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QueryAtomContainer.java
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QueryAtomContainer.java
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/* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project
*
* 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.isomorphism.matchers;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IElectronContainer;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.ISingleElectron;
import org.openscience.cdk.interfaces.IStereoElement;
/**
* @cdk.module isomorphism
* @cdk.githash
*/
public class QueryAtomContainer extends QueryChemObject implements IQueryAtomContainer {
private static final long serialVersionUID = -1876912362585898476L;
@Override
public String toString() {
StringBuilder s = new StringBuilder();
s.append("QueryAtomContainer(");
s.append(this.hashCode());
s.append(", #A:").append(getAtomCount());
s.append(", #EC:").append(getElectronContainerCount());
for (int i = 0; i < getAtomCount(); i++) {
s.append(", ").append(getAtom(i).toString());
}
for (int i = 0; i < getBondCount(); i++) {
s.append(", ").append(getBond(i).toString());
}
for (int i = 0; i < getLonePairCount(); i++) {
s.append(", ").append(getLonePair(i).toString());
}
for (int i = 0; i < getSingleElectronCount(); i++) {
s.append(", ").append(getSingleElectron(i).toString());
}
s.append(')');
return s.toString();
}
/**
* 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 List<IStereoElement> stereoElements;
/**
* Constructs an empty AtomContainer.
*/
public QueryAtomContainer(IChemObjectBuilder builder) {
this(10, 10, 0, 0, builder);
}
/**
* 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 QueryAtomContainer(IAtomContainer container, IChemObjectBuilder builder) {
super(builder);
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 ArrayList<IStereoElement>(atomCount / 2);
for (int f = 0; f < container.getAtomCount(); f++) {
atoms[f] = container.getAtom(f);
container.getAtom(f).addListener(this);
}
for (int f = 0; f < this.bondCount; f++) {
bonds[f] = container.getBond(f);
container.getBond(f).addListener(this);
}
for (int f = 0; f < this.lonePairCount; f++) {
lonePairs[f] = container.getLonePair(f);
container.getLonePair(f).addListener(this);
}
for (int f = 0; f < this.singleElectronCount; f++) {
singleElectrons[f] = container.getSingleElectron(f);
container.getSingleElectron(f).addListener(this);
}
}
/**
* 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 QueryAtomContainer(int atomCount, int bondCount, int lpCount, int seCount, IChemObjectBuilder builder) {
super(builder);
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 ArrayList<IStereoElement>(atomCount / 2);
}
/** {@inheritDoc} */
@Override
public void addStereoElement(IStereoElement element) {
stereoElements.add(element);
}
/** {@inheritDoc} */
@Override
public Iterable<IStereoElement> stereoElements() {
return new Iterable<IStereoElement>() {
@Override
public Iterator<IStereoElement> iterator() {
return stereoElements.iterator();
}
};
}
/**
* Sets the array of atoms of this AtomContainer.
*
*@param atoms The array of atoms to be assigned to this AtomContainer
*@see #getAtom
*/
@Override
public void setAtoms(IAtom[] atoms) {
this.atoms = atoms;
for (IAtom atom : atoms) {
atom.addListener(this);
}
this.atomCount = atoms.length;
notifyChanged();
}
/**
* Sets the array of bonds of this AtomContainer.
*
* @param bonds The array of bonds to be assigned to
* this AtomContainer
* @see #getBond
*/
@Override
public void setBonds(IBond[] bonds) {
this.bonds = bonds;
for (IBond bond : bonds) {
bond.addListener(this);
}
this.bondCount = bonds.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;
atom.addListener(this);
oldAtom.removeListener(this);
// replace in 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);
}
notifyChanged();
}
/**
* {@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];
}
/**
* Returns an Iterable for looping over all atoms in this container.
*
*@return An Iterable with the atoms in this container
*/
@Override
public Iterable<IAtom> atoms() {
return new Iterable<IAtom>() {
@Override
public Iterator<IAtom> iterator() {
return new AtomIterator();
}
};
}
/**
* The inner AtomIterator class.
