/
AtomContainer.java
1485 lines (1317 loc) · 40.6 KB
/
AtomContainer.java
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/* Copyright (C) 1997-2007 Christoph Steinbeck
*
* Contact: cdk-devel@lists.sourceforge.net
*
* 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.
*
* 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.silent;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
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.CDKConstants;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.IElectronContainer;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.ISingleElectron;
import org.openscience.cdk.interfaces.IStereoElement;
import org.openscience.cdk.interfaces.IBond.Order;
/**
* Base class for all chemical objects that maintain a list of Atoms and
* ElectronContainers. <p>
* <p>
* Looping over all Bonds in the AtomContainer is typically done like: <pre>
* Iterator iter = atomContainer.bonds();
* while (iter.hasNext()) {
* IBond aBond = (IBond) iter.next();
* }
* <p>
* </pre>
*
* @author steinbeck
* @cdk.module silent
* @cdk.githash
* @cdk.created 2000-10-02
*/
public class AtomContainer extends ChemObject implements IAtomContainer, IChemObjectListener, Serializable, Cloneable {
private static final int DEFAULT_CAPACITY = 20;
/**
* Determines if a de-serialized object is compatible with this class.
* <p>
* This value must only be changed if and only if the new version
* of this class is incompatible with the old version. See Sun docs
* for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
* /serialization/spec/version.doc.html>details</a>.
*/
private static final long serialVersionUID = 5678100348445919254L;
/**
* Number of atoms contained by this object.
*/
protected int atomCount;
/**
* Number of bonds contained by this object.
*/
protected int bondCount;
/**
* Number of lone pairs contained by this object.
*/
protected int lonePairCount;
/**
* Number of single electrons contained by this object.
*/
protected int singleElectronCount;
/**
* Amount by which the bond and atom arrays grow when elements are added and
* the arrays are not large enough for that.
*/
protected int growArraySize = 10;
/**
* Internal array of atoms.
*/
protected IAtom[] atoms;
/**
* Internal array of bonds.
*/
protected IBond[] bonds;
/**
* Internal array of lone pairs.
*/
protected ILonePair[] lonePairs;
/**
* Internal array of single electrons.
*/
protected ISingleElectron[] singleElectrons;
/**
* Internal list of atom parities.
*/
protected Set<IStereoElement> stereoElements;
/**
* Constructs an empty AtomContainer.
*/
public AtomContainer() {
this(0, 0, 0, 0);
}
/**
* Constructs an AtomContainer with a copy of the atoms and electronContainers
* of another AtomContainer (A shallow copy, i.e., with the same objects as in
* the original AtomContainer).
*
* @param container An AtomContainer to copy the atoms and electronContainers from
*/
public AtomContainer(IAtomContainer container) {
this.atomCount = container.getAtomCount();
this.bondCount = container.getBondCount();
this.lonePairCount = container.getLonePairCount();
this.singleElectronCount = container.getSingleElectronCount();
this.atoms = new IAtom[this.atomCount];
this.bonds = new IBond[this.bondCount];
this.lonePairs = new ILonePair[this.lonePairCount];
this.singleElectrons = new ISingleElectron[this.singleElectronCount];
stereoElements = new HashSet<IStereoElement>(atomCount / 2);
for (IStereoElement element : container.stereoElements()) {
addStereoElement(element);
}
for (int f = 0; f < container.getAtomCount(); f++) {
atoms[f] = container.getAtom(f);
}
for (int f = 0; f < this.bondCount; f++) {
bonds[f] = container.getBond(f);
}
for (int f = 0; f < this.lonePairCount; f++) {
lonePairs[f] = container.getLonePair(f);
}
for (int f = 0; f < this.singleElectronCount; f++) {
singleElectrons[f] = container.getSingleElectron(f);
}
}
/**
* Constructs an empty AtomContainer that will contain a certain number of
* atoms and electronContainers. It will set the starting array lengths to the
* defined values, but will not create any Atom or ElectronContainer's.
