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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#ifndef UTILS_UTILITY_HPP
#define UTILS_UTILITY_HPP
#include <vector>
#include <math.h>
#include "config.h"
#include "utils/next_combination.hpp"

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
   * std::vector<std::string> sv;
   * std::vector<std::vector<std::string>::iterator> sic;
   * std::vector<std::string> resultString;
   * sv.push_back("H");
   * sv.push_back("C");
   * sv.push_back("N");

   * while (replaceWithWildCard(sic, sv, resultString)) {   
   *     for(std::vector<std::string>::iterator i = resultString.begin(); i != resultString.end(); ++i) {
   *         std::cout << *i << "\t";
   *     }
   *     std::cout << std::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(std::vector<std::vector<std::string>::iterator>& cont,
                           std::vector<std::string>& sequence, std::vector<std::string>& result, const std::string& wildCard = "X");
}
#endif

Revision:	1442
Committed:	Mon May 10 17:28:26 2010 UTC (14 years, 11 months ago) by gezelter
File size:	3950 byte(s)
Log Message:	Adding property set to svn entries
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42			#ifndef UTILS_UTILITY_HPP
43			#define UTILS_UTILITY_HPP
44	gezelter	2	#include <vector>
45			#include <math.h>
46	tim	963	#include "config.h"
47	gezelter	246	#include "utils/next_combination.hpp"
48
49	gezelter	1390	namespace OpenMD {
50	tim	963	inline RealType roundMe( RealType x ){
51	gezelter	507	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
52			}
53	gezelter	246
54	gezelter	507	/**
55			* @brief iteratively replace the sequence with wild cards
56			* @return true if more combination sequence is avaliable, otherwise return true
57			* @param cont iterator container, if expect the whole series of combinations, pass an empty iterator
58			* container. The user should not modify this iterator container
59			* @param sequence the whole sequence used to generate combination
60			* @param result a possible combination sequence which is set on return
61			* @param wildCard the wild card string. Its value is "X" by default
62			* @note since next_combination never returns an empty sequence, replaceWildCard will not generate
63			* one special combination, which is n identical wild cards (n is equal to the size of the passing sequence)
64			*
65			* @code
66			* std::vector<std::string> sv;
67			* std::vector<std::vector<std::string>::iterator> sic;
68			* std::vector<std::string> resultString;
69			* sv.push_back("H");
70			* sv.push_back("C");
71			* sv.push_back("N");
72	gezelter	246
73	gezelter	507	* while (replaceWithWildCard(sic, sv, resultString)) {
74			* for(std::vector<std::string>::iterator i = resultString.begin(); i != resultString.end(); ++i) {
75			* std::cout << *i << "\t";
76			* }
77			* std::cout << std::endl;
78			* }
79			* //output
80			* //H X X
81			* //X C X
82			* //X X N
83			* //H C X
84			* //H X N
85			* //X C N
86			* //H C N
87			* @endcode
88			*/
89			bool replaceWithWildCard(std::vector<std::vector<std::string>::iterator>& cont,
90			std::vector<std::string>& sequence, std::vector<std::string>& result, const std::string& wildCard = "X");
91	gezelter	246	}
92	gezelter	2	#endif
93	gezelter	246