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DoubleBondStereochemistry.java
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DoubleBondStereochemistry.java
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/* Copyright (C) 2012 Egon Willighagen <egonw@users.sf.net>
*
* 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.stereo;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
import org.openscience.cdk.interfaces.IStereoElement;
import java.util.List;
import java.util.Map;
/**
* Stereochemistry specification for double bonds. See {@link IDoubleBondStereochemistry} for
* further details.
*
* @cdk.module core
* @cdk.githash
*
* @see org.openscience.cdk.interfaces.IDoubleBondStereochemistry
*/
public class DoubleBondStereochemistry
extends AbstractStereo<IBond,IBond>
implements IDoubleBondStereochemistry {
/**
* Creates a new double bond stereo chemistry. The path of length three is defined by
* <code>ligandBonds[0]</code>, <code>stereoBonds</code>, and <code>ligandBonds[1]</code>.
*/
public DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, Conformation stereo) {
this(stereoBond, ligandBonds, Conformation.toConfig(stereo));
}
public DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, int config) {
super(stereoBond, ligandBonds, CT | (CFG_MASK & config));
}
public void setBuilder(IChemObjectBuilder builder) {
super.setBuilder(builder);
}
/** {@inheritDoc} */
@Override
public IBond[] getBonds() {
return getCarriers().toArray(new IBond[0]);
}
/** {@inheritDoc} */
@Override
public IBond getStereoBond() {
return getFocus();
}
/** {@inheritDoc} */
@Override
public Conformation getStereo() {
return Conformation.toConformation(getConfigOrder());
}
@Override
public IDoubleBondStereochemistry map(Map<IAtom, IAtom> atoms,
Map<IBond, IBond> bonds) {
return (IDoubleBondStereochemistry) super.map(atoms, bonds);
}
@Override
protected IStereoElement<IBond, IBond> create(IBond focus, List<IBond> carriers,
int cfg) {
return new DoubleBondStereochemistry(focus, carriers.toArray(new IBond[2]), cfg);
}
}