*
* @param atomCount Number of atoms to be in this container
* @param bondCount Number of bonds to be in this container
* @param lpCount Number of lone pairs to be in this container
* @param seCount Number of single electrons to be in this container
*/
public AtomContainer(int atomCount, int bondCount, int lpCount,
int seCount) {
this.atomCount = 0;
this.bondCount = 0;
this.lonePairCount = 0;
this.singleElectronCount = 0;
atoms = new IAtom[atomCount];
bonds = new IBond[bondCount];
lonePairs = new ILonePair[lpCount];
singleElectrons = new ISingleElectron[seCount];
stereoElements = new HashSet<IStereoElement>(atomCount / 2);
}
/**
* {@inheritDoc}
*/
@Override
public void addStereoElement(IStereoElement element) {
stereoElements.add(element);
}
/**
* {@inheritDoc}
*/
@Override
public void setStereoElements(List<IStereoElement> elements) {
this.stereoElements = new HashSet<IStereoElement>();
this.stereoElements.addAll(elements);
}
/**
* {@inheritDoc}
*/
@Override
public Iterable<IStereoElement> stereoElements() {
return Collections.unmodifiableSet(stereoElements);
}
/**
* {@inheritDoc}
*/
@Override
public void setAtoms(IAtom[] newAtoms) {
ensureAtomCapacity(newAtoms.length);
System.arraycopy(newAtoms, 0, this.atoms, 0, newAtoms.length);
if (newAtoms.length < this.atoms.length)
Arrays.fill(atoms, newAtoms.length, this.atoms.length, null);
this.atomCount = newAtoms.length;
}
/**
* {@inheritDoc}
*/
@Override
public void setBonds(IBond[] newBonds) {
ensureBondCapacity(newBonds.length);
System.arraycopy(newBonds, 0, this.bonds, 0, newBonds.length);
if (newBonds.length < this.bonds.length)
Arrays.fill(bonds, newBonds.length, this.bonds.length, null);
this.bondCount = newBonds.length;
}
/**
* {@inheritDoc}
*/
@Override
public void setAtom(int idx, IAtom atom) {
if (idx >= atomCount)
throw new IndexOutOfBoundsException("No atom at index: " + idx);
int aidx = indexOf(atom);
if (aidx >= 0)
throw new IllegalArgumentException("Atom already in container at index: " + idx);
final IAtom oldAtom = atoms[idx];
atoms[idx] = atom;
// update electron containers
for (IBond bond : bonds()) {
for (int i = 0; i < bond.getAtomCount(); i++) {
if (oldAtom.equals(bond.getAtom(i))) {
bond.setAtom(atom, i);
}
}
}
for (ISingleElectron ec : singleElectrons()) {
if (oldAtom.equals(ec.getAtom()))
ec.setAtom(atom);
}
for (ILonePair lp : lonePairs()) {
if (oldAtom.equals(lp.getAtom()))
lp.setAtom(atom);
}
// update stereo
IStereoElement oldStereo = null;
IStereoElement newStereo = null;
for (IStereoElement se : stereoElements()) {
if (se.contains(oldAtom)) {
oldStereo = se;
Map<IAtom, IAtom> amap = Collections.singletonMap(oldAtom, atom);
Map<IBond, IBond> bmap = Collections.emptyMap();
newStereo = se.map(amap, bmap);
}
}
if (oldStereo != null) {
stereoElements.remove(oldStereo);
stereoElements.add(newStereo);
}
}
/**
* {@inheritDoc}
*/
@Override
public IAtom getAtom(int idx) {
if (idx < 0 || idx >= atomCount)
throw new IndexOutOfBoundsException("Atom index out of bounds: 0 <= " + idx + " < " + atomCount);
return atoms[idx];
}
/**
* {@inheritDoc}
*/
@Override
public IBond getBond(int idx) {
if (idx < 0 || idx >= bondCount)
throw new IndexOutOfBoundsException("Bond index out of bounds: 0 <= " + idx + " < " + bondCount);
return bonds[idx];
}
/**
* {@inheritDoc}
*/
@Override
public ILonePair getLonePair(int idx) {
if (idx < 0 || idx >= lonePairCount)
throw new IndexOutOfBoundsException("Lone Pair index out of bounds: 0 <= " + idx + " < " + lonePairCount);
return lonePairs[idx];
}
/**
* {@inheritDoc}
*/
@Override
public ISingleElectron getSingleElectron(int idx) {
if (idx < 0 || idx >= singleElectronCount)
throw new IndexOutOfBoundsException("Single Electrong index out of bounds: 0 <= " + idx + " < " + singleElectronCount);
return singleElectrons[idx];
}
/**
* {@inheritDoc}
*/
@Override
public Iterable<IAtom> atoms() {
return new Iterable<IAtom>() {
@Override
public Iterator<IAtom> iterator() {
return new AtomIterator();
}
};
}
/**
* {@inheritDoc}
*/
@Override
public Iterable<IBond> bonds() {
