org.openscience.cdk.ringsearch.RingPartitioner Maven / Gradle / Ivy
/* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
*
* 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.
* 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.ringsearch;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;
import java.util.ArrayList;
import java.util.List;
/**
* Partitions a RingSet into RingSets of connected rings. Rings which share an
* Atom, a Bond or three or more atoms with at least on other ring in the
* RingSet are considered connected.
*
*
* @cdk.module standard
* @cdk.githash
*/
public class RingPartitioner {
/**
* Debugging on/off
*/
public final static boolean debug = false;
// minimum details
/**
* Partitions a RingSet into RingSets of connected rings. Rings which share
* an Atom, a Bond or three or more atoms with at least on other ring in
* the RingSet are considered connected. Thus molecules such as azulene and
* indole will return a List with 1 element.
*
* Note that an isolated ring is considered to be self-connect. As a result
* a molecule such as biphenyl will result in a 2-element List being returned (each
* element corresponding to a phenyl ring).
*
*@param ringSet The RingSet to be partitioned
*@return A {@link List} of connected RingSets
*/
public static List partitionRings(IRingSet ringSet) {
List ringSets = new ArrayList();
if (ringSet.getAtomContainerCount() == 0) return ringSets;
IRing ring = (IRing) ringSet.getAtomContainer(0);
if (ring == null) return ringSets;
IRingSet rs = ring.getBuilder().newInstance(IRingSet.class);
for (int f = 0; f < ringSet.getAtomContainerCount(); f++) {
rs.addAtomContainer(ringSet.getAtomContainer(f));
}
do {
ring = (IRing) rs.getAtomContainer(0);
IRingSet newRs = ring.getBuilder().newInstance(IRingSet.class);
newRs.addAtomContainer(ring);
ringSets.add(walkRingSystem(rs, ring, newRs));
} while (rs.getAtomContainerCount() > 0);
return ringSets;
}
/**
* Converts a RingSet to an AtomContainer.
*
*@param ringSet The RingSet to be converted.
*@return The AtomContainer containing the bonds and atoms of the ringSet.
*/
public static IAtomContainer convertToAtomContainer(IRingSet ringSet) {
IRing ring = (IRing) ringSet.getAtomContainer(0);
if (ring == null) return null;
IAtomContainer ac = ring.getBuilder().newInstance(IAtomContainer.class);
for (int i = 0; i < ringSet.getAtomContainerCount(); i++) {
ring = (IRing) ringSet.getAtomContainer(i);
for (int r = 0; r < ring.getBondCount(); r++) {
IBond bond = ring.getBond(r);
if (!ac.contains(bond)) {
for (int j = 0; j < bond.getAtomCount(); j++) {
ac.addAtom(bond.getAtom(j));
}
ac.addBond(bond);
}
}
}
return ac;
}
/**
* Perform a walk in the given RingSet, starting at a given Ring and
* recursively searching for other Rings connected to this ring. By doing
* this it finds all rings in the RingSet connected to the start ring,
* putting them in newRs, and removing them from rs.
*
*@param rs The RingSet to be searched
*@param ring The ring to start with
*@param newRs The RingSet containing all Rings connected to ring
*@return newRs The RingSet containing all Rings connected to ring
*/
private static IRingSet walkRingSystem(IRingSet rs, IRing ring, IRingSet newRs) {
IRing tempRing;
IRingSet tempRings = rs.getConnectedRings(ring);
// logger.debug("walkRingSystem -> tempRings.size(): " + tempRings.size());
rs.removeAtomContainer(ring);
for (IAtomContainer container : tempRings.atomContainers()) {
tempRing = (IRing) container;
if (!newRs.contains(tempRing)) {
newRs.addAtomContainer(tempRing);
newRs.add(walkRingSystem(rs, tempRing, newRs));
}
}
return newRs;
}
}