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AtomSignature.java
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AtomSignature.java
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/* Copyright (C) 2009-2010 maclean {gilleain.torrance@gmail.com}
*
* 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.signature;
import java.util.List;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import signature.AbstractVertexSignature;
/**
* The signature for a molecule rooted at a particular atom.
*
* @cdk.module signature
* @author maclean
*
*/
@TestClass("org.openscience.cdk.signature.AtomSignatureTest")
public class AtomSignature extends AbstractVertexSignature {
/**
* The atom container to make signatures from
*/
private IAtomContainer molecule;
/**
* Create an atom signature starting at <code>atomIndex</code>.
*
* @param atomIndex the index of the atom that roots this signature
* @param molecule the molecule to create the signature from
*/
public AtomSignature(int atomIndex, IAtomContainer molecule) {
super();
this.molecule = molecule;
super.createMaximumHeight(atomIndex, molecule.getAtomCount());
}
/**
* Create an atom signature starting at <code>atomIndex</code> and with a
* maximum height of <code>h</code>.
*
* @param atomIndex the index of the atom that roots this signature
* @param height the maximum height of the signature
* @param molecule the molecule to create the signature from
*/
public AtomSignature(int atomIndex, int height, IAtomContainer molecule) {
super();
this.molecule = molecule;
super.create(atomIndex, molecule.getAtomCount(), height);
}
public AtomSignature(int atomIndex, int height,
InvariantType invariantType, IAtomContainer molecule) {
super(invariantType);
}
public int getIntLabel(int vertexIndex) {
IAtom atom = molecule.getAtom(vertexIndex);
return atom.getMassNumber();
}
/* (non-Javadoc)
* @see signature.AbstractVertexSignature#getConnected(int)
*/
@Override
public int[] getConnected(int vertexIndex) {
IAtom atom = this.molecule.getAtom(vertexIndex);
List<IAtom> connected = this.molecule.getConnectedAtomsList(atom);
int[] connectedIndices = new int[connected.size()];
int i = 0;
for (IAtom otherAtom : connected) {
connectedIndices[i++] = this.molecule.getAtomNumber(otherAtom);
}
return connectedIndices;
}
/* (non-Javadoc)
* @see signature.AbstractVertexSignature#getEdgeLabel(int, int)
*/
@Override
public String getEdgeLabel(int vertexIndex, int otherVertexIndex) {
IAtom atomA = this.molecule.getAtom(vertexIndex);
IAtom atomB = this.molecule.getAtom(otherVertexIndex);
IBond bond = this.molecule.getBond(atomA, atomB);
if (bond != null) {
switch (bond.getOrder()) {
// case SINGLE: return "-";
case SINGLE: return "";
case DOUBLE: return "=";
case TRIPLE: return "#";
case QUADRUPLE: return "$";
default: return "";
}
} else {
return "";
}
}
/* (non-Javadoc)
* @see signature.AbstractVertexSignature#getVertexSymbol(int)
*/
@Override
public String getVertexSymbol(int vertexIndex) {
return this.molecule.getAtom(vertexIndex).getSymbol();
}
}