*
*/
private class AtomIterator implements Iterator<IAtom> {
private int pointer = 0;
@Override
public boolean hasNext() {
return pointer < atomCount;
}
@Override
public IAtom next() {
return atoms[pointer++];
}
@Override
public void remove() {
removeAtomOnly(--pointer);
}
}
/**
* Returns an Iterable for looping over all bonds in this container.
*
*@return An Iterable with the bonds in this container
*/
@Override
public Iterable<IBond> bonds() {
return new Iterable<IBond>() {
@Override
public Iterator<IBond> iterator() {
return new BondIterator();
}
};
}
/**
* The inner BondIterator class.
*
*/
private class BondIterator implements Iterator<IBond> {
private int pointer = 0;
@Override
public boolean hasNext() {
return pointer < bondCount;
}
@Override
public IBond next() {
return bonds[pointer++];
}
@Override
public void remove() {
removeBond(--pointer);
}
}
/**
* Returns an Iterable for looping over all lone pairs in this container.
*
*@return An Iterable with the lone pairs in this container
*/
@Override
public Iterable<ILonePair> lonePairs() {
return new Iterable<ILonePair>() {
@Override
public Iterator<ILonePair> iterator() {
return new LonePairIterator();
}
};
}
/**
* The inner LonePairIterator class.
*
*/
private class LonePairIterator implements Iterator<ILonePair> {
private int pointer = 0;
@Override
public boolean hasNext() {
return pointer < lonePairCount;
}
@Override
public ILonePair next() {
return lonePairs[pointer++];
}
@Override
public void remove() {
removeLonePair(--pointer);
}
}
/**
* Returns an Iterable for looping over all single electrons in this container.
*
*@return An Iterable with the single electrons in this container
*/
@Override
public Iterable<ISingleElectron> singleElectrons() {
return new Iterable<ISingleElectron>() {
@Override
public Iterator<ISingleElectron> iterator() {
return new SingleElectronIterator();
}
};
}
/**
* The inner SingleElectronIterator class.
*
*/
private class SingleElectronIterator implements Iterator<ISingleElectron> {
private int pointer = 0;
@Override
public boolean hasNext() {
return pointer < singleElectronCount;
}
@Override
public ISingleElectron next() {
return singleElectrons[pointer++];
}
@Override
public void remove() {
removeSingleElectron(--pointer);
}
}
/**
* Returns an Iterable for looping over all electron containers in this container.
*
*@return An Iterable with the electron containers in this container
*/
@Override
public Iterable<IElectronContainer> electronContainers() {
return new Iterable<IElectronContainer>() {
@Override
public Iterator<IElectronContainer> iterator() {
return new ElectronContainerIterator();
}
};
}
/**
* The inner ElectronContainerIterator class.
*
*/
private class ElectronContainerIterator implements Iterator<IElectronContainer> {
private int pointer = 0;
@Override
public boolean hasNext() {
return pointer < (bondCount + lonePairCount + singleElectronCount);
}
@Override
public IElectronContainer next() {
if (pointer < bondCount)
return bonds[pointer++];
else if (pointer < bondCount + lonePairCount)
return lonePairs[(pointer++) - bondCount];
else if (pointer < bondCount + lonePairCount + singleElectronCount)
return singleElectrons[(pointer++) - bondCount - lonePairCount];
return null;
}
@Override
public void remove() {
if (pointer <= bondCount)
removeBond(--pointer);
else if (pointer <= bondCount + lonePairCount)
removeLonePair((--pointer) - bondCount);
else if (pointer <= bondCount + lonePairCount + singleElectronCount)
removeSingleElectron((--pointer) - bondCount - lonePairCount);
}
}
/**
* Returns the atom at position 0 in the container.
*
*@return The atom at position 0 .
*/
@Override
public IAtom getFirstAtom() {
return atoms[0];
}
/**
* Returns the atom at the last position in the container.
*
*@return The atom at the last position
*/
@Override
public IAtom getLastAtom() {
return getAtomCount() > 0 ? (IAtom) atoms[getAtomCount() - 1] : null;
}
/**
* Returns the position of a given atom in the atoms array. It returns -1 if
* the atom does not exist.
*
*@param atom The atom to be sought
*@return The Position of the atom in the atoms array in [0,..].
