Hi Matthew,
the VicinitySampler is a crime that I committed a long time ago.
It has not been tested through at least four years of CDK development
and is therefore quite unlikeyl to work out of the box.
The sampler will not need hydrogens attached but assigned as implicit.
What exactly do you mean by "not working"? :-)
It seems that the sampler produces "something".
Cheers,
Chris
Ketterer, Matthew James wrote:
> Hello,
> I am an undergraduate trying to write some code to generate some
> molecules from random smiles strings. I want to use the
> VicinitySampler or other constitutional isomer generator, but I tried
> to input some code based on the VicinitySamplertest and it isn't
> working. I am using the CDK by importing the jar files into Eclipse.
> I'm not sure if I need to add hydrogens after creating the molecule. I
> also tried using a simple smiles string from the test rather than the
> one created below but the molecule seems to be built. Thanks for any
> help. Here is my code:
>
> import org.openscience.cdk.exception.InvalidSmilesException;
> import org.openscience.cdk.graph.ConnectivityChecker;
> import org.openscience.cdk.interfaces.IMolecule;
> import org.openscience.cdk.smiles.*;
> import org.openscience.cdk.structgen.*;
>
> import org.openscience.cdk.DefaultChemObjectBuilder;
> import java.util.List;
> import java.util.Random;
>
>
> public class RandomString {
>
> static final char[] _chars =
> { 'C','C','C','O','O','N','N','C', };
>
> static Random _r = new Random();
>
> static void randomStr(char[] buf, int len) {
> for (int i = 0; i < len; i++) {
> buf[i] = _chars[_r.nextInt(8)];
> }
> }
>
>
>
> public static void main(String[] args) throws InvalidSmilesException {
> char[] buf = new char[5];
> String s;
> randomStr(buf, 5);
> s = new String(buf);
> SmilesParser sp = new
> SmilesParser(DefaultChemObjectBuilder.getInstance());
> IMolecule mol = sp.parseSmiles(s);
>
> List structures = VicinitySampler.sample(mol);
> System.out.print(structures.size() + "\n");
> System.out.print(mol.getAtomCount()+ "\n");
> System.out.print(mol.getFirstAtom() + " \n");
> System.out.print(ConnectivityChecker.isConnected(mol));
>
>
> }
> }
> ## And here is the output
>
> 5
> 4
> Atom(9532399, C, H:3, SP:0, 2D:[null], 3D:[null], Fract3D:[null],
> C:0.0, FC:0, AtomType(null, MBO:0.0, BOS:0.0, FC:0, H:0, NC:0, CR:0.0,
> VDWR:0.0, EV:0, Isotope(0, EM:-1.0, AB:-1.0, Element(C, ID:null,
> AN:0))))
> true
>
>
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--
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
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