/* $RCSfile$
* $Author$
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*
* Copyright (C) 2003-2007 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.
* 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.
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package org.openscience.cdk.tools.manipulator;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IElectronContainer;
import org.openscience.cdk.interfaces.IMoleculeSet;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* @cdk.module standard
* @cdk.githash
*
* @see ChemModelManipulator
*/
@TestClass("org.openscience.cdk.tools.manipulator.AtomContainerSetManipulatorTest")
public class AtomContainerSetManipulator {
@TestMethod("testGetAtomCount_IAtomContainerSet")
public static int getAtomCount(IAtomContainerSet set) {
int count = 0;
for (IAtomContainer atomContainer : set.atomContainers()) {
count += (atomContainer).getAtomCount();
}
return count;
}
@TestMethod("testGetBondCount_IAtomContainerSet")
public static int getBondCount(IAtomContainerSet set) {
int count = 0;
for (IAtomContainer atomContainer : set.atomContainers()) {
count += (atomContainer).getBondCount();
}
return count;
}
@TestMethod("testRemoveAtomAndConnectedElectronContainers_IAtomContainerSet_IAtom")
public static void removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom) {
for (IAtomContainer atomContainer : set.atomContainers()) {
if (atomContainer.contains(atom)) {
atomContainer.removeAtomAndConnectedElectronContainers(atom);
IMoleculeSet molecules = ConnectivityChecker.partitionIntoMolecules(atomContainer);
if (molecules.getAtomContainerCount() > 1) {
set.removeAtomContainer(atomContainer);
for (int k = 0; k < molecules.getAtomContainerCount(); k++) {
set.addAtomContainer(molecules.getAtomContainer(k));
}
}
return;
}
}
}
@TestMethod("testRemoveElectronContainer_IAtomContainerSet_IElectronContainer")
public static void removeElectronContainer(IAtomContainerSet set, IElectronContainer electrons) {
for (IAtomContainer atomContainer : set.atomContainers()) {
if (atomContainer.contains(electrons)) {
atomContainer.removeElectronContainer(electrons);
IMoleculeSet molecules = ConnectivityChecker.partitionIntoMolecules(atomContainer);
if (molecules.getAtomContainerCount() > 1) {
set.removeAtomContainer(atomContainer);
for (int k = 0; k < molecules.getAtomContainerCount(); k++) {
set.addAtomContainer(molecules.getMolecule(k));
}
}
return;
}
}
}
/**
* Returns all the AtomContainer's of a MoleculeSet.
*
* @param set The collection of IAtomContainer objects
* @return A list of individual IAtomContainer's
*/
@TestMethod("testGetAllAtomContainers_IAtomContainerSet")
public static List<IAtomContainer> getAllAtomContainers(IAtomContainerSet set) {
List<IAtomContainer> atomContainerList = new ArrayList<IAtomContainer>();
for (IAtomContainer atomContainer : set.atomContainers()) {
atomContainerList.add(atomContainer);
}
return atomContainerList;
}
/**
* @param set The collection of IAtomContainer objects
* @return The summed charges of all atoms in this set.
*/
@TestMethod("testGetTotalCharge_IAtomContainerSet")
public static double getTotalCharge(IAtomContainerSet set) {
double charge = 0;
for (int i = 0; i < set.getAtomContainerCount(); i++) {
int thisCharge = AtomContainerManipulator.getTotalFormalCharge(set.getAtomContainer(i));
double stoich = set.getMultiplier(i);
charge += stoich * thisCharge;
}
return charge;
}
/**
* @param set The collection of IAtomContainer objects
* @return The summed formal charges of all atoms in this set.
*/
@TestMethod("testGetTotalFormalCharge_IAtomContainerSet")
public static double getTotalFormalCharge(IAtomContainerSet set) {
int charge = 0;
for (int i = 0; i < set.getAtomContainerCount(); i++) {
int thisCharge = AtomContainerManipulator.getTotalFormalCharge(set.getAtomContainer(i));
double stoich = set.getMultiplier(i);
charge += stoich * thisCharge;
}
return charge;
}
/**
* @param set The collection of IAtomContainer objects
* @return The summed implicit hydrogens of all atoms in this set.