return new Iterable<IBond>() {
@Override
public Iterator<IBond> iterator() {
return new BondIterator();
}
};
}
/**
* {@inheritDoc}
*/
@Override
public Iterable<ILonePair> lonePairs() {
return new Iterable<ILonePair>() {
@Override
public Iterator<ILonePair> iterator() {
return new LonePairIterator();
}
};
}
/**
* {@inheritDoc}
*/
@Override
public Iterable<ISingleElectron> singleElectrons() {
return new Iterable<ISingleElectron>() {
@Override
public Iterator<ISingleElectron> iterator() {
return new SingleElectronIterator();
}
};
}
/**
* {@inheritDoc}
*/
@Override
public Iterable<IElectronContainer> electronContainers() {
return new Iterable<IElectronContainer>() {
@Override
public Iterator<IElectronContainer> iterator() {
return new ElectronContainerIterator();
}
};
}
/**
* {@inheritDoc}
*/
@Override
public IAtom getFirstAtom() {
return atoms[0];
}
/**
* {@inheritDoc}
*/
@Override
public IAtom getLastAtom() {
return getAtomCount() > 0 ? (IAtom) atoms[getAtomCount() - 1] : null;
}
/**
* {@inheritDoc}
*/
@Override
public int getAtomNumber(IAtom atom) {
return indexOf(atom);
}
/**
* {@inheritDoc}
*/
@Override
public int getBondNumber(IAtom atom1, IAtom atom2) {
return indexOf(getBond(atom1, atom2));
}
/**
* {@inheritDoc}
*/
@Override
public int getBondNumber(IBond bond) {
return indexOf(bond);
}
/**
* {@inheritDoc}
*/
@Override
public int getLonePairNumber(ILonePair lonePair) {
return indexOf(lonePair);
}
/**
* {@inheritDoc}
*/
@Override
public int getSingleElectronNumber(ISingleElectron singleElectron) {
return indexOf(singleElectron);
}
/**
* {@inheritDoc}
*/
@Override
public int indexOf(IAtom atom) {
for (int i = 0; i < atomCount; i++) {
if (atoms[i] == atom) return i;
}
return -1;
}
/**
* {@inheritDoc}
*/
@Override
public int indexOf(IBond bond) {
for (int i = 0; i < bondCount; i++) {
if (bonds[i] == bond) return i;
}
return -1;
}
/**
* {@inheritDoc}
*/
@Override
public int indexOf(ISingleElectron electron) {
for (int i = 0; i < singleElectronCount; i++) {
if (singleElectrons[i] == electron) return i;
}
return -1;
}
/**
* {@inheritDoc}
*/
@Override
public int indexOf(ILonePair pair) {
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i] == pair) return i;
}
return -1;
}
/**
* {@inheritDoc}
*/
@Override
public IElectronContainer getElectronContainer(int number) {
if (number < this.bondCount) return bonds[number];
number -= this.bondCount;
if (number < this.lonePairCount) return lonePairs[number];
number -= this.lonePairCount;
if (number < this.singleElectronCount) return singleElectrons[number];
return null;
}
/**
* {@inheritDoc}
*/
@Override
public IBond getBond(IAtom atom1, IAtom atom2) {
for (int i = 0; i < getBondCount(); i++) {
if (bonds[i].contains(atom1) && bonds[i].getOther(atom1) == atom2) {
return bonds[i];
}
}
return null;
}
/**
* {@inheritDoc}
*/
@Override
public int getAtomCount() {
return this.atomCount;
}
/**
* {@inheritDoc}
*/
@Override
public int getBondCount() {
return this.bondCount;
}
/**
* {@inheritDoc}
*/
@Override
public int getLonePairCount() {
return this.lonePairCount;
}
/**
* {@inheritDoc}
*/
@Override
public int getSingleElectronCount() {
return this.singleElectronCount;
}
/**
* {@inheritDoc}
*/
@Override
public int getElectronContainerCount() {
return this.bondCount + this.lonePairCount + this.singleElectronCount;
}
/**
* {@inheritDoc}
*/
@Override
public List<IAtom> getConnectedAtomsList(IAtom atom) {
List<IAtom> atomsList = new ArrayList<IAtom>();
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) atomsList.add(bonds[i].getOther(atom));
}
return atomsList;
}
/**
* {@inheritDoc}
*/
@Override
public List<IBond> getConnectedBondsList(IAtom atom) {
List<IBond> bondsList = new ArrayList<IBond>();
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) bondsList.add(bonds[i]);
}
return bondsList;
}
/**
* {@inheritDoc}
*/
@Override
public List<ILonePair> getConnectedLonePairsList(IAtom atom) {
List<ILonePair> lps = new ArrayList<ILonePair>();
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i].contains(atom)) lps.add(lonePairs[i]);
}
