--- trunk/SHAPES/RigidBody.cpp	2004/06/21 15:54:27	1283
+++ trunk/SHAPES/RigidBody.cpp	2004/06/23 23:19:43	1292
@@ -48,8 +48,6 @@ void RigidBody::setEuler( double phi, double theta, do
     A[2][1] = -cos(phi) * sin(theta);
     A[2][2] = cos(theta);
 
-    printf("A[2][x] = %lf\t%lf\t%lf\n", A[2][0], A[2][1], A[2][2]);
-
 }
 
 void RigidBody::getQ( double q[4] ){
@@ -320,28 +318,27 @@ void RigidBody::calcRefCoords( ) {
     pAxisMat[i][0] = sU[i][maxAxis];
   }
     
+  
   //calculate the proper rotation matrix
   transposeMat3(pAxisMat, pAxisRotMat);
   
   
-  for (i=0; i<myAtoms.size(); i++){
-    apos = refCoords[i];
-    printf("%f\t%f\t%f\n",apos[0],apos[1],apos[2]);
-  }
-    
   //rotate the rigid body to the principle axis frame
   for (i = 0; i < myAtoms.size(); i++) {
     matVecMul3(pAxisRotMat, refCoords[i].vec, refCoords[i].vec);
     myAtoms[i]->setPos(refCoords[i].vec);
   }
-   
-  for (i=0; i<myAtoms.size(); i++){
-    apos = refCoords[i];
-    printf("%f\t%f\t%f\n",apos[0],apos[1],apos[2]);
-  }
   
   identityMat3(iMat);
   setA(iMat);
+  
+  //and resort the moments of intertia to match the new orientation
+  for (i=0; i<3; i++)
+    if (evals[i]<momIntTol)
+      evals[i] = 0.0;
+  I[0][0] = evals[maxAxis];
+  I[1][1] = evals[midAxis];
+  I[2][2] = evals[pAxis];
 }
 
 void RigidBody::doEulerToRotMat(double euler[3], double myA[3][3] ){
@@ -548,3 +545,9 @@ double RigidBody::getAtomEps(int index){
   return myAtoms[index]->getEps();
   
 }
+
+char *RigidBody::getAtomBase(int index){
+  
+  return myAtoms[index]->getBase();
+  
+}