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

Go to download
/**
 *    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 java.util.ArrayList;
import java.util.List;

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.cml.element.CMLBondSet;
import org.xmlcml.euclid.Util;

/**
 * tool to support a ring. not fully developed
 * 
 * @author pmr
 * 
 */
public class Junction extends AbstractTool {
	private final static Logger LOG = Logger.getLogger(Junction.class.getName());
	private List ringAtomSetList;
	private List ringBondSetList;
	private List ringList;
	private CMLAtomSet commonAtomSet;
	private CMLBondSet commonBondSet;
	//list of atoms and bonds in junction
	// run in same direction as ring0
	private List commonBondList = null;
	private List commonAtomList = null;
	// are ringList running in same direction?
	private int direction;
	private List bridgeAtomList;

	/** get junction between two ringList.
	 * 
	 * @param ring0
	 * @param ring1
	 * @param commonAtomSet
	 */
	Junction(Ring ring0, Ring ring1, CMLAtomSet commonAtomSet) {
		if (ring0 == null || ring1 == null) {
			throw new RuntimeException("null ring in junction");
		}
		if (ring0.equals(ring1)) {
			throw new RuntimeException("cannot form junction with self");
		}
		this.ringAtomSetList = new ArrayList();
		ringAtomSetList.add(ring0.getAtomSet());
		ringAtomSetList.add(ring1.getAtomSet());
		this.ringBondSetList = new ArrayList();
		ringBondSetList.add(ring0.getBondSet());
		ringBondSetList.add(ring1.getBondSet());
		
		this.commonAtomSet = commonAtomSet;
		this.ringList = new ArrayList();
		this.ringList.add(ring0);
		this.ringList.add(ring1);
		commonBondSet = ringBondSetList.get(0).intersection(ringBondSetList.get(1));
		makeJunction();
		ring0.add(ring1, this);
		ring1.add(ring0, this);
	}

	/** factory for Junction
	 * 
	 * @param ring0
	 * @param ring1
	 * @return null if ringList have no atoms in common
	 */
	public static Junction createJunction(Ring ring0, Ring ring1) {
		Junction junction = null;
		CMLAtomSet commonAtomSet = ring0.getAtomSet().intersection(ring1.getAtomSet());
		if (commonAtomSet.size() > 0) {
			junction = new Junction(ring0, ring1, commonAtomSet);
		}
		return junction;
	}
	
	/** 
	 */
	private void makeJunction() {
		if (commonAtomSet.size() != commonBondSet.size()+1) {
			throw new RuntimeException("commonAtomSet ("+commonAtomSet.size()+") should be 1 larger than commonBondSet ("+commonBondSet.size()+")");
		}
		// make sure ringList are distinct
		if (ringList.get(0).size() == ringList.get(1).size()) {
			CMLBondSet bs = ringBondSetList.get(0).complement(ringBondSetList.get(1));
			if (bs.size() == 0) {
				throw new RuntimeException("identical ringList");
			}
		}
		commonBondList = new ArrayList();
		commonAtomList = new ArrayList();
		if (commonBondSet.size() > 0) {
			sortAtomsAndBonds();
		} else {
			commonAtomList.add(commonAtomSet.getAtom(0));
		}
	}
	
	private void sortAtomsAndBonds() {
		CyclicList cyclicAtomList0 = this.ringList.get(0).getCyclicAtomList();
		CyclicList cyclicBondList0 = this.ringList.get(0).getCyclicBondList();
		CyclicList cyclicBondList1 = this.ringList.get(1).getCyclicBondList();
		int atom2BondOffset = ringList.get(0).getCanonicalBondToAtomOffset();
		
		// traverse bond until in junction
		CMLBond bond = cyclicBondList0.get(0);
		// sets internalPointer
		cyclicBondList0.getIndexOfAndCache(bond);
		// if in common area keep going
		CMLBond startBond = bond;
		while (ringBondSetList.get(1).contains(bond)) {
			bond = cyclicBondList0.getNext();
			if (bond.equals(startBond)) {
				LOG.debug(cyclicBondList0);
				LOG.debug(cyclicBondList1);
				throw new RuntimeException("all bonds are contained in one ring");
			}
		}
		startBond = bond;
		// out, now continue till we re-enter
		while (!ringBondSetList.get(1).contains(bond)) {
			bond = cyclicBondList0.getNext();
			if (bond.equals(startBond)) {
				LOG.debug(cyclicBondList0);
				LOG.debug(cyclicBondList1);
				throw new RuntimeException("NO bonds are contained in one ring");
			}
		}
		
		startBond = bond;
		// now record bonds
		int startBondIdx = cyclicBondList0.getIndexOfAndCache(bond);
		int startAtomIdx = (startBondIdx + atom2BondOffset) % cyclicBondList0.size();
		CMLAtom atom = cyclicAtomList0.get(startAtomIdx);
		while (ringBondSetList.get(1).contains(bond)) {
			commonBondList.add(bond);
			commonAtomList.add(atom);
			bond = cyclicBondList0.getNext();
			atom = cyclicAtomList0.getNext();
			if (bond.equals(startBond)) {
				LOG.debug(cyclicBondList0);
				LOG.debug(cyclicBondList1);
				throw new RuntimeException("All/NO bonds are contained in one ring");
			}
		}
		// get last atom
//		CMLAtom lastAtom = bond.getOtherAtom(atom);
		commonAtomList.add(atom);
		
