--- trunk/src/utils/Utility.hpp	2004/09/24 04:16:43	2
+++ branches/development/src/utils/Utility.hpp	2011/11/22 20:38:56	1665
@@ -1,8 +1,101 @@
-#ifndef _UTILITY_H_
-#define _UTILITY_H_
+/*
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ *
+ * The University of Notre Dame grants you ("Licensee") a
+ * non-exclusive, royalty free, license to use, modify and
+ * redistribute this software in source and binary code form, provided
+ * that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded.  The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * arising out of the use of or inability to use software, even if the
+ * University of Notre Dame has been advised of the possibility of
+ * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
+ */
+ 
+#ifndef UTILS_UTILITY_HPP
+#define UTILS_UTILITY_HPP
 #include <vector>
 #include <math.h>
+#include "config.h"
+#include "utils/next_combination.hpp"
+
 using namespace std;
-double dotProduct(vector<double>& v1, vector<double>& v2);
-double norm2(vector<double>& x); 
+namespace OpenMD {
+  inline RealType roundMe( RealType x ){
+    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
+  }
+
+  /**
+   * @brief iteratively replace the sequence with wild cards
+   * @return true if more combination sequence is avaliable, otherwise
+   * return true
+   * @param cont iterator container, if expect the whole series of
+   * combinations, pass an empty iterator container. The user should
+   * not modify this iterator container
+   * @param sequence the whole sequence used to generate combination
+   * @param result a possible combination sequence which is set on return
+   * @param wildCard the wild card string. Its value is "X" by default
+   * @note since next_combination never returns an empty sequence,
+   * replaceWildCard will not generate one special combination, which
+   * is n identical wild cards (n is equal to the size of the passing
+   * sequence)
+   * 
+   * @code
+   * vector<string> sv;
+   * vector<vector<string>::iterator> sic;
+   * vector<string> resultString;
+   * sv.push_back("H");
+   * sv.push_back("C");
+   * sv.push_back("N");
+
+   * while (replaceWithWildCard(sic, sv, resultString)) {   
+   *     for(vector<string>::iterator i = resultString.begin(); 
+   *          i != resultString.end(); ++i) {
+   *         cout << *i << "\t";
+   *     }
+   *     cout << endl;
+   * }
+   * //output
+   * //H X X
+   * //X C X
+   * //X X N
+   * //H C X
+   * //H X N
+   * //X C N
+   * //H C N
+   * @endcode
+   */
+  bool replaceWithWildCard(vector<vector<string>::iterator>& cont,
+			   vector<string>& sequence, vector<string>& result, 
+                           const string& wildCard = "X");
+}
 #endif
+