/* $Id$
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*
* Copyright (C) 1997-2007 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.
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package org.openscience.cdk.structgen;
import java.util.Random;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.SaturationChecker;
import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* Randomly generates a single, connected, correctly bonded structure for
* a given molecular formula.
* To see it working run the graphical
* test org.openscience.cdk.test.SingleStructureRandomGeneratorTest
* and add more structures to the panel using the "More" button.
* In order to use this class, use MFAnalyser to get an AtomContainer from
* a molecular formula string.
*
* <p>Assign hydrogen counts to each heavy atom. The hydrogens should not be
* in the atom pool but should be assigned implicitly to the heavy atoms in
* order to reduce computational cost.
* Assign this AtomContainer to the
* SingleStructureRandomGenerator and retrieve a randomly generated, but correctly bonded
* structure by using the generate() method. You can then repeatedly call
* the generate() method in order to retrieve further structures.
*
* <p>Agenda:
* <ul>
* <li>add a method for randomly adding hydrogens to the atoms
* <li>add a seed for random generator for reproducability
* </ul>
*
* @author steinbeck
* @cdk.created 2001-09-04
* @cdk.module structgen
* @cdk.githash
*/
public class SingleStructureRandomGenerator {
ILoggingTool logger =
LoggingToolFactory.createLoggingTool(SingleStructureRandomGenerator.class);
IAtomContainer atomContainer;
SaturationChecker satCheck;
Random random = null;
/**
* Constructor for the SingleStructureRandomGenerator object.
*/
public SingleStructureRandomGenerator(long seed) throws java.lang.Exception
{
satCheck = new SaturationChecker();
random = new Random(seed);
}
/**
* Constructor for the SingleStructureRandomGenerator object.
*/
public SingleStructureRandomGenerator() throws java.lang.Exception
{
this((long)11000);
}
/**
* Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.
*
* @param ac The new AtomContainer value
*/
public void setAtomContainer(IAtomContainer ac)
{
this.atomContainer = ac;
}
/**
* Generates a random structure based on the atoms in the given IAtomContainer.
*/
public IMolecule generate() throws CDKException
{
boolean structureFound = false;
boolean bondFormed;
double order;
double max, cmax1, cmax2;
int iteration = 0;
IAtom partner;
IAtom atom;
do
{
iteration++;
atomContainer.removeAllElectronContainers();
do
{
bondFormed = false;
for (int f = 0; f < atomContainer.getAtomCount(); f++)
{
atom = atomContainer.getAtom(f);
if (!satCheck.isSaturated(atom, atomContainer))
{
partner = getAnotherUnsaturatedNode(atom);
if (partner != null)
{
cmax1 = satCheck.getCurrentMaxBondOrder(atom, atomContainer);
cmax2 = satCheck.getCurrentMaxBondOrder(partner, atomContainer);
max = Math.min(cmax1, cmax2);
order = Math.min(Math.max(1.0, random.nextInt((int)Math.round(max))), 3.0);
logger.debug("Forming bond of order ", order);
atomContainer.addBond(
atomContainer.getBuilder().newBond(
atom, partner, BondManipulator.createBondOrder(order)
)
);
bondFormed = true;
}
}
}
} while (bondFormed);
if (ConnectivityChecker.isConnected(atomContainer)
&& satCheck.allSaturated(atomContainer))
{
structureFound = true;
}
} while (!structureFound && iteration < 20);
logger.debug("Structure found after #iterations: ", iteration);
return atomContainer.getBuilder().newMolecule(atomContainer);
}
/**
* Gets the AnotherUnsaturatedNode attribute of the SingleStructureRandomGenerator object.
*
* @return The AnotherUnsaturatedNode value
*/
private IAtom getAnotherUnsaturatedNode(IAtom exclusionAtom) throws CDKException
{
IAtom atom;
int next = random.nextInt(atomContainer.getAtomCount());
for (int f = next; f < atomContainer.getAtomCount(); f++)
{
atom = atomContainer.getAtom(f);
if (!satCheck.isSaturated(atom, atomContainer)
&& exclusionAtom != atom
&& !atomContainer.getConnectedAtomsList(exclusionAtom).contains(atom))
{
return atom;
}
}
for (int f = 0; f < next; f++)
{
atom = atomContainer.getAtom(f);
if (!satCheck.isSaturated(atom, atomContainer)
&& exclusionAtom != atom
&& !atomContainer.getConnectedAtomsList(exclusionAtom).contains(atom))
{
return atom;
}
}
return null;
}
}