src/utils/Utility.hpp

/*
 * 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, 234107 (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;
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

Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	3998 byte(s)
Log Message:	Fixed a widespread typo in the license
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifndef UTILS_UTILITY_HPP
44	#define UTILS_UTILITY_HPP
45	#include <vector>
46	#include <math.h>
47	#include "config.h"
48	#include "utils/next_combination.hpp"
49
50	using namespace std;
51	namespace OpenMD {
52	inline RealType roundMe( RealType x ){
53	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
54	}
55
56	/**
57	* @brief iteratively replace the sequence with wild cards
58	* @return true if more combination sequence is avaliable, otherwise
59	* return true
60	* @param cont iterator container, if expect the whole series of
61	* combinations, pass an empty iterator container. The user should
62	* not modify this iterator container
63	* @param sequence the whole sequence used to generate combination
64	* @param result a possible combination sequence which is set on return
65	* @param wildCard the wild card string. Its value is "X" by default
66	* @note since next_combination never returns an empty sequence,
67	* replaceWildCard will not generate one special combination, which
68	* is n identical wild cards (n is equal to the size of the passing
69	* sequence)
70	*
71	* @code
72	* vector<string> sv;
73	* vector<vector<string>::iterator> sic;
74	* vector<string> resultString;
75	* sv.push_back("H");
76	* sv.push_back("C");
77	* sv.push_back("N");
78
79	* while (replaceWithWildCard(sic, sv, resultString)) {
80	* for(vector<string>::iterator i = resultString.begin();
81	* i != resultString.end(); ++i) {
82	* cout << *i << "\t";
83	* }
84	* cout << endl;
85	* }
86	* //output
87	* //H X X
88	* //X C X
89	* //X X N
90	* //H C X
91	* //H X N
92	* //X C N
93	* //H C N
94	* @endcode
95	*/
96	bool replaceWithWildCard(vector<vector<string>::iterator>& cont,
97	vector<string>& sequence, vector<string>& result,
98	const string& wildCard = "X");
99	}
100	#endif
101