--- trunk/tcProps/tcProps.c	2004/02/27 20:39:17	1072
+++ trunk/tcProps/tcProps.c	2004/02/28 16:45:57	1073
@@ -11,7 +11,7 @@
 #include "scdCorr.h"
 #include "directorHead.h"
 #include "directorWhole.h"
-#inlcude "rmsd.h"
+#include "rmsd.h"
 
 
 #define VERSION_MAJOR 0
@@ -48,7 +48,8 @@ int main( int argC, char *argV[] ){
   int scdCorr;
   double startTime;
   double maxLength;
-  int directorHead, directorWhole;
+  int directorHead, directorWhole, doRMSD;
+  enum atomNames rmsdType;
 
   // system initialization
   
@@ -68,6 +69,7 @@ int main( int argC, char *argV[] ){
   startTime = 0.0;
   directorHead = 0;
   directorWhole = 0;
+  doRMSD = 0;
   
 
   // parse the command line
@@ -84,27 +86,31 @@ int main( int argC, char *argV[] ){
 
 	// parse long word options
 	
-	if( !strcmp( argV[i], "--gofr" ) ){
+	if( !strcmp( argV[i], "--rmsd" ) ){
 
+	  doRMSD = 1;
 	  i++;
 	  if( i>=argC ){
 	    fprintf( stderr,
 		     "\n"
-		     "not enough arguments for --gofr\n");
+		     "not enough arguments for --rmsd\n");
 	    usage();
 	    exit(0);
 	  }	  
 	  pair1 = argV[i];
 
-	  i++;
-	  if( i>=argC ){
-	    fprintf( stderr,
-		     "\n"
-		     "not enough arguments for --gofr\n");
-	    usage();
+	  if( !strcmp(pair1, "HEAD") )    rmsdType = HEAD;
+	  else if( !strcmp(pair1, "CH") ) rmsdType = CH;
+	  else if( !strcmp(pair1, "CH2") )rmsdType = CH2;
+	  else if( !strcmp(pair1, "CH3") )rmsdType = CH3;
+	  else if( !strcmp(pair1, "SSD") )rmsdType = SSD;
+	  else if( !strcmp(pair1, "COM") )rmsdType = COM;
+	  else{
+	    fprintf( stderr,
+		     "Unrecognized rmsd atom type \"%s\"\n",
+		     pair1 );
 	    exit(0);
-	  }	  
-	  pair2 = argV[i];
+	  }
 
 	}
 
@@ -478,6 +484,15 @@ int main( int argC, char *argV[] ){
     fflush( stdout );
     
     calcDirWholeCorr( startTime, atoms, outPrefix );
+  }
+
+  if(doRMSD){
+
+    fprintf ( stdout,
+	      "Calculating the RMSD\n" );
+    fflush( stdout );
+    
+    rmsd( rmsdType, startTime, outPrefix );
   }
   
 
@@ -509,7 +524,7 @@ void usage(){
 		"\n"
 		"   long:\n"
 		"   -----\n"
-		"   --gofr <atom1> <atom2>         g(r) for atom1 and atom2\n"
+		"   --rmsd <atom1>                 rmsd for atom1\n"
 		"   --gofrTheta <atom1> <atom2>    g(r, theta) for atom1 and atom2\n"
 		"   --gofrOmega <atom1> <atom2>    g(r, omega) for atom1 and atom2\n"
 		"   --version                      displays the version number\n"