/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.
*/
package org.openscience.cdk.tools.manipulator;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.*;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* Class with convenience methods that provide methods from
* methods from ChemObjects within the ChemFile.
*
* @see org.openscience.cdk.AtomContainer#removeAtomAndConnectedElectronContainers(IAtom)
*
* @cdk.module standard
* @cdk.githash
*/
@TestClass("org.openscience.cdk.tools.manipulator.ChemFileManipulatorTest")
public class ChemFileManipulator {
/**
* Get the total number of atoms inside an IChemFile.
*
* @param file The IChemFile object.
* @return The number of Atom object inside.
*/
@TestMethod("testGetAtomCount_IChemFile")
public static int getAtomCount(IChemFile file) {
int count = 0;
for (int i=0; i<file.getChemSequenceCount(); i++) {
count += ChemSequenceManipulator.getAtomCount(file.getChemSequence(i));
}
return count;
}
/**
* Get the total number of bonds inside an IChemFile.
*
* @param file The IChemFile object.
* @return The number of Bond object inside.
*/
@TestMethod("testGetBondCount_IChemFile")
public static int getBondCount(IChemFile file) {
int count = 0;
for (int i=0; i<file.getChemSequenceCount(); i++) {
count += ChemSequenceManipulator.getBondCount(file.getChemSequence(i));
}
return count;
}
/**
* Returns a List of all IChemObject inside a ChemFile.
*
* @return A list of all ChemObjects
*/
@TestMethod("testGetAllChemObjects_IChemFile")
public static List<IChemObject> getAllChemObjects(IChemFile file) {
List<IChemObject> list = new ArrayList<IChemObject>();
//list.add(file); // should not add the original file
for (int i=0; i<file.getChemSequenceCount(); i++) {
list.add(file.getChemSequence(i));
list.addAll(ChemSequenceManipulator.getAllChemObjects(
file.getChemSequence(i)
));
}
return list;
}
@TestMethod("testGetAllIDs_IChemFile")
public static List<String> getAllIDs(IChemFile file) {
List<String> list = new ArrayList<String>();
if (file.getID() != null) list.add(file.getID());
for (int i=0; i<file.getChemSequenceCount(); i++) {
list.addAll(ChemSequenceManipulator.getAllIDs(
file.getChemSequence(i)
));
}
return list;
}
/**
* Returns all the AtomContainer's of a ChemFile.
*/
@TestMethod("testGetAllAtomContainers_IChemFile")
public static List<IAtomContainer> getAllAtomContainers(IChemFile file) {
List<IAtomContainer> acList = new ArrayList<IAtomContainer>();
for (IChemSequence sequence : file.chemSequences()) {
acList.addAll(ChemSequenceManipulator.getAllAtomContainers(sequence));
}
return acList;
}
/**
* Get a list of all ChemModels inside an IChemFile.
*
* @param file The IChemFile object.
* @return The List of IChemModel objects inside.
*/
@TestMethod("testGetAllChemModels_IChemFile")
public static List<IChemModel> getAllChemModels(IChemFile file) {
List<IChemModel> modelsList = new ArrayList<IChemModel>();
for (int f = 0; f < file.getChemSequenceCount(); f++){
for (IChemModel model : file.getChemSequence(f).chemModels()) {
modelsList.add(model);
}
}
return modelsList;
}
/**
* Get a list of all IReaction inside an IChemFile.
*
* @param file The IChemFile object.
* @return The List of IReaction objects inside.
*/
@TestMethod("testGetAllReactions_IChemFile")
public static List<IReaction> getAllReactions(IChemFile file) {
List<IReaction> reactonList = new ArrayList<IReaction>();
List<IChemModel> chemModel = getAllChemModels(file);
for (int f = 0; f < chemModel.size(); f++){
for (IReaction reaction : chemModel.get(f).getReactionSet().reactions()) {
reactonList.add(reaction);
}
}
return reactonList;
}
}