--- trunk/OOPSE/libBASS/MoleculeStamp.cpp	2003/10/28 16:03:06	828
+++ trunk/OOPSE/libBASS/MoleculeStamp.cpp	2004/04/15 16:18:26	1113
@@ -13,18 +13,22 @@ MoleculeStamp::MoleculeStamp(){
   n_bonds = 0;
   n_bends = 0;
   n_torsions = 0;
+  n_rigidbodies = 0;
+  n_integrable = 0;
 
   unhandled = NULL;
   atoms = NULL;
   bonds = NULL;
   bends = NULL;
   torsions = NULL;
+  rigidBodies = NULL;
 
   have_name = 0;
   have_atoms = 0;
   have_bonds = 0;
   have_bends = 0;
   have_torsions = 0;
+  have_rigidbodies = 0;
 
 }
 
@@ -32,7 +36,11 @@ MoleculeStamp::~MoleculeStamp(){
   int i;
   
   if( unhandled != NULL) delete unhandled;
-
+  
+  if( rigidBodies != NULL ) {
+    for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i];
+  }
+  
   if( atoms != NULL ){
     for( i=0; i<n_atoms; i++ ) delete atoms[i];
   }
@@ -74,7 +82,7 @@ char* MoleculeStamp::assignDouble( char* lhs, double r
     if( have_atoms ){
       sprintf( errMsg,
 	       "MoleculeStamp error, n_atoms already declared"
-	       "for molecule: %s\n",
+	       " for molecule: %s\n",
 	       name);
       return strdup( errMsg );
     }
@@ -127,6 +135,22 @@ char* MoleculeStamp::assignDouble( char* lhs, double r
     torsions = new TorsionStamp*[n_torsions];
     for( i=0; i<n_torsions; i++ ) torsions[i] = NULL;
   }
+
+  else if( !strcmp( lhs, "nRigidBodies" ) ){
+    n_rigidbodies = (int)rhs;
+
+    if( have_rigidbodies ){
+      sprintf( errMsg,
+	       "MoleculeStamp error, n_rigidbodies already declared for"
+	       " molecule: %s\n",
+	       name );
+      return strdup( errMsg );
+    }
+    have_rigidbodies = 1;
+    rigidBodies = new RigidBodyStamp*[n_rigidbodies];
+    for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
+  }
+
   else{
     if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
     else unhandled->add( lhs, rhs );
@@ -197,6 +221,21 @@ char*  MoleculeStamp::assignInt( char* lhs, int rhs ){
     torsions = new TorsionStamp*[n_torsions];
     for( i=0; i<n_torsions; i++ ) torsions[i] = NULL;
   }
+
+  else if( !strcmp( lhs, "nRigidBodies" ) ){
+    n_rigidbodies = rhs;
+
+    if( have_rigidbodies ){
+      sprintf( errMsg,
+	       "RigidBodyStamp error, n_rigidbodies already declared for"
+	       " molecule: %s\n",
+	       name);
+      return strdup( errMsg );
+    }
+    have_rigidbodies = 1;
+    rigidBodies = new RigidBodyStamp*[n_rigidbodies];
+    for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL;
+  }
   else{
     if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs );
     else unhandled->add( lhs, rhs );
@@ -208,16 +247,34 @@ 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 );
       return strdup( errMsg );
     }
     else return strdup("MoleculeStamp error, nAtoms not given before"
-		       "first atom declaration." );
+		       " first atom declaration." );
   }
 
+  return NULL;
+}
+
+char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, 
+                                   int rigidBodyIndex ){
+  
+  if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) 
+    rigidBodies[rigidBodyIndex] = the_rigidbody;
+  else {
+    if( have_rigidbodies ){
+      sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", 
+	       rigidBodyIndex );
+      return strdup( errMsg );
+    }
+    else return strdup("MoleculeStamp error, nRigidBodies not given before"
+		       " first rigidBody declaration." );
+  }
+  
   return NULL;
 }
 
@@ -276,14 +333,27 @@ char* MoleculeStamp::checkMe( void ){
 char* MoleculeStamp::checkMe( void ){
   
   int i;
-  short int no_atom;
+  short int no_atom, no_rigidbody;
+
+  if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name"
+                                  " was not given.\n" );
   
-  if( !have_name || !have_atoms ){
-    if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name"
-				    " was not given.\n" );
-    else return strdup( "MoleculeStamp error. Molecule contains no atoms." );
+  if( !have_atoms ){
+    return strdup( "MoleculeStamp error. Molecule contains no atoms." );
   }
   
+  no_rigidbody = 0;
+  for( i=0; i<n_rigidbodies; i++ ){
+    if( rigidBodies[i] == NULL ) no_rigidbody = 1;
+  }
+
+  if( no_rigidbody ){
+    sprintf( errMsg, 
+	     "MoleculeStamp error. Not all of the RigidBodies 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;
@@ -296,5 +366,17 @@ char* MoleculeStamp::checkMe( void ){
     return strdup( errMsg );
   }
 
+
+  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 NULL;
-}
+}