org.xmlcml.cml.tools.Sprout Maven / Gradle / Ivy

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/**
 *    Copyright 2011 Peter Murray-Rust et. al.
 *
 *    Licensed under the Apache License, Version 2.0 (the "License");
 *    you may not use this file except in compliance with the License.
 *    You may obtain a copy of the License at
 *
 *        http://www.apache.org/licenses/LICENSE-2.0
 *
 *    Unless required by applicable law or agreed to in writing, software
 *    distributed under the License is distributed on an "AS IS" BASIS,
 *    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *    See the License for the specific language governing permissions and
 *    limitations under the License.
 */

package org.xmlcml.cml.tools;

import org.apache.log4j.Logger;
import org.xmlcml.cml.base.AbstractTool;
import org.xmlcml.cml.element.CMLAtom;
import org.xmlcml.cml.element.CMLAtomSet;
import org.xmlcml.cml.element.CMLBond;
import org.xmlcml.euclid.Real2;
import org.xmlcml.euclid.Vector2;

/**
 * tool to support a ring. not fully developed
 * 
 * @author pmr
 * 
 */
public class Sprout extends AbstractTool {
	final static Logger LOG = Logger.getLogger(Sprout.class);

	private CMLAtom ringAtom;
	private CMLAtom firstAtom;
	private CMLBond bond;
	private Chain chain;
	private CMLAtomSet ringAtomSet;
	private RingNucleus ringNucleus;
	private MoleculeLayout moleculeDraw;
	
//	private Sprout() {
//		// 
//	}
	/** constructor.
	 * @param ringAtom
	 * @param bond
	 * @param ringNucleus
	 */
	public Sprout(CMLAtom ringAtom,	CMLBond bond, 
			RingNucleus ringNucleus) {
		this.bond = bond;
		this.ringAtom = ringAtom;
		this.firstAtom = bond.getOtherAtom(ringAtom);
		this.ringNucleus = ringNucleus;
		this.moleculeDraw = ringNucleus.getMoleculeDraw();
	}

	/**
	 */
	public void generateCoordinates() {
		if (chain == null) {
			throw new RuntimeException("null chain");
		}
		Real2 sproutVector = getSproutVector();
		if (sproutVector != null) {
			firstAtom.setXY2(ringAtom.getXY2().plus(sproutVector));
			chain.calculate2DCoordinates(this, moleculeDraw);
		}
	}
	/**
	 * @return vector
	 * @throws RuntimeException
	 */
	Real2 getSproutVector() throws RuntimeException {
		Real2 vv = null;
		double bondLength = ((MoleculeDisplay)ringNucleus.getMoleculeDraw().getAbstractDisplay()).getBondLength();
		if (ringAtom.getX2Attribute() == null) {
			LOG.error("ringAtom has no coordinates; "+ringAtom.getId());
		} else {
			if (ringAtomSet == null) {
				ringAtomSet = new CMLAtomSet();
				for (CMLAtom atom : ringAtom.getLigandAtoms()) {
					if (ringNucleus.getAtomSet().contains(atom)) {
						if (atom.getX2Attribute() == null) {
							// this happens when adding sprout to ring within
							// ringSet
	//						System.err.println("ring has no coordinates: ");
						} else {
							ringAtomSet.addAtom(atom);
						}
					}
				}
			}
			if (ringAtomSet.size() < 2) {
				LOG.error("Must have at list 2 ring atoms");
			} else {
				// calculate sprout coordinates and then recurse to chain
				Real2 centroid = ringAtomSet.getCentroid2D();
				Vector2 v = new Vector2(ringAtom.getXY2().subtract(centroid));
				if (v.getLength() < 0.00001) {
					v = new Vector2(1., 0.);
				}
				vv = v.getUnitVector().multiplyBy(bondLength);
			}
		}
		return vv;
	}

	/**
	 * @return the bond
	 */
	public CMLBond getBond() {
		return bond;
	}
	/**
	 * @return the chain
	 */
	public Chain getChain() {
		return chain;
	}
	/**
	 * @return the firstAtom
	 */
	public CMLAtom getFirstAtom() {
		return firstAtom;
	}
	/**
	 * @return the ringAtom
	 */
	public CMLAtom getRingAtom() {
		return ringAtom;
	}
	/**
	 * @return string
	 */
	public String toString() {
		String s = ringAtom.getId()+" -> "+firstAtom.getId();
		return s;
	}
	/**
	 * @return the ringAtomSet
	 */
	public CMLAtomSet getRingAtomSet() {
		return ringAtomSet;
	}
	/**
	 * @return the moleculeDraw
	 */
	public MoleculeLayout getMoleculeDraw() {
		return moleculeDraw;
	}
	/**
	 * @param moleculeDraw the moleculeDraw to set
	 */
	public void setMoleculeDraw(MoleculeLayout moleculeDraw) {
		this.moleculeDraw = moleculeDraw;
	}
	/**
	 * @return the ringNucleus
	 */
	public RingNucleus getRingNucleus() {
		return ringNucleus;
	}
	/**
	 * @param chain the chain to set
	 */
	public void setChain(Chain chain) {
		this.chain = chain;
	}
}