*/
@Override
public int getAtomNumber(IAtom atom) {
return indexOf(atom);
}
/**
* Returns the position of the bond between two given atoms in the
* electronContainers array. It returns -1 if the bond does not exist.
*
*@param atom1 The first atom
*@param atom2 The second atom
*@return The Position of the bond between a1 and a2 in the
* electronContainers array.
*/
@Override
public int getBondNumber(IAtom atom1, IAtom atom2) {
return indexOf(getBond(atom1, atom2));
}
/**
* Returns the position of a given bond in the electronContainers array. It
* returns -1 if the bond does not exist.
*
*@param bond The bond to be sought
*@return The Position of the bond in the electronContainers array in [0,..].
*/
@Override
public int getBondNumber(IBond bond) {
return indexOf(bond);
}
/**
* Returns the position of a given lone pair in the lone pair array.
* It returns -1 if the lone pair does not exist.
*
*@param lonePair The lone pair to be sought
*@return The Position of the lone pair in the array..
*/
@Override
public int getLonePairNumber(ILonePair lonePair) {
return indexOf(lonePair);
}
/**
* Returns the position of a given single electron in the single electron array.
* It returns -1 if the single electron does not exist.
*
*@param singleElectron The single electron to be sought
*@return The Position of the single electron in the array.
*/
@Override
public int getSingleElectronNumber(ISingleElectron singleElectron) {
return indexOf(singleElectron);
}
@Override
public int indexOf(IAtom atom) {
for (int i = 0; i < atomCount; i++) {
if (atoms[i].equals(atom)) return i;
}
return -1;
}
@Override
public int indexOf(IBond bond) {
for (int i = 0; i < bondCount; i++) {
if (bonds[i].equals(bond)) return i;
}
return -1;
}
@Override
public int indexOf(ISingleElectron electron) {
for (int i = 0; i < singleElectronCount; i++) {
if (singleElectrons[i] == electron) return i;
}
return -1;
}
@Override
public int indexOf(ILonePair pair) {
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i] == pair) return i;
}
return -1;
}
/**
* Returns the ElectronContainer at position <code>number</code> in the
* container.
*
* @param number The position of the ElectronContainer to be returned.
* @return The ElectronContainer at position <code>number</code>.
*/
@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;
}
/**
* Returns the bond that connects the two given atoms.
*
* @param atom1 The first atom
* @param atom2 The second atom
* @return The bond that connects the two atoms
*/
@Override
public IBond getBond(IAtom atom1, IAtom atom2) {
for (int i = 0; i < getBondCount(); i++) {
if (bonds[i].contains(atom1) && bonds[i].getOther(atom1).equals(atom2)) {
return bonds[i];
}
}
return null;
}
/**
* Returns the number of Atoms in this Container.
*
*@return The number of Atoms in this Container
*/
@Override
public int getAtomCount() {
return this.atomCount;
}
/**
* Returns the number of Bonds in this Container.
*
*@return The number of Bonds in this Container
*/
@Override
public int getBondCount() {
return this.bondCount;
}
/**
* Returns the number of LonePairs in this Container.
*
*@return The number of LonePairs in this Container
*/
@Override
public int getLonePairCount() {
return this.lonePairCount;
}
/**
* Returns the number of the single electrons in this container,
*
*@return The number of SingleElectron objects of this AtomContainer
*/
@Override
public int getSingleElectronCount() {
return this.singleElectronCount;
}
/**
* Returns the number of ElectronContainers in this Container.
*
* @return The number of ElectronContainers in this Container
*/
@Override
public int getElectronContainerCount() {
return this.bondCount + this.lonePairCount + this.singleElectronCount;
}
/**
* Returns an ArrayList of all atoms connected to the given atom.
*
*@param atom The atom the bond partners are searched of.
*@return The ArrayList with the connected atoms
*/
@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;
}
/**
* Returns an ArrayList of all Bonds connected to the given atom.
*
*@param atom The atom the connected bonds are searched of
*@return The ArrayList with connected atoms
*/
@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;
}
/**
* Returns the array of lone pairs connected to an atom.
*
* @param atom The atom for which to get lone pairs
* @return The array of LonePairs of this AtomContainer
* @see #getElectronContainer
* @see #electronContainers()
* @see #getBond
*/
@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;
}
/**
* Returns an array of all SingleElectron connected to the given atom.
