--- trunk/OOPSE/libBASS/MoleculeStamp.cpp	2004/01/26 18:52:42	981
+++ trunk/OOPSE/libBASS/MoleculeStamp.cpp	2004/06/01 21:44:54	1216
@@ -14,6 +14,8 @@ MoleculeStamp::MoleculeStamp(){
   n_bends = 0;
   n_torsions = 0;
   n_rigidbodies = 0;
+  n_cutoffgroups = 0;
+  n_integrable = 0;
 
   unhandled = NULL;
   atoms = NULL;
@@ -21,6 +23,7 @@ MoleculeStamp::MoleculeStamp(){
   bends = NULL;
   torsions = NULL;
   rigidBodies = NULL;
+  cutoffGroups = NULL;
 
   have_name = 0;
   have_atoms = 0;
@@ -28,6 +31,7 @@ MoleculeStamp::MoleculeStamp(){
   have_bends = 0;
   have_torsions = 0;
   have_rigidbodies = 0;
+  have_cutoffgroups = 0;
 
 }
 
@@ -39,23 +43,36 @@ MoleculeStamp::~MoleculeStamp(){
   if( rigidBodies != NULL ) {
     for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i];
   }
+  delete[] rigidBodies;
+
+  if( cutoffGroups != NULL ) {
+    for( i=0; i<n_cutoffgroups; i++ ) delete cutoffGroups[i];
+  }
+  delete[] cutoffGroups;
   
   if( atoms != NULL ){
     for( i=0; i<n_atoms; i++ ) delete atoms[i];
   }
+  delete[] atoms;
   
   if( bonds != NULL ){
     for( i=0; i<n_bonds; i++ ) delete bonds[i];
   }
+  delete[] bonds;
   
   if( bends != NULL ){
     for( i=0; i<n_bends; i++ ) delete bends[i];
   }
+  delete[] bends;
   
   if( torsions != NULL ){
     for( i=0; i<n_torsions; i++ ) delete torsions[i];
   }
+  delete[] torsions;
   
+
+
+
 }
 
 char* MoleculeStamp::assignString( char* lhs, char* rhs ){
@@ -150,6 +167,21 @@ char* MoleculeStamp::assignDouble( char* lhs, double r
     for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
   }
 
+  else if( !strcmp( lhs, "nCutoffGroups" ) ){
+    n_cutoffgroups = (int)rhs;
+
+    if( have_cutoffgroups ){
+      sprintf( errMsg,
+	       "MoleculeStamp error, n_cutoffgroups already declared for"
+	       " molecule: %s\n",
+	       name );
+      return strdup( errMsg );
+    }
+    have_cutoffgroups = 1;
+    cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups];
+    for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL;
+  }
+  
   else{
     if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
     else unhandled->add( lhs, rhs );
@@ -226,7 +258,7 @@ char*  MoleculeStamp::assignInt( char* lhs, int rhs ){
 
     if( have_rigidbodies ){
       sprintf( errMsg,
-	       "RigidBodyStamp error, n_rigidbodies already declared for"
+	       "MoleculeStamp error, n_rigidbodies already declared for"
 	       " molecule: %s\n",
 	       name);
       return strdup( errMsg );
@@ -235,6 +267,20 @@ char*  MoleculeStamp::assignInt( char* lhs, int rhs ){
     rigidBodies = new RigidBodyStamp*[n_rigidbodies];
     for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
   }
+  else if( !strcmp( lhs, "nCutoffGroups" ) ){
+    n_cutoffgroups = rhs;
+
+    if( have_cutoffgroups ){
+      sprintf( errMsg,
+	       "MoleculeStamp error, n_cutoffgroups already declared for"
+	       " molecule: %s\n",
+	       name);
+      return strdup( errMsg );
+    }
+    have_cutoffgroups = 1;
+    cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups];
+    for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL;
+  }
   else{
     if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
     else unhandled->add( lhs, rhs );
@@ -246,7 +292,7 @@ char* MoleculeStamp::addAtom( AtomStamp* the_atom, int
 char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){
   
