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added working implementations for PartialFilledStructureMerger and Cr…
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…ossoverMachine
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@egonw
Stefan Kuhn authored and egonw committed Feb 27, 2010
1 parent 6441b75 commit 089103e
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Showing 3 changed files with 230 additions and 223 deletions.
165 changes: 75 additions & 90 deletions src/main/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java
View file
Expand Up @@ -25,37 +25,21 @@
package org.openscience.cdk.structgen.stochastic;

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.IAtomContainerSet;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.SaturationChecker;
import org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator;
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.
*
* Randomly generates a single, connected, correctly bonded structure from
* a number of fragments.
* <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.
*
* <p>Assign this AtomContainer to the
* PartialFilledStructureMerger 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
Expand All @@ -67,110 +51,111 @@ public class PartialFilledStructureMerger {
private ILoggingTool logger =
LoggingToolFactory.createLoggingTool(PartialFilledStructureMerger.class);

IAtomContainer atomContainer;
SaturationChecker satCheck;

/**
* Constructor for the PartialFilledStructureMerger object.
*/
public PartialFilledStructureMerger() throws java.lang.Exception
public PartialFilledStructureMerger()
{
satCheck = new SaturationChecker();
}


/**
* Sets the AtomContainer attribute of the PartialFilledStructureMerger object
*
* @param gc The new AtomContainer value
* Randomly generates a single, connected, correctly bonded structure from
* a number of fragments.
*
* @param atomContainers The fragments to generate for. IMPORTANT: The AtomContainers in the set must be connected.
* If an AtomContainer is disconnected, the generated structure is not guaranteed to be connected.
* @return
* @throws CDKException
*/
public void setAtomContainer(IAtomContainer gc)
{
this.atomContainer = gc;
}

public IAtomContainer getAtomContainer()
{
return this.atomContainer;
}

public IAtomContainer generate() throws CDKException
public IAtomContainerSet generate(IAtomContainerSet atomContainers) throws CDKException
{
boolean structureFound = false;
boolean bondFormed;
double order;
double max, cmax1, cmax2;
int iteration = 0;
IAtom partner;
IAtom atom;
IAtomContainer backup = atomContainer.getBuilder().newAtomContainer(atomContainer);
boolean structureFound = false;
do
{
iteration++;

atomContainer = backup;
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)
boolean bondFormed;
do{
bondFormed=false;
for(IAtomContainer ac : atomContainers.atomContainers()){
for(IAtom atom : ac.atoms()){
if (!satCheck.isSaturated(atom, ac))
{
cmax1 = satCheck.getCurrentMaxBondOrder(atom, atomContainer);
cmax2 = satCheck.getCurrentMaxBondOrder(partner, atomContainer);
max = Math.min(cmax1, cmax2);
order = Math.min(Math.max(1.0, (double)Math.round(Math.random() * max)), 3.0);
logger.debug("cmax1, cmax2, max, order: " + cmax1 + ", " + cmax2 + ", " + max + ", " + order);

atomContainer.addBond(
atomContainer.getBuilder().newBond(
atom, partner, BondManipulator.createBondOrder(order)
)
);
bondFormed = true;
}
}
IAtom partner = getAnotherUnsaturatedNode(atom, atomContainers);
if (partner != null)
{
IAtomContainer toadd = AtomContainerSetManipulator.getRelevantAtomContainer(atomContainers, partner);
double cmax1 = satCheck.getCurrentMaxBondOrder(atom, ac);
double cmax2 = satCheck.getCurrentMaxBondOrder(partner, toadd);
double max = Math.min(cmax1, cmax2);
double order = Math.min(Math.max(1.0, max), 3.0);//(double)Math.round(Math.random() * max)
logger.debug("cmax1, cmax2, max, order: " + cmax1 + ", " + cmax2 + ", " + max + ", " + order);
if(toadd!=ac){
atomContainers.removeAtomContainer(toadd);
ac.add(toadd);
}
ac.addBond(
ac.getBuilder().newBond(
atom, partner, BondManipulator.createBondOrder(order)
)
);
bondFormed = true;
}
}
}
}
} while (bondFormed);
if (ConnectivityChecker.isConnected(atomContainer) && satCheck.allSaturated(atomContainer))
}while(bondFormed);
if (atomContainers.getAtomContainerCount()==1 && satCheck.allSaturated(atomContainers.getAtomContainer(0)))
{
structureFound = true;
}
} while (!structureFound && iteration < 300);
System.out.println("Structure found after " + iteration + " iterations.");
return atomContainer;
} while (!structureFound && iteration < 5);
if (atomContainers.getAtomContainerCount()==1 && satCheck.allSaturated(atomContainers.getAtomContainer(0)))
{
structureFound = true;
}
if(!structureFound)
throw new CDKException("Could not combine the fragments to combine a valid, satured structure");
return atomContainers;
}