*
*@param atom The atom on which the single electron is located
*@return The array of SingleElectron of this AtomContainer
*/
@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;
}
/**
* Returns an ArrayList of all electronContainers connected to the given atom.
*
*@param atom The atom the connected electronContainers are searched of
*@return The ArrayList with the connected atoms
*/
@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;
}
/**
* Returns the number of atoms connected to the given atom.
*
*@param atom The atom the number of bond partners are searched of.
*@return The the size of connected atoms
*/
@Override
public int getConnectedAtomsCount(IAtom atom) {
int count = 0;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) ++count;
}
return count;
}
/**
* Returns the number of Bonds for a given Atom.
*
*@param atom The atom
*@return The number of Bonds for this atom
*/
@Override
public int getConnectedBondsCount(IAtom atom) {
return getConnectedAtomsCount(atom);
}
/**
* Returns the number of connected atoms (degree) to the given atom.
*
*@param idx The atomnumber the degree is searched for
*@return The number of connected atoms (degree)
*/
@Override
public int getConnectedBondsCount(int idx) {
return getConnectedAtomsCount(atoms[idx]);
}
/**
* Returns the number of LonePairs for a given Atom.
*
*@param atom The atom
*@return The number of LonePairs for this atom
*/
@Override
public int getConnectedLonePairsCount(IAtom atom) {
int count = 0;
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i].contains(atom)) ++count;
}
return count;
}
/**
* Returns the sum of the SingleElectron for a given Atom.
*
*@param atom The atom on which the single electron is located
*@return The array of SingleElectron of this AtomContainer
*/
@Override
public int getConnectedSingleElectronsCount(IAtom atom) {
int count = 0;
for (int i = 0; i < singleElectronCount; i++) {
if (singleElectrons[i].contains(atom)) ++count;
}
return count;
}
/**
* Returns the sum of the bond orders for a given Atom.
*
* @param atom The atom
* @return The number of bond orders for this atom
*
* @deprecated Replaced by <code>AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)</code>
*/
@Override
public double getBondOrderSum(IAtom atom) {
double count = 0;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) {
if (bonds[i].getOrder() == IBond.Order.SINGLE) {
count += 1;
} else if (bonds[i].getOrder() == IBond.Order.DOUBLE) {
count += 2;
} else if (bonds[i].getOrder() == IBond.Order.TRIPLE) {
count += 3;
} else if (bonds[i].getOrder() == IBond.Order.QUADRUPLE) {
count += 4;
}
}
}
return count;
}
/**
* Returns the maximum bond order that this atom currently has in the context
* of this AtomContainer.
*
* @param atom The atom
* @return The maximum bond order that this atom currently has
*/
@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().ordinal() > max.ordinal()) {
max = bonds[i].getOrder();
}
}
return max;
}
/**
* Returns the minimum bond order that this atom currently has in the context
* of this AtomContainer.
*
*@param atom The atom
*@return The minimum bond order that this atom currently has
*/
@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().ordinal() < min.ordinal()) {
min = bonds[i].getOrder();
}
}
return min;
}
/**
* Adds all atoms and electronContainers of a given atomcontainer to this
* container.
*
*@param atomContainer The atomcontainer to be added
*/
@Override
public void add(IAtomContainer atomContainer) {
if (atomContainer instanceof QueryAtomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
if (!contains(atomContainer.getAtom(f))) {
addAtom(atomContainer.getAtom(f));
}
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
if (!contains(atomContainer.getBond(f))) {
addBond(atomContainer.getBond(f));
}
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
if (!contains(atomContainer.getLonePair(f))) {
addLonePair(atomContainer.getLonePair(f));
}
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
if (!contains(atomContainer.getSingleElectron(f))) {
addSingleElectron(atomContainer.getSingleElectron(f));
}
}
notifyChanged();
} else {
throw new IllegalArgumentException("AtomContainer is not of type QueryAtomContainer");
}
}
/**
* Adds an atom to this container.
*
*@param atom The atom to be added to this container
*/
@Override
public void addAtom(IAtom atom) {
if (contains(atom)) {