[Cdk-commits] CVS: cdk/org/openscience/cdk/structgen RandomGenerator.java,1.9,1.10

[Christoph S. <ste...@us...>]

Update of /cvsroot/cdk/cdk/org/openscience/cdk/structgen
In directory usw-pr-cvs1:/tmp/cvs-serv8957/org/openscience/cdk/structgen

Modified Files:
	RandomGenerator.java 
Log Message:
Changes to the RandomStructureGenerator

Index: RandomGenerator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/org/openscience/cdk/structgen/RandomGenerator.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -r1.9 -r1.10
*** RandomGenerator.java	2001/10/10 13:01:00	1.9
--- RandomGenerator.java	2001/10/15 16:36:58	1.10
***************
*** 83,108 ****
  	public Molecule proposeStructure()
  	{
  		do
  		{
! 			trial.removeAllBonds();
! 			trial.addBonds(molecule);
  			mutate(trial);
! 			if (true)
  			{
! 			String s = "BondCounts:    ";
! 			for (int f = 0; f < trial.getAtomCount(); f++)
! 			{
! 				s += trial.getBondCount(trial.getAtomAt(f)) + " ";
! 			}
! 			System.out.println(s);
! 			s = "BondOrderSums: ";
! 			for (int f = 0; f < trial.getAtomCount(); f++)
! 			{
! 				s += trial.getBondOrderSum(trial.getAtomAt(f)) + " ";
! 			}
! 			System.out.println(s);
  			}
- 
- 
  		}
  		while(!cc.isConnected(trial));
--- 83,108 ----
  	public Molecule proposeStructure()
  	{
+ 		if(debug) System.out.println("RandomGenerator->proposeStructure() Start");
  		do
  		{
! 			//System.out.println("molecule: " + molecule);
! 			trial = (Molecule)molecule.clone();
! 			//System.out.println("trial: " + trial);
  			mutate(trial);
! 			if(debug)
  			{
! 				String s = "BondCounts:    ";
! 				for (int f = 0; f < trial.getAtomCount(); f++)
! 				{
! 					s += trial.getBondCount(trial.getAtomAt(f)) + " ";
! 				}
! 				System.out.println(s);
! 				s = "BondOrderSums: ";
! 				for (int f = 0; f < trial.getAtomCount(); f++)
! 				{
! 					s += trial.getBondOrderSum(trial.getAtomAt(f)) + " ";
! 				}
! 				System.out.println(s);
  			}
  		}
  		while(!cc.isConnected(trial));
***************
*** 135,138 ****
--- 135,139 ----
  	protected void mutate(AtomContainer ac)
  	{
+ 		if(debug) System.out.println("RandomGenerator->mutate() Start");
  		int nrOfAtoms = ac.getAtomCount();
  		int x1 = 0, x2 = 0, y1 = 0, y2 = 0;
***************
*** 159,162 ****
--- 160,164 ----
  					y1 = (int)(Math.random() * nrOfAtoms);
  					y2 = (int)(Math.random() * nrOfAtoms);
+ 					if (debug) System.out.println("RandomGenerator->mutate(): x1, x2, y1, y2: " + x1 + ", " + x2 + ", " + y1 + ", " + y2);
  				}
  				while (!(x1 != x2 && x1 != y1 && x1 != y2 && x2 != y1 && x2 != y2 && y1 != y2));
***************
*** 210,213 ****
--- 212,216 ----
  					a22 = 0;
  				}
+ 				if(debug) System.out.println("RandomGenerator->mutate()->The old bond orders: a11, a12, a21, a22: " +  + a11 + ", " + a12 + ", " + a21 + ", " + a22);
  			}while(nonZeroBondsCounter < 2);