return lps;
}
/**
* {@inheritDoc}
*/
@Override
public List<ISingleElectron> getConnectedSingleElectronsList(IAtom atom) {
List<ISingleElectron> lps = new ArrayList<ISingleElectron>();
for (int i = 0; i < singleElectronCount; i++) {
if (singleElectrons[i].contains(atom)) lps.add(singleElectrons[i]);
}
return lps;
}
/**
* {@inheritDoc}
*/
@Override
public List<IElectronContainer> getConnectedElectronContainersList(
IAtom atom) {
List<IElectronContainer> lps = new ArrayList<IElectronContainer>();
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) lps.add(bonds[i]);
}
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i].contains(atom)) lps.add(lonePairs[i]);
}
for (int i = 0; i < singleElectronCount; i++) {
if (singleElectrons[i].contains(atom)) lps.add(singleElectrons[i]);
}
return lps;
}
/**
* {@inheritDoc}
*/
@Override
public int getConnectedAtomsCount(IAtom atom) {
int count = 0;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) ++count;
}
return count;
}
/**
* {@inheritDoc}
*/
@Override
public int getConnectedBondsCount(IAtom atom) {
return getConnectedAtomsCount(atom);
}
/**
* {@inheritDoc}
*/
@Override
public int getConnectedBondsCount(int atomNumber) {
return getConnectedAtomsCount(atoms[atomNumber]);
}
/**
* {@inheritDoc}
*/
@Override
public int getConnectedLonePairsCount(IAtom atom) {
int count = 0;
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i].contains(atom)) ++count;
}
return count;
}
/**
* {@inheritDoc}
*/
@Override
public int getConnectedSingleElectronsCount(IAtom atom) {
int count = 0;
for (int i = 0; i < singleElectronCount; i++) {
if (singleElectrons[i].contains(atom)) ++count;
}
return count;
}
/**
* {@inheritDoc}
*/
@Override
public double getBondOrderSum(IAtom atom) {
double count = 0;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) {
IBond.Order order = bonds[i].getOrder();
if (order != null) {
count += order.numeric();
}
}
}
return count;
}
/**
* {@inheritDoc}
*/
@Override
public Order getMaximumBondOrder(IAtom atom) {
IBond.Order max = IBond.Order.SINGLE;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom) && bonds[i].getOrder().numeric() > max.numeric()) {
max = bonds[i].getOrder();
}
}
return max;
}
/**
* {@inheritDoc}
*/
@Override
public Order getMinimumBondOrder(IAtom atom) {
IBond.Order min = IBond.Order.QUADRUPLE;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom) && bonds[i].getOrder().numeric() < min.numeric()) {
min = bonds[i].getOrder();
}
}
return min;
}
/**
* {@inheritDoc}
*/
@Override
public void add(IAtomContainer that) {
atoms = Arrays.copyOf(atoms, atomCount + that.getAtomCount());
bonds = Arrays.copyOf(bonds, bondCount + that.getBondCount());
for (IAtom atom : that.atoms())
atom.setFlag(CDKConstants.VISITED, false);
for (IBond bond : that.bonds())
bond.setFlag(CDKConstants.VISITED, false);
for (IAtom atom : this.atoms())
atom.setFlag(CDKConstants.VISITED, true);
for (IBond bond : this.bonds())
bond.setFlag(CDKConstants.VISITED, true);
for (IAtom atom : that.atoms()) {
if (!atom.getFlag(CDKConstants.VISITED)) {
atom.setFlag(CDKConstants.VISITED, true);
atoms[atomCount++] = atom;
}
}
for (IBond bond : that.bonds()) {
if (!bond.getFlag(CDKConstants.VISITED)) {
bond.setFlag(CDKConstants.VISITED, true);
bonds[bondCount++] = bond;
}
}
for (ILonePair lp : that.lonePairs()) {
if (!contains(lp)) {
addLonePair(lp);
}
}
for (ISingleElectron se : that.singleElectrons()) {
if (!contains(se)) {
addSingleElectron(se);
}
}
for (IStereoElement se : that.stereoElements())
stereoElements.add(se);
}
/**
* {@inheritDoc}
*/
@Override
public void addAtom(IAtom atom) {
if (contains(atom)) {
return;
}
ensureAtomCapacity(atomCount+1);
atoms[atomCount++] = atom;
}
/**
* {@inheritDoc}
*/
@Override
public void addBond(IBond bond) {
ensureBondCapacity(bondCount+1);
bonds[bondCount++] = bond;
}
/**
* {@inheritDoc}
*/
@Override
public void addLonePair(ILonePair lonePair) {
ensureLonePairCapacity(lonePairCount+1);
lonePairs[lonePairCount++] = lonePair;
}
/**
* {@inheritDoc}
*/
@Override
public void addSingleElectron(ISingleElectron singleElectron) {
