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root/OpenMD/trunk/src/selection/NameFinder.hpp
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Comparing trunk/src/selection/NameFinder.hpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

# Line 35 | Line 35
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   #ifndef SELECTION_NAMEFINDER_HPP
43   #define SELECTION_NAMEFINDER_HPP
# Line 44 | Line 45
45   #include <string>
46   #include <map>
47   #include "brains/SimInfo.hpp"
48 < #include "utils/OpenMDBitSet.hpp"
48 > #include "selection/SelectionSet.hpp"
49   namespace OpenMD {
50  
51    class TreeNode{
52    public:
53      ~TreeNode();
54      std::string name;
55 <    OpenMDBitSet bs;
55 >    SelectionSet bs;
56      std::map<std::string, TreeNode*> children;
57    };
58  
# Line 59 | Line 60 | namespace OpenMD {
60    public:
61      NameFinder(SimInfo* info);
62      ~NameFinder();
63 <    OpenMDBitSet  match(const std::string& name);
63 >    SelectionSet  match(const std::string &name);
64  
65    private:
66      void loadNames();
67 <    void matchMolecule(const std::string& molName, OpenMDBitSet& bs);
68 <    void matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs);
69 <    void matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs);
67 >    void matchMolecule(const std::string &molName, SelectionSet &bs);
68 >    void matchStuntDouble(const std::string &molName, const std::string &sdName, SelectionSet &bs);
69 >    void matchRigidAtoms(const std::string &molName, const std::string &rbName, const std::string &rbAtomName, SelectionSet &bs);
70 >    void matchBond(const std::string &molName, const std::string &bondName,  SelectionSet &bs);
71 >    void matchBend(const std::string &molName, const std::string &bendName, SelectionSet &bs);
72 >    void matchTorsion(const std::string &molName, const std::string &torsionName, SelectionSet &bs);
73 >    void matchInversion(const std::string &molName, const std::string &inversionName, SelectionSet &bs);
74  
75 <    void matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs);
75 >    void matchInternalIndex(const std::string &name, int internalIndex, SelectionSet &bs);
76  
77 <    TreeNode* createNode(TreeNode* parent, const std::string& name);
78 <    std::vector<TreeNode*> getMatchedChildren(TreeNode* node, const std::string& name);
79 <    bool isMatched(const std::string& str, const std::string& wildcard);
77 >    TreeNode* createNode(TreeNode* parent, const std::string &name);
78 >    std::vector<TreeNode*> getAllChildren(TreeNode* node);
79 >    std::vector<TreeNode*> getMatchedChildren(TreeNode* node, const std::string &name);
80 >    bool isMatched(const std::string &str, const std::string &wildcard);
81  
82 <    bool isInteger(const std::string str);
82 >    bool isInteger(const std::string &str);
83  
84      SimInfo* info_;
85 <    int nStuntDouble_;
85 >    vector<int> nObjects_;
86      TreeNode* root_;
87    };
82 –
83 –
88   }
89   #endif

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