| 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). |
| 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 |
| 47 |
|
#include "config.h" |
| 48 |
|
#include "utils/next_combination.hpp" |
| 49 |
|
|
| 50 |
+ |
using namespace std; |
| 51 |
|
namespace OpenMD { |
| 52 |
< |
inline RealType roundMe( RealType x ){ |
| 52 |
> |
inline RealType roundMe( const 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 return true |
| 59 |
< |
* @param cont iterator container, if expect the whole series of combinations, pass an empty iterator |
| 60 |
< |
* container. The user should not modify this iterator container |
| 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, replaceWildCard will not generate |
| 67 |
< |
* one special combination, which is n identical wild cards (n is equal to the size of the passing sequence) |
| 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 |
< |
* std::vector<std::string> sv; |
| 73 |
< |
* std::vector<std::vector<std::string>::iterator> sic; |
| 74 |
< |
* std::vector<std::string> resultString; |
| 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(std::vector<std::string>::iterator i = resultString.begin(); i != resultString.end(); ++i) { |
| 81 |
< |
* std::cout << *i << "\t"; |
| 80 |
> |
* for(vector<string>::iterator i = resultString.begin(); |
| 81 |
> |
* i != resultString.end(); ++i) { |
| 82 |
> |
* cout << *i << "\t"; |
| 83 |
|
* } |
| 84 |
< |
* std::cout << std::endl; |
| 84 |
> |
* cout << endl; |
| 85 |
|
* } |
| 86 |
|
* //output |
| 87 |
|
* //H X X |
| 93 |
|
* //H C N |
| 94 |
|
* @endcode |
| 95 |
|
*/ |
| 96 |
< |
bool replaceWithWildCard(std::vector<std::vector<std::string>::iterator>& cont, |
| 97 |
< |
std::vector<std::string>& sequence, std::vector<std::string>& result, const std::string& wildCard = "X"); |
| 96 |
> |
bool replaceWithWildCard(vector<vector<string>::iterator>& cont, |
| 97 |
> |
vector<string>& sequence, vector<string>& result, |
| 98 |
> |
const string& wildCard = "X"); |
| 99 |
|
} |
| 100 |
|
#endif |
| 101 |
|
|