*/
@TestMethod("testGetTotalHydrogenCount_IAtomContainerSet")
public static int getTotalHydrogenCount(IAtomContainerSet set) {
int hCount = 0;
for (int i = 0; i < set.getAtomContainerCount(); i++) {
hCount += AtomContainerManipulator.getTotalHydrogenCount(set.getAtomContainer(i));
}
return hCount;
}
@TestMethod("testGetAllIDs_IAtomContainerSet")
public static List<String> getAllIDs(IAtomContainerSet set) {
List<String> idList = new ArrayList<String>();
if (set != null) {
if (set.getID() != null) idList.add(set.getID());
for (int i = 0; i < set.getAtomContainerCount(); i++) {
idList.addAll(AtomContainerManipulator.getAllIDs(set.getAtomContainer(i)));
}
}
return idList;
}
@TestMethod("testSetAtomProperties_IAtomContainerSet_Object_Object")
public static void setAtomProperties(IAtomContainerSet set, Object propKey, Object propVal) {
if (set != null) {
for (int i = 0; i < set.getAtomContainerCount(); i++) {
AtomContainerManipulator.setAtomProperties(set.getAtomContainer(i), propKey, propVal);
}
}
}
@TestMethod("testGetRelevantAtomContainer_IAtomContainerSet_IAtom")
public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet containerSet, IAtom atom) {
for (IAtomContainer atomContainer : containerSet.atomContainers()) {
if (atomContainer.contains(atom)) {
return atomContainer;
}
}
return null;
}
@TestMethod("testGetRelevantAtomContainer_IAtomContainerSet_IBond")
public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet containerSet, IBond bond) {
for (IAtomContainer atomContainer : containerSet.atomContainers()) {
if (atomContainer.contains(bond)) {
return atomContainer;
}
}
return null;
}
/**
* Does not recursively return the contents of the AtomContainer.
*
* @param set The collection of IAtomContainer objects
* @return a list of individual ChemObject's
*/
@TestMethod("testGetAllChemObjects_IAtomContainerSet")
public static List<IChemObject> getAllChemObjects(IAtomContainerSet set) {
ArrayList<IChemObject> list = new ArrayList<IChemObject>();
list.add(set);
for (IAtomContainer atomContainer : set.atomContainers()) {
list.add(atomContainer);
}
return list;
}
/**
* <p>Sorts the IAtomContainers in the given IAtomContainerSet by the following
* criteria with decreasing priority:</p>
* <ul>
* <li>Compare atom count
* <li>Compare molecular weight (heavy atoms only)
* <li>Compare bond count
* <li>Compare sum of bond orders (heavy atoms only)
* </ul>
* <p>If no difference can be found with the above criteria, the IAtomContainers are
* considered equal.</p>
* @param atomContainerSet The collection of IAtomContainer objects
*/
@TestMethod("testSort_IAtomContainerSet")
public static void sort(IAtomContainerSet atomContainerSet) {
List<IAtomContainer> atomContainerList = AtomContainerSetManipulator.getAllAtomContainers(atomContainerSet);
Collections.sort(atomContainerList, new AtomContainerComparator());
atomContainerSet.removeAllAtomContainers();
for (Object anAtomContainerList : atomContainerList)
atomContainerSet.addAtomContainer((IAtomContainer) anAtomContainerList);
}
/**
* Tells if an AtomContainerSet contains at least one AtomContainer with the
* same ID as atomContainer. Note this checks getID() for equality, not pointers.
*
* @param id The IAtomContainer to look for
* @param atomContainerSet The collection of IAtomContainer objects
*/
@TestMethod("testContainsByID_IAtomContainerSet_IAtomContainer")
public static boolean containsByID(IAtomContainerSet atomContainerSet,
String id) {
for(IAtomContainer ac : atomContainerSet.atomContainers()){
if(ac.getID()!=null && ac.getID().equals(id))
return true;
}
return false;
}
}