ensureElectronCapacity(singleElectronCount+1);
singleElectrons[singleElectronCount++] = singleElectron;
}
/**
* {@inheritDoc}
*/
@Override
public void addElectronContainer(IElectronContainer electronContainer) {
if (electronContainer instanceof IBond)
this.addBond((IBond) electronContainer);
if (electronContainer instanceof ILonePair)
this.addLonePair((ILonePair) electronContainer);
if (electronContainer instanceof ISingleElectron)
this.addSingleElectron((ISingleElectron) electronContainer);
}
/**
* {@inheritDoc}
*/
@Override
public void remove(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
removeAtomOnly(atomContainer.getAtom(f));
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
removeBond(atomContainer.getBond(f));
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
removeLonePair(atomContainer.getLonePair(f));
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
removeSingleElectron(atomContainer.getSingleElectron(f));
}
}
/**
* {@inheritDoc}
*/
@Override
public void removeAtomOnly(int position) {
for (int i = position; i < atomCount - 1; i++) {
atoms[i] = atoms[i + 1];
}
atoms[atomCount - 1] = null;
atomCount--;
}
/**
* {@inheritDoc}
*/
@Override
public void removeAtomOnly(IAtom atom) {
int position = getAtomNumber(atom);
if (position != -1) {
removeAtomOnly(position);
}
}
/**
* {@inheritDoc}
*/
@Override
public IBond removeBond(int position) {
IBond bond = bonds[position];
for (int i = position; i < bondCount - 1; i++) {
bonds[i] = bonds[i + 1];
}
bonds[bondCount - 1] = null;
bondCount--;
return bond;
}
/**
* {@inheritDoc}
*/
@Override
public IBond removeBond(IAtom atom1, IAtom atom2) {
int pos = indexOf(getBond(atom1, atom2));
IBond bond = null;
if (pos != -1) {
bond = bonds[pos];
removeBond(pos);
}
return bond;
}
/**
* {@inheritDoc}
*/
@Override
public void removeBond(IBond bond) {
int pos = getBondNumber(bond);
if (pos != -1) removeBond(pos);
}
/**
* {@inheritDoc}
*/
@Override
public ILonePair removeLonePair(int position) {
ILonePair lp = lonePairs[position];
for (int i = position; i < lonePairCount - 1; i++) {
lonePairs[i] = lonePairs[i + 1];
}
lonePairs[lonePairCount - 1] = null;
lonePairCount--;
return lp;
}
/**
* {@inheritDoc}
*/
@Override
public void removeLonePair(ILonePair lonePair) {
int pos = indexOf(lonePair);
if (pos != -1) removeLonePair(pos);
}
/**
* {@inheritDoc}
*/
@Override
public ISingleElectron removeSingleElectron(int position) {
ISingleElectron se = singleElectrons[position];
for (int i = position; i < singleElectronCount - 1; i++) {
singleElectrons[i] = singleElectrons[i + 1];
}
singleElectrons[singleElectronCount - 1] = null;
singleElectronCount--;
return se;
}
/**
* {@inheritDoc}
*/
@Override
public void removeSingleElectron(ISingleElectron singleElectron) {
int pos = indexOf(singleElectron);
if (pos != -1) removeSingleElectron(pos);
}
/**
* {@inheritDoc}
*/
@Override
public IElectronContainer removeElectronContainer(int number) {
if (number < this.bondCount) return removeBond(number);
number -= this.bondCount;
if (number < this.lonePairCount) return removeLonePair(number);
number -= this.lonePairCount;
if (number < this.singleElectronCount)
return removeSingleElectron(number);
return null;
}
/**
* {@inheritDoc}
*/
@Override
public void removeElectronContainer(IElectronContainer electronContainer) {
if (electronContainer instanceof IBond)
removeBond((IBond) electronContainer);
else if (electronContainer instanceof ILonePair)
removeLonePair((ILonePair) electronContainer);
else if (electronContainer instanceof ISingleElectron)
removeSingleElectron((ISingleElectron) electronContainer);
}
/**
* {@inheritDoc}
*/
@Override
@Deprecated
public void removeAtomAndConnectedElectronContainers(IAtom atom) {
removeAtom(atom);
}
/**
* {@inheritDoc}
*/
@Override
public void removeAtom(IAtom atom) {
int position = getAtomNumber(atom);
if (position != -1) {
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) {
removeBond(i);
--i;
}
}
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i].contains(atom)) {