/**
* Gets the AnotherUnsaturatedNode attribute of the PartialFilledStructureMerger object
* Gets a randomly selected unsaturated atom from the set. If there are any, it will be from another
* container than exclusionAtom.
*
* @return The AnotherUnsaturatedNode value
* @return The unsaturated atom.
*/
private IAtom getAnotherUnsaturatedNode(IAtom exclusionAtom) throws CDKException
private IAtom getAnotherUnsaturatedNode(IAtom exclusionAtom, IAtomContainerSet atomContainers) throws CDKException
{
IAtom atom;
int next = (int) (Math.random() * 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(IAtomContainer ac : atomContainers.atomContainers()){
if(!ac.contains(exclusionAtom)){
int next = 0;//(int) (Math.random() * ac.getAtomCount());
for (int f = next; f < ac.getAtomCount(); f++)
{
atom = ac.getAtom(f);
if (!satCheck.isSaturated(atom, ac) && exclusionAtom != atom && !ac.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))
for(IAtomContainer ac : atomContainers.atomContainers()){
int next = ac.getAtomCount();//(int) (Math.random() * ac.getAtomCount());
for (int f = 0; f < next; f++)
{
return atom;
atom = ac.getAtom(f);
if (!satCheck.isSaturated(atom, ac) && exclusionAtom != atom && !ac.getConnectedAtomsList(exclusionAtom).contains(atom))
{
return atom;
}
}
}
return null;
Expand Down
20 changes: 10 additions & 10 deletions src/main/org/openscience/cdk/structgen/stochastic/operator/ChemGraph.java
View file
Expand Up @@ -47,7 +47,7 @@ public class ChemGraph
/*Flag: true if atom visited during a traversal*/
protected boolean[] visited;
/*Depth first traversal of the graph*/
protected List subGraph;
protected List<Integer> subGraph;

public ChemGraph(IAtomContainer chrom)
{
Expand All @@ -57,12 +57,12 @@ public ChemGraph(IAtomContainer chrom)
contab = ConnectionMatrix.getMatrix(chrom);
}

public List pickDFgraph()
public List<Integer> pickDFgraph()
{
//depth first search from a randomly selected atom

travIndex = 0;
subGraph = new ArrayList();
subGraph = new ArrayList<Integer>();
visited = new boolean[dim];
for (int atom = 0; atom < dim; atom++) visited[atom] = false;
int seedAtom = RandomNumbersTool.randomInt(0,dim-1);
Expand All @@ -81,7 +81,7 @@ private void recursiveDFT(int atom)

// for (int nextAtom = 0; nextAtom < dim; nextAtom++) //not generalized
// if (contab[atom][nextAtom] != 0) recursiveDFT(nextAtom);
List adjSet = new ArrayList();
List<Integer> adjSet = new ArrayList<Integer>();
for (int nextAtom = 0; nextAtom < dim; nextAtom++)
{
if ((int)contab[atom][nextAtom] != 0)
Expand All @@ -99,17 +99,17 @@ private void recursiveDFT(int atom)
}
}

public List pickBFgraph()
public List<Integer> pickBFgraph()
{
//breadth first search from a randomly selected atom

travIndex = 0;
subGraph = new ArrayList();
subGraph = new ArrayList<Integer>();
visited = new boolean[dim];
for (int atom = 0; atom < dim; atom++) visited[atom] = false;
int seedAtom = RandomNumbersTool.randomInt(0,dim-1);

List atomQueue = new ArrayList();
List<Integer> atomQueue = new ArrayList<Integer>();
atomQueue.add(Integer.valueOf(seedAtom));
visited[seedAtom] = true;

Expand All @@ -120,7 +120,7 @@ public List pickBFgraph()
atomQueue.remove(0);
travIndex++;

List adjSet = new ArrayList();
List<Integer> adjSet = new ArrayList<Integer>();
for (int nextAtom = 0; nextAtom < dim; nextAtom++)
{
if (((int)contab[foreAtom][nextAtom] != 0)&&(!visited[nextAtom]))
Expand All @@ -140,12 +140,12 @@ public List pickBFgraph()
return subGraph;
}

public List getSubgraph()
public List<Integer> getSubgraph()
{
return subGraph;
}

public void setSubgraph(List subgraph)
public void setSubgraph(List<Integer> subgraph)
{
subGraph = subgraph;
}
Expand Down

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