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/* Copyright (C) 2003-2007  Miguel Howard 
 *
 * Contact: [email protected]
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the
 * beginning of your source code files, and to any copyright notice that
 * you may distribute with programs based on this work.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.graph.rebond;

import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;

import java.util.Iterator;

/**
 * Provides tools to rebond a molecule from 3D coordinates only.
 * The algorithm uses an efficient algorithm using a
 * Binary Space Partitioning Tree (Bspt). It requires that the
 * atom types are configured such that the covalent bond radii
 * for all atoms are set. The AtomTypeFactory can be used for this.
 *
 * @cdk.keyword rebonding
 * @cdk.keyword bond, recalculation
 * @cdk.dictref blue-obelisk:rebondFrom3DCoordinates
 *
 * @author      Miguel Howard
 * @cdk.created 2003-05-23
 * @cdk.module  standard
 * @cdk.githash
 *
 * @see org.openscience.cdk.graph.rebond.Bspt
 */
public class RebondTool {

    private double maxCovalentRadius;
    private double minBondDistance;
    private double bondTolerance;

    private Bspt   bspt;

    public RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance) {
        this.maxCovalentRadius = maxCovalentRadius;
        this.bondTolerance = bondTolerance;
        this.minBondDistance = minBondDistance;
        this.bspt = null;
    }

    /**
     * Rebonding using a Binary Space Partition Tree. Note, that any bonds
     * defined will be deleted first. It assumes the unit of 3D space to
     * be 1 Å.
     */
    public void rebond(IAtomContainer container) throws CDKException {
        container.removeAllBonds();
        maxCovalentRadius = 0.0;
        // construct a new binary space partition tree
        bspt = new Bspt(3);
        Iterator atoms = container.atoms().iterator();
        while (atoms.hasNext()) {
            IAtom atom = atoms.next();
            double myCovalentRadius = atom.getCovalentRadius();
            if (myCovalentRadius == 0.0) {
                throw new CDKException("Atom(s) does not have covalentRadius defined.");
            }
            if (myCovalentRadius > maxCovalentRadius) maxCovalentRadius = myCovalentRadius;
            TupleAtom tupleAtom = new TupleAtom(atom);
            bspt.addTuple(tupleAtom);
        }
        // rebond all atoms
        atoms = container.atoms().iterator();
        while (atoms.hasNext()) {
            bondAtom(container, (IAtom) atoms.next());
        }
    }

    /**
     * Rebonds one atom by looking up nearby atom using the binary space partition tree.
     */
    private void bondAtom(IAtomContainer container, IAtom atom) {
        double myCovalentRadius = atom.getCovalentRadius();
        double searchRadius = myCovalentRadius + maxCovalentRadius + bondTolerance;
        Point tupleAtom = new Point(atom.getPoint3d().x, atom.getPoint3d().y, atom.getPoint3d().z);
        for (Bspt.EnumerateSphere e = bspt.enumHemiSphere(tupleAtom, searchRadius); e.hasMoreElements();) {
            IAtom atomNear = ((TupleAtom) e.nextElement()).getAtom();
            if (!atomNear.equals(atom) && container.getBond(atom, atomNear) == null) {
                boolean bonded = isBonded(myCovalentRadius, atomNear.getCovalentRadius(), e.foundDistance2());
                if (bonded) {
                    IBond bond = atom.getBuilder().newInstance(IBond.class, atom, atomNear, IBond.Order.SINGLE);
                    container.addBond(bond);
                }
            }
        }
    }

    /**
     * Returns the bond order for the bond. At this moment, it only returns
     * 0 or 1, but not 2 or 3, or aromatic bond order.
     */

    private boolean isBonded(double covalentRadiusA, double covalentRadiusB, double distance2) {
        double maxAcceptable = covalentRadiusA + covalentRadiusB + bondTolerance;
        double maxAcceptable2 = maxAcceptable * maxAcceptable;
        double minBondDistance2 = this.minBondDistance * this.minBondDistance;
        if (distance2 < minBondDistance2) return false;
        return distance2 <= maxAcceptable2;
    }

    class TupleAtom implements Bspt.Tuple {

        IAtom atom;

        TupleAtom(IAtom atom) {
            this.atom = atom;
        }

        @Override
        public double getDimValue(int dim) {
            if (dim == 0) return atom.getPoint3d().x;
            if (dim == 1) return atom.getPoint3d().y;
            return atom.getPoint3d().z;
        }

        public IAtom getAtom() {
            return this.atom;
        }

        @Override
        public String toString() {
            return ("<" + atom.getPoint3d().x + "," + atom.getPoint3d().y + "," + atom.getPoint3d().z + ">");
        }
    }

}