--- trunk/src/selection/NameFinder.hpp	2005/02/04 05:42:49	287
+++ branches/development/src/selection/NameFinder.hpp	2013/02/20 15:39:39	1850
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 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.
@@ -37,6 +28,16 @@
  * 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 SELECTION_NAMEFINDER_HPP
 #define SELECTION_NAMEFINDER_HPP
@@ -44,37 +45,42 @@
 #include <string>
 #include <map>
 #include "brains/SimInfo.hpp"
-#include "utils/BitSet.hpp"
-namespace oopse {
+#include "utils/OpenMDBitSet.hpp"
+namespace OpenMD {
 
-class TreeNode{
-    public:
-        ~TreeNode();
-        std::string name;
-        BitSet bs;
-        std::map<std::string, TreeNode*> children;
-};
+  class TreeNode{
+  public:
+    ~TreeNode();
+    std::string name;
+    OpenMDBitSet bs;
+    std::map<std::string, TreeNode*> children;
+  };
 
-class NameFinder{
-    public:
-        NameFinder(SimInfo* info);
-        ~NameFinder();
-        bool match(const std::string& name, BitSet& bs);
+  class NameFinder{
+  public:
+    NameFinder(SimInfo* info);
+    ~NameFinder();
+    OpenMDBitSet  match(const std::string& name);
 
-    private:
-        void loadNames();
-        void matchMolecule(const std::string& molName, BitSet& bs);
-        void matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs);
-        void matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs);
+  private:
+    void loadNames();
+    void matchMolecule(const std::string& molName, OpenMDBitSet& bs);
+    void matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs);
+    void matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs);
 
-        std::vector<TreeNode*> getMatchedChildren(TreeNode* node, const std::string& name);
-        bool isMatched(const std::string& str, const std::string& wildcard);
+    void matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs);
 
-        SimInfo* info_;
-        int nStuntDouble_;
-        TreeNode* root_;
-};
+    TreeNode* createNode(TreeNode* parent, const std::string& name);
+    std::vector<TreeNode*> getMatchedChildren(TreeNode* node, const std::string& name);
+    bool isMatched(const std::string& str, const std::string& wildcard);
 
+    bool isInteger(const std::string str);
 
+    SimInfo* info_;
+    int nStuntDouble_;
+    TreeNode* root_;
+  };
+
+
 }
 #endif