src/selection/NameFinder.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, 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
#include <set>
#include <string>
#include <map>
#include "brains/SimInfo.hpp"
#include "selection/SelectionSet.hpp"
namespace OpenMD {

  class TreeNode{
  public:
    ~TreeNode();
    std::string name;
    SelectionSet bs;
    std::map<std::string, TreeNode*> children;
  };

  class NameFinder{
  public:
    NameFinder(SimInfo* info);
    ~NameFinder();
    SelectionSet  match(const std::string &name);

  private:
    void loadNames();
    void matchMolecule(const std::string &molName, SelectionSet &bs);
    void matchStuntDouble(const std::string &molName, const std::string &sdName, SelectionSet &bs);
    void matchRigidAtoms(const std::string &molName, const std::string &rbName, const std::string &rbAtomName, SelectionSet &bs);
    void matchBond(const std::string &molName, const std::string &bondName,  SelectionSet &bs);
    void matchBend(const std::string &molName, const std::string &bendName, SelectionSet &bs);
    void matchTorsion(const std::string &molName, const std::string &torsionName, SelectionSet &bs);
    void matchInversion(const std::string &molName, const std::string &inversionName, SelectionSet &bs);

    void matchInternalIndex(const std::string &name, int internalIndex, SelectionSet &bs);

    TreeNode* createNode(TreeNode* parent, const std::string &name);
    std::vector<TreeNode*> getAllChildren(TreeNode* node);
    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_;
    vector<int> nObjects_;
    TreeNode* root_;
  };
}
#endif
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 10 months ago) by gezelter
File size:	3896 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	Content
1	/*
2	* 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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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).
41	*/
42	#ifndef SELECTION_NAMEFINDER_HPP
43	#define SELECTION_NAMEFINDER_HPP
44	#include <set>
45	#include <string>
46	#include <map>
47	#include "brains/SimInfo.hpp"
48	#include "selection/SelectionSet.hpp"
49	namespace OpenMD {
50
51	class TreeNode{
52	public:
53	~TreeNode();
54	std::string name;
55	SelectionSet bs;
56	std::map<std::string, TreeNode*> children;
57	};
58
59	class NameFinder{
60	public:
61	NameFinder(SimInfo* info);
62	~NameFinder();
63	SelectionSet match(const std::string &name);
64
65	private:
66	void loadNames();
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, SelectionSet &bs);
76
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);
83
84	SimInfo* info_;
85	vector<int> nObjects_;
86	TreeNode* root_;
87	};
88	}
89	#endif