> 1 3 2 0 0 0
> 1 2 1 0 0 0
> 4 5 1 0 0 0
> 4 9 1 0 0 0
> 4 10 1 0 0 0
> 5 6 1 0 0 0
> 5 11 1 0 0 0
> 5 12 1 0 0 0
> 6 8 1 0 0 0
> 6 7 2 0 0 0
> M END
> $$$$
> ==============================
> *** Open Babel Error in OpenBabel::OBForceFieldMMFF94::ParseParamFile
> Cannot open parameter file
> ==============================
> *** Open Babel Error in OpenBabel::OBForceFieldUFF::ParseParamFile
> Cannot open UFF.prm
> ==============================
> *** Open Babel Error in OpenBabel::OBForceFieldUFF::SetTypes
> Cannot open UFF.prm
You need to set BABEL_DATADIR or else the ring templates and
forcefields are not going to work.
> Next, I will compare the 3D geometries generated by CDK and those generated
> by OpenBabel by overlaying the two resultant geometries with PM6 and
> B3LYP/6-311+G(d,p) optimized geometries (with G09) and calculating the RMSD
> for a few hundred compounds, for each approach to see which method is most
> accurate. I am guessing you guys would bet that both should be very similar,
> as the methodology used by OpenBabel and CDK is essentially the same?
Just to note, comp chem does a local optimisation. To do a global
optimisation you need to do a conformer search and locally optimise
each. With OB, what you're actually comparing is the accuracy of
MMFF94 geometries and those from B3LYP. This is already well studied.
> In any case, thank you for the help, I don't need to do it through system
> calls and writing to disk now.
> Regards,
> Leonid Chepelev
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