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package org.openscience.cdk.tools;

import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;

import org.openscience.cdk.interfaces.IAtom;

/**
 * Methods 'borrowed' (stolen) from Jmol to determine or check the stereo
 * class of a set of atoms.

gilleain

import java.util.Random;

/**
 * General permutation generator, that uses orderly generation by ranking and
 * unranking. The basic idea is that all permutations of length N can be ordered
 * (lexicographically) like:
 * <pre>
 * 0 [0, 1, 2]

gilleain

import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.openscience.cdk.Atom;
import org.openscience.cdk.Molecule;

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import org.junit.Test;
import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;

import signature.chemistry.MoleculeSignature;

gilleain

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;

import signature.chemistry.Molecule.BondOrder;


/**
 * Adapts a CDK IAtomContainer class to a signature.chemistry.Molecule class, 

gilleain

package test;

import java.util.ArrayList;
import java.util.List;

import tmp.IGenerator;
import tmp.Model;
import tmp.MyGenerator;

import static tmp.MyGenerator.BOND_DISTANCE;

gilleain

package tmp;

public class MyGenerator extends BaseGenerator {
    
    public static final String BOND_DISTANCE = "BondDistance";
    
    public MyGenerator() {
        super.register(BOND_DISTANCE, Double.class, 5.0);
    }

gilleain

package tmp;

import java.util.HashMap;
import java.util.Map;
import java.util.Set;

public class BaseGenerator implements IGenerator {
    
    public Map<String, Class> parameterTypes;
    

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package tmp;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

public class Model {
    
    public Map<String, Class> parameterTypes;
    

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  public static IChemObjectBuilder builder = 
        NoNotificationChemObjectBuilder.getInstance();
    
    public IMolecule makeCHXFragment(int hCount) {
        IMolecule mol = builder.newMolecule();
        mol.addAtom(builder.newAtom("C"));
        mol.getAtom(0).setHydrogenCount(hCount);
        return mol;
    }