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[Cdk-commits] CVS: cdk/org/openscience/cdk/structgen VicinitySampler.java,1.1,1.2
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From: Christoph S. <ste...@us...> - 2002-05-23 09:48:45
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Update of /cvsroot/cdk/cdk/org/openscience/cdk/structgen
In directory usw-pr-cvs1:/tmp/cvs-serv17783/structgen
Modified Files:
VicinitySampler.java
Log Message:
Bugfixes for the VicinitySampler
Index: VicinitySampler.java
===================================================================
RCS file: /cvsroot/cdk/cdk/org/openscience/cdk/structgen/VicinitySampler.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -r1.1 -r1.2
*** VicinitySampler.java 21 May 2002 13:45:50 -0000 1.1
--- VicinitySampler.java 23 May 2002 09:48:42 -0000 1.2
***************
*** 52,55 ****
--- 52,56 ----
public boolean debug = false;
private int[] correctBondOrderSums;
+ int molCounter = 0;
/**
***************
*** 83,88 ****
if(debug) System.out.println("RandomGenerator->mutate() Start");
Vector structures = new Vector();
int nrOfAtoms = ac.getAtomCount();
- int x1 = 0, x2 = 0, y1 = 0, y2 = 0;
double a11 = 0, a12 = 0, a22 = 0, a21 = 0;
double b11 = 0, lowerborder = 0, upperborder = 0;
--- 84,89 ----
if(debug) System.out.println("RandomGenerator->mutate() Start");
Vector structures = new Vector();
+ ConnectivityChecker conCheck = new ConnectivityChecker();
int nrOfAtoms = ac.getAtomCount();
double a11 = 0, a12 = 0, a22 = 0, a21 = 0;
double b11 = 0, lowerborder = 0, upperborder = 0;
***************
*** 92,95 ****
--- 93,97 ----
double[] cmax = new double[4];
double[] cmin = new double[4];
+ AtomContainer newAc = (AtomContainer)ac.clone();
Atom ax1 = null, ax2 = null, ay1 = null, ay2 = null;
***************
*** 99,118 ****
/* We need at least two non-zero bonds in order to be successful */
int nonZeroBondsCounter = 0;
! for (x1 = 0; x1 < nrOfAtoms; x1++)
{
! for (x2 = x1 + 1; x2 < nrOfAtoms; x2++)
{
! for (y1 = x2 + 1; y1 < nrOfAtoms; y1++)
{
! for (y2 = y1 + 1; y2 < nrOfAtoms; y2++)
{
nonZeroBondsCounter = 0;
! ax1 = ac.getAtomAt(x1);
! ay1 = ac.getAtomAt(y1);
! ax2 = ac.getAtomAt(x2);
! ay2 = ac.getAtomAt(y2);
/* Get four bonds for these four atoms */
! b1 = ac.getBond(ax1, ay1);
if (b1 != null)
{
--- 101,124 ----
/* We need at least two non-zero bonds in order to be successful */
int nonZeroBondsCounter = 0;
! boolean changed = false;
! for (int x1 = 0; x1 < nrOfAtoms; x1++)
{
! for (int x2 = x1 + 1; x2 < nrOfAtoms; x2++)
{
! for (int y1 = x2 + 1; y1 < nrOfAtoms; y1++)
{
! for (int y2 = y1 + 1; y2 < nrOfAtoms; y2++)
{
+ if (changed) newAc = (AtomContainer)ac.clone();
nonZeroBondsCounter = 0;
! ax1 = newAc.getAtomAt(x1);
! ay1 = newAc.getAtomAt(y1);
! ax2 = newAc.getAtomAt(x2);
! ay2 = newAc.getAtomAt(y2);
!
!
