Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/* Copyright (C) 2010 Egon Willighagen
* 2012 John May
*
* Contact: [email protected]
*
* 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;
import org.openscience.cdk.formula.AdductFormula;
import org.openscience.cdk.formula.MolecularFormula;
import org.openscience.cdk.formula.MolecularFormulaSet;
import org.openscience.cdk.interfaces.IAdductFormula;
import org.openscience.cdk.interfaces.IAminoAcid;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBioPolymer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.ICDKObject;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
import org.openscience.cdk.interfaces.IElectronContainer;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IFragmentAtom;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.IMapping;
import org.openscience.cdk.interfaces.IMolecularFormula;
import org.openscience.cdk.interfaces.IMolecularFormulaSet;
import org.openscience.cdk.interfaces.IMonomer;
import org.openscience.cdk.interfaces.IPDBAtom;
import org.openscience.cdk.interfaces.IPDBMonomer;
import org.openscience.cdk.interfaces.IPDBPolymer;
import org.openscience.cdk.interfaces.IPDBStructure;
import org.openscience.cdk.interfaces.IPolymer;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionScheme;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.interfaces.ISingleElectron;
import org.openscience.cdk.interfaces.IStrand;
import org.openscience.cdk.interfaces.ISubstance;
import org.openscience.cdk.interfaces.ITetrahedralChirality;
import org.openscience.cdk.protein.data.PDBAtom;
import org.openscience.cdk.protein.data.PDBMonomer;
import org.openscience.cdk.protein.data.PDBPolymer;
import org.openscience.cdk.protein.data.PDBStructure;
import org.openscience.cdk.stereo.DoubleBondStereochemistry;
import org.openscience.cdk.stereo.TetrahedralChirality;
import java.util.Locale;
/**
* A factory class to provide implementation independent {@link ICDKObject}s.
*
*
*
* @author egonw
* @author john may
* @cdk.module data
* @cdk.githash
*/
public class DefaultChemObjectBuilder implements IChemObjectBuilder {
// Improved over System.getBoolean(), if we don't recognize the value we throw
// an error rather than return false. The default can also be specified.
private static boolean getSystemProp(final String key, final boolean defaultValue) {
String val = System.getProperty(key);
if (val == null)
val = System.getenv(key);
if (val == null) {
return defaultValue;
} else if (val.isEmpty()) {
return true;
} else {
switch (val.toLowerCase(Locale.ROOT)) {
case "t":
case "true":
case "1":
return true;
case "f":
case "false":
case "0":
return false;
default:
throw new IllegalArgumentException("Invalid value, expected true/false: " + val);
}
}
}
private static final boolean CDK_LEGACY_AC
= getSystemProp("CdkUseLegacyAtomContainer", true);
private static volatile IChemObjectBuilder instance = null;
private static final Object LOCK = new Object();
private final DynamicFactory factory = new DynamicFactory(200);
private DefaultChemObjectBuilder() {
// self reference required for stereo-elements
final IChemObjectBuilder self = this;
// elements
factory.register(IAtom.class, Atom.class);
factory.register(IPseudoAtom.class, PseudoAtom.class);
factory.register(IElement.class, Element.class);
factory.register(IAtomType.class, AtomType.class);
factory.register(IFragmentAtom.class, FragmentAtom.class);
factory.register(IPDBAtom.class, PDBAtom.class);
factory.register(IIsotope.class, Isotope.class);
// electron containers
factory.register(IBond.class, Bond.class);
factory.register(IElectronContainer.class, ElectronContainer.class);
factory.register(ISingleElectron.class, SingleElectron.class);
factory.register(ILonePair.class, LonePair.class);
// atom containers
if (CDK_LEGACY_AC) {
factory.register(IAtomContainer.class, AtomContainer.class);
} else {
factory.register(IAtomContainer.class, AtomContainer2.class);
}
factory.register(IRing.class, Ring.class);
factory.register(ICrystal.class, Crystal.class);
factory.register(IPolymer.class, Polymer.class);
factory.register(IPDBPolymer.class, PDBPolymer.class);
factory.register(IMonomer.class, Monomer.class);
factory.register(IPDBMonomer.class, PDBMonomer.class);
factory.register(IBioPolymer.class, BioPolymer.class);
factory.register(IPDBStructure.class, PDBStructure.class);
factory.register(IAminoAcid.class, AminoAcid.class);
factory.register(IStrand.class, Strand.class);
// reactions
factory.register(IReaction.class, Reaction.class);
factory.register(IReactionScheme.class, ReactionScheme.class);
// formula
factory.register(IMolecularFormula.class, MolecularFormula.class);
factory.register(IAdductFormula.class, AdductFormula.class);
// chem object sets
factory.register(IAtomContainerSet.class, AtomContainerSet.class);
factory.register(IMolecularFormulaSet.class, MolecularFormulaSet.class);
factory.register(IReactionSet.class, ReactionSet.class);
factory.register(IRingSet.class, RingSet.class);
factory.register(IChemModel.class, ChemModel.class);
factory.register(IChemFile.class, ChemFile.class);
factory.register(IChemSequence.class, ChemSequence.class);
factory.register(ISubstance.class, Substance.class);
// stereo components (requires some modification after instantiation)
factory.register(ITetrahedralChirality.class, TetrahedralChirality.class,
new DynamicFactory.CreationModifier() {
@Override
public void modify(TetrahedralChirality instance) {
instance.setBuilder(self);
}
});
factory.register(IDoubleBondStereochemistry.class, DoubleBondStereochemistry.class,
new DynamicFactory.CreationModifier() {
@Override
public void modify(DoubleBondStereochemistry instance) {
instance.setBuilder(self);
}
});
// miscellaneous
factory.register(IMapping.class, Mapping.class);
factory.register(IChemObject.class, ChemObject.class);
}
/**
* Access the singleton instance of this DefaultChemObjectBuilder.
*
{@code
*
* // get the builder instance
* IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
*
* // using the builder...
* // create an IAtom using the default constructor
* IAtom atom = builder.newInstance(IAtom.class);
*
* // create a carbon atom
* IAtom c1 = builder.newInstance(IAtom.class, "C");
* }
*
* @return a DefaultChemObjectBuilder instance
*/
public static IChemObjectBuilder getInstance() {
IChemObjectBuilder result = instance;
if (result == null) {
result = instance;
synchronized (LOCK) {
if (result == null) {
instance = result = new DefaultChemObjectBuilder();
}
}
}
return result;
}
/**
*{@inheritDoc}
*/
@Override
public T newInstance(Class clazz, Object... params) {
return factory.ofClass(clazz, params);
}
/**
* {@inheritDoc}
*/
@Override
public IAtom newAtom() {
return new Atom();
}
/**
* {@inheritDoc}
*/
@Override
public IBond newBond() {
return new Bond();
}
/**
* {@inheritDoc}
*/
@Override
public IAtomContainer newAtomContainer() {
if (CDK_LEGACY_AC)
return new AtomContainer();
else
return new AtomContainer2();
}
}