		// check direction
		CyclicList cyclicAtomList1 = this.ringList.get(1).getCyclicAtomList();
		direction = getDirection(commonAtomList, cyclicAtomList1);
		if (direction == 0) {
			throw new RuntimeException("bad direction");
		}
	}
	
	private int getDirection(List atomList, CyclicList cyclicAtomList) {
		int direction = 0;
		CMLAtom startAtom = atomList.get(0);
		int idx = cyclicAtomList.getIndexOfAndCache(startAtom);
		if (idx == -1) {
			throw new RuntimeException("atom lists do not intersect");
		}
		direction = 1;
		if (!testDirection(direction, atomList, cyclicAtomList)) {
			direction = -1;
			if (!testDirection(direction, atomList, cyclicAtomList)) {
				direction = 0;
			}
		}
		return direction;
	}
	
	private boolean testDirection(int direction, List atomList, 
		CyclicList cyclicAtomList) {
		CMLAtom startAtom = atomList.get(0);
		CMLAtom cyclicAtom = startAtom;
		cyclicAtomList.getIndexOfAndCache(startAtom);
		boolean ok = true;
		for (int i = 0; i < atomList.size(); i++) {
			CMLAtom atom = atomList.get(i);
			if (!atom.equals(cyclicAtom)) {
				ok = false;
				break;
			}
			cyclicAtom = (direction == 1) ? cyclicAtomList.getNext() : cyclicAtomList.getPrevious();
		}
		return ok;
	}
	

	/** get bridge atoms between two ringList.
	 * 
	 * @return null if nothing in common
	 */
	public List getBridgeAtomList() {
		if (bridgeAtomList == null) {
			bridgeAtomList = new ArrayList();
			bridgeAtomList.add(new BridgeAtom(this, commonAtomList.get(0)));
			bridgeAtomList.add(new BridgeAtom(this, commonAtomList.get(commonAtomList.size()-1)));
		}
		return bridgeAtomList;
	}

	/** has 1 atom in common.
	 * 
	 * @return true if 1 atom
	 */
	public boolean isSpiro() {
		return (commonAtomSet.size() == 1 && commonBondSet.size() == 0);
	}

	/** has 1 bond in common.
	 * 
	 * @return true if 1 bond
	 */
	public boolean isFusion() {
		return (commonAtomSet.size() == 2 && commonBondSet.size() == 1);
	}

	/** has > 1 bond in common.
	 * 
	 * @return true if > 1 bond
	 */
	public boolean isBridge() {
		return (commonBondSet.size() > 1);
	}

	/**
	 * @return the commonAtomSet
	 */
	public CMLAtomSet getCommonAtomSet() {
		return commonAtomSet;
	}

	/**
	 * @return the commonBondList
	 */
	public List getCommonBondList() {
		return commonBondList;
	}

	/**
	 * @return the commonBondSet
	 */
	public CMLBondSet getCommonBondSet() {
		return commonBondSet;
	}

	/**
	 * @return the direction
	 */
	public int getDirection() {
		return direction;
	}

	/**
	 * @return the ringAtomSetList
	 */
	public List getRingAtomSetList() {
		return ringAtomSetList;
	}

	/**
	 * @return the ringBondSetList
	 */
	public List getRingBondSetList() {
		return ringBondSetList;
	}

	/** get ordered atom list
	 * @return list
	 */
	public List getCommonAtomList() {
		return commonAtomList;
	}
	
	/** get ring list
	 * @return list
	 */
	public List getRingList() {
		return ringList;
	}
	
	/** debug.
	 */
	public void debug() {
		ringList.get(0).debug();
		if (commonBondList.size() > 0) {
			Util.print("..bond");
			for (CMLBond bond : commonBondList) {
				Util.print(" ... "+bond.getId());
			}
			Util.println();
			Util.println("..atom");
			for (CMLAtom atom : commonAtomList) {
				Util.print(" ... "+atom.getId());
			}
//			LOG.debug();
		} else {
			LOG.info("..atom "+commonAtomSet.getAtoms().get(0).getId());
		}
		
	}
}