/* Get four bonds for these four atoms */
! b1 = newAc.getBond(ax1, ay1);
if (b1 != null)
{
***************
*** 125,129 ****
}
! b2 = ac.getBond(ax1, ay2);
if (b2 != null)
{
--- 131,135 ----
}
! b2 = newAc.getBond(ax1, ay2);
if (b2 != null)
{
***************
*** 136,140 ****
}
! b3 = ac.getBond(ax2, ay1);
if (b3 != null)
{
--- 142,146 ----
}
! b3 = newAc.getBond(ax2, ay1);
if (b3 != null)
{
***************
*** 147,151 ****
}
! b4 = ac.getBond(ax2, ay2);
if (b4 != null)
{
--- 153,157 ----
}
! b4 = newAc.getBond(ax2, ay2);
if (b4 != null)
{
***************
*** 179,184 ****
b21 = a11 + a21 - b11;
b22 = a22 - a11 + b11;
! change(ac, ax1, ay1, ax2, ay2, b1, b2, b3, b4, b11, b12, b21, b22);
! structures.add(ac.clone());
}
}
--- 185,199 ----
b21 = a11 + a21 - b11;
b22 = a22 - a11 + b11;
! System.out.println("Trying atom combination : " + x1 + ":" + x2 + ":"+ y1 + ":"+ y2);
! changed = true;
! newAc = change(newAc, ax1, ay1, ax2, ay2, b1, b2, b3, b4, b11, b12, b21, b22);
! if (conCheck.isConnected(newAc))
! {
! structures.add(newAc);
! }
! else
! {
! System.out.println("not connected");
! }
}
}
***************
*** 230,239 ****
}
! private void change(AtomContainer ac, Atom ax1, Atom ay1, Atom ax2, Atom ay2, Bond b1, Bond b2, Bond b3, Bond b4, double b11, double b12, double b21, double b22)
{
if (b11 > 0)
{
if (b1 == null)
{
b1 = new Bond(ax1, ay1, b11);
ac.addBond(b1);
--- 245,269 ----
}
! private AtomContainer change(AtomContainer ac, Atom ax1, Atom ay1, Atom ax2, Atom ay2, Bond b1, Bond b2, Bond b3, Bond b4, double b11, double b12, double b21, double b22)
{
+ int x1 = -1, x2 = -1, y1 = -1, y2 = -1;
+ System.out.println("About to make modification " + molCounter);
+ molCounter ++;
+ try
+ {
+ x1 = ac.getAtomNumber(ax1);
+ x2 = ac.getAtomNumber(ax2);
+ y1 = ac.getAtomNumber(ay1);
+ y2 = ac.getAtomNumber(ay2);
+ }
+ catch(Exception exc)
+ {
+ exc.printStackTrace();
+ }
if (b11 > 0)
{
if (b1 == null)
{
+ System.out.println("no bond " + x1 + "-" + y1 + ". Adding it with order " + b11);
b1 = new Bond(ax1, ay1, b11);
ac.addBond(b1);
***************
*** 247,250 ****
--- 277,281 ----
{
ac.removeBond(b1);
+ System.out.println("removing bond " + x1 + "-" + y1);
}
***************
*** 253,256 ****
--- 284,288 ----
if (b2 == null)
{
+ System.out.println("no bond " + x1 + "-" + y2 + ". Adding it with order " + b12);
b2 = new Bond(ax1, ay2, b12);
ac.addBond(b2);
***************
*** 264,267 ****
--- 296,300 ----
{
ac.removeBond(b2);
+ System.out.println("removing bond " + x1 + "-" + y2);
}
***************
*** 270,273 ****
--- 303,307 ----
if (b3 == null)
{
+ System.out.println("no bond " + x2 + "-" + y1 + ". Adding it with order " + b21);
b3 = new Bond(ax2, ay1, b21);
ac.addBond(b3);
***************
*** 281,284 ****
--- 315,319 ----
{
ac.removeBond(b3);
+ System.out.println("removing bond " + x2 + "-" + y1);
}
***************
*** 287,290 ****
--- 322,326 ----
if (b4 == null)
{
+ System.out.println("no bond " + x2 + "-" + y2 + ". Adding it with order " + b22);
b4 = new Bond(ax2, ay2, b22);
ac.addBond(b4);
***************
*** 298,303 ****
{
ac.removeBond(b4);
}
!
}
--- 334,340 ----
{
ac.removeBond(b4);
+ System.out.println("removing bond " + x2 + "-" + y2);
}
! return ac;
}
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