   if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom;
-  else{
+  else {
     if( have_atoms ){
       sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", 
 	       atomIndex );
@@ -264,7 +310,7 @@ char* MoleculeStamp::addRigidBody( RigidBodyStamp* the
   
   if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) 
     rigidBodies[rigidBodyIndex] = the_rigidbody;
-  else{
+  else {
     if( have_rigidbodies ){
       sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", 
 	       rigidBodyIndex );
@@ -272,6 +318,24 @@ char* MoleculeStamp::addRigidBody( RigidBodyStamp* the
     }
     else return strdup("MoleculeStamp error, nRigidBodies not given before"
 		       " first rigidBody declaration." );
+  }
+  
+  return NULL;
+}
+
+char* MoleculeStamp::addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, 
+                                     int cutoffGroupIndex ){
+  
+  if( have_cutoffgroups && cutoffGroupIndex < n_cutoffgroups ) 
+    cutoffGroups[cutoffGroupIndex] = the_cutoffgroup;
+  else {
+    if( have_cutoffgroups ){
+      sprintf( errMsg, "MoleculeStamp error, %d out of nCutoffGroups range", 
+	       cutoffGroupIndex );
+      return strdup( errMsg );
+    }
+    else return strdup("MoleculeStamp error, nCutoffGroups not given before"
+		       " first CutoffGroup declaration." );
   }
   
   return NULL;
@@ -332,18 +396,13 @@ char* MoleculeStamp::checkMe( void ){
 char* MoleculeStamp::checkMe( void ){
   
   int i;
-  short int no_atom, no_rigidbody;
+  short int no_atom, no_rigidbody, no_cutoffgroup;
 
-  // Fix for Rigid Bodies!!!  Molecules may not have any atoms that 
-  // they know about.  They might have only rigid bodies (which then
-  // know about the atoms!
-  
-
   if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name"
                                   " was not given.\n" );
-
-  if( !have_rigidbodies && !have_atoms ){
-    return strdup( "MoleculeStamp error. Molecule contains no atoms or RigidBodies." );
+  
+  if( !have_atoms ){
+    return strdup( "MoleculeStamp error. Molecule contains no atoms." );
   }
   
   no_rigidbody = 0;
@@ -358,6 +417,18 @@ char* MoleculeStamp::checkMe( void ){
     return strdup( errMsg );
   }
 
+  no_cutoffgroup = 0;
+  for( i=0; i<n_cutoffgroups; i++ ){
+    if( cutoffGroups[i] == NULL ) no_cutoffgroup = 1;
+  }
+
+  if( no_cutoffgroup ){
+    sprintf( errMsg, 
+	     "MoleculeStamp error. Not all of the CutoffGroups were"
+	     " declared in molecule \"%s\".\n", name );
+    return strdup( errMsg );
+  }
+  
   no_atom = 0;
   for( i=0; i<n_atoms; i++ ){
     if( atoms[i] == NULL ) no_atom = 1;
@@ -370,21 +441,16 @@ char* MoleculeStamp::checkMe( void ){
     return strdup( errMsg );
   }
 
-  return NULL;
-}
-
-
-int MoleculeStamp::getTotAtoms() {
-  int total_atoms;
-  int i;
-
-  total_atoms = n_atoms;
-
-  if( rigidBodies != NULL ) {
-    for( i=0; i<n_rigidbodies; i++ ) 
-      total_atoms += rigidBodies[i]->getNAtoms();
+  n_integrable = n_atoms;
+  for (i = 0; i < n_rigidbodies; i++) 
+    n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object
+  
+  if (n_integrable <= 0 || n_integrable > n_atoms) {
+    sprintf( errMsg, 
+	     "MoleculeStamp error. n_integrable is either <= 0 or"
+	     " greater than n_atoms in molecule \"%s\".\n", name );
+    return strdup( errMsg );
   }
 
-  return total_atoms;
-}
-  
+  return NULL;
+}