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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