| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
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* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* 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). |
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*/ |
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|
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|
#ifndef UTILS_UTILITY_HPP |
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#include "config.h" |
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#include "utils/next_combination.hpp" |
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|
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< |
namespace oopse { |
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> |
using namespace std; |
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> |
namespace OpenMD { |
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inline RealType roundMe( RealType x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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|
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/** |
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* @brief iteratively replace the sequence with wild cards |
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* @return true if more combination sequence is avaliable, otherwise return true |
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< |
* @param cont iterator container, if expect the whole series of combinations, pass an empty iterator |
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< |
* container. The user should not modify this iterator container |
| 58 |
> |
* @return true if more combination sequence is avaliable, otherwise |
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> |
* return true |
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> |
* @param cont iterator container, if expect the whole series of |
| 61 |
> |
* combinations, pass an empty iterator container. The user should |
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> |
* not modify this iterator container |
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|
* @param sequence the whole sequence used to generate combination |
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* @param result a possible combination sequence which is set on return |
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* @param wildCard the wild card string. Its value is "X" by default |
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< |
* @note since next_combination never returns an empty sequence, replaceWildCard will not generate |
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< |
* 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 |
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> |
* is n identical wild cards (n is equal to the size of the passing |
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> |
* sequence) |
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|
* |
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|
* @code |
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* std::vector<std::string> sv; |
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* std::vector<std::vector<std::string>::iterator> sic; |
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* std::vector<std::string> resultString; |
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> |
* vector<string> sv; |
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> |
* vector<vector<string>::iterator> sic; |
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> |
* vector<string> resultString; |
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* sv.push_back("H"); |
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* sv.push_back("C"); |
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* sv.push_back("N"); |
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|
|
| 79 |
|
* while (replaceWithWildCard(sic, sv, resultString)) { |
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< |
* for(std::vector<std::string>::iterator i = resultString.begin(); i != resultString.end(); ++i) { |
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< |
* std::cout << *i << "\t"; |
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> |
* for(vector<string>::iterator i = resultString.begin(); |
| 81 |
> |
* i != resultString.end(); ++i) { |
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> |
* cout << *i << "\t"; |
| 83 |
|
* } |
| 84 |
< |
* std::cout << std::endl; |
| 84 |
> |
* cout << endl; |
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* } |
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* //output |
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* //H X X |
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* //H C N |
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* @endcode |
| 95 |
|
*/ |
| 96 |
< |
bool replaceWithWildCard(std::vector<std::vector<std::string>::iterator>& cont, |
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< |
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 |
|
} |
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|
#endif |
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|
