FAS/src/fasmodel.h

/**********************************************************************
*           Copyright (C) 2002-2003 by Gezelter's Group
*This program is free software; you can redistribute it and/or modify
*it under the terms of the GNU General Public License as published by
*the Free Software Foundation version 2 of the License.
*
*This program is distributed in the hope that it will be useful,
*but WITHOUT ANY WARRANTY; without even the implied warranty of
*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
*GNU General Public License for more details.
*
************************************************************************
*Author: Teng Lin               Email:  tlin@nd.edu
*Date: 08/13/2002               Version: 1.0
*
************************************************************************
*Description:
*
***********************************************************************/
#ifndef FASMOL_H
#define FASMOL_H

#include <iostream>
#include <vector>
#include <string>
#include "keylist.h"
#include "animation.h"
using namespace std;

class TFASAtom;
class TFASResidue;
class TFASBond;
class TFASMolecule;

/*******************************************************************************
  In next version,I would like to declare TFASModel as template using class
  partial specialization.So if you want to derived a class from TAnimation,( the
  reason we want to do this is that if the trajectory file is too huge, we can
  not load all the frames to memory at one time, we would like to load part of
  it,and then we can doing the job of swapping as OS by ourself) and then we
  can derive TFASmodel from the new Animation class easily.

  declaration:

  class TMyAnimation : public TAnimation
  {
    public:
      vector<TFrames *> _frames
      int _activeFrame;
      int _totalFrames;
      int _numFrames;
      void SwapFromDisk();
      void SwapToDisk();
      GetCoor(int frameIndex, int frameNum)
      {
        if (frameNum = -1)
          frameNum = _activeFrame;
        if (framNum > frameNum && frameNum <totalNum)
        {
        //here we know that the frame we want to acces is not now in memory
        //so we trigger a exception, and the exception handler will swap some
        //frames in and some out or we can just hard code here
          throw exception

        }
      }

  }

  template<class T> class TFASModel : public T
  {
    public:
      vector<TFASAtom<T> *> _atomList;

  };

  template<class T> class TFASAtom
  {
    public:
      TFASModel<T> _parent;
      GetRX(int frameNum = -1)
      {
        _parent.GetCoor(frameIndex, frameNum);
      }

  };

  so what we only need to do is

  TFASModel<TMyAnimation> fasModel;
  TFASAtom<TMyAnimation> fasAtom;
  and then build up the structure of model
  so if you want to get the coordinate of an atom,you can use below

  fasAtom.GetRX();

  Actually, we can declare the TFASModel without deriving from TAnimation, just
  delegate the operation about coordinate to TAnimation.


*******************************************************************************/
class TFASModel : public TAnimation
{
        protected:
          string _modelName;
                unsigned int _natoms;
                unsigned int _nbonds;
                unsigned int _nresidues;
                unsigned int _nmols;

                vector<TFASAtom *> _atomList;
                vector<TFASResidue *> _resList;
                vector<TFASBond *> _bondList;
                vector<TFASMolecule *> _molList;

                TNameList _atomNames;
                TNameList _atomTypes;
                TNameList _resNames;
                TNameList _resIds;
                TNameList _chainNames;
                TNameList _segNames;

        public:

                TFASModel();
                ~TFASModel();

                string GetModelName() { return _modelName;}
                void SetModelName(string modelName) { _modelName = modelName;}
                void SetModelName(char * modelName) {_modelName = modelName;}

                void FindMolecules();
};


#endif
Revision:	88
Committed:	Mon Aug 19 20:49:08 2002 UTC (21 years, 10 months ago) by tim
Content type:	text/plain
File size:	3790 byte(s)
Log Message:	* empty log message *
#	User	Rev	Content
1	tim	86	/**********************************************************************
2			* Copyright (C) 2002-2003 by Gezelter's Group
3			*This program is free software; you can redistribute it and/or modify
4			*it under the terms of the GNU General Public License as published by
5			*the Free Software Foundation version 2 of the License.
6			*
7			*This program is distributed in the hope that it will be useful,
8			*but WITHOUT ANY WARRANTY; without even the implied warranty of
9			*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10			*GNU General Public License for more details.
11			*
12			************************************************************************
13			*Author: Teng Lin Email: tlin@nd.edu
14			*Date: 08/13/2002 Version: 1.0
15			*
16			************************************************************************
17			*Description:
18			*
19			***********************************************************************/
20	tim	66	#ifndef FASMOL_H
21			#define FASMOL_H
22
23			#include <iostream>
24			#include <vector>
25			#include <string>
26	tim	86	#include "keylist.h"
27			#include "animation.h"
28	tim	66	using namespace std;
29
30			class TFASAtom;
31			class TFASResidue;
32			class TFASBond;
33			class TFASMolecule;
34
35	tim	88	/*******************************************************************************
36			In next version,I would like to declare TFASModel as template using class
37			partial specialization.So if you want to derived a class from TAnimation,( the
38			reason we want to do this is that if the trajectory file is too huge, we can
39			not load all the frames to memory at one time, we would like to load part of
40			it,and then we can doing the job of swapping as OS by ourself) and then we
41			can derive TFASmodel from the new Animation class easily.
42
43			declaration:
44
45			class TMyAnimation : public TAnimation
46			{
47			public:
48			vector<TFrames *> _frames
49			int _activeFrame;
50			int _totalFrames;
51			int _numFrames;
52			void SwapFromDisk();
53			void SwapToDisk();
54			GetCoor(int frameIndex, int frameNum)
55			{
56			if (frameNum = -1)
57			frameNum = _activeFrame;
58			if (framNum > frameNum && frameNum <totalNum)
59			{
60			//here we know that the frame we want to acces is not now in memory
61			//so we trigger a exception, and the exception handler will swap some
62			//frames in and some out or we can just hard code here
63			throw exception
64
65			}
66			}
67
68			}
69
70			template<class T> class TFASModel : public T
71			{
72			public:
73			vector<TFASAtom<T> *> _atomList;
74
75			};
76
77			template<class T> class TFASAtom
78			{
79			public:
80			TFASModel<T> _parent;
81			GetRX(int frameNum = -1)
82			{
83			_parent.GetCoor(frameIndex, frameNum);
84			}
85
86			};
87
88			so what we only need to do is
89
90			TFASModel<TMyAnimation> fasModel;
91			TFASAtom<TMyAnimation> fasAtom;
92			and then build up the structure of model
93			so if you want to get the coordinate of an atom,you can use below
94
95			fasAtom.GetRX();
96
97			Actually, we can declare the TFASModel without deriving from TAnimation, just
98			delegate the operation about coordinate to TAnimation.
99
100
101			*******************************************************************************/
102	tim	86	class TFASModel : public TAnimation
103	tim	66	{
104			protected:
105			string _modelName;
106			unsigned int _natoms;
107			unsigned int _nbonds;
108			unsigned int _nresidues;
109			unsigned int _nmols;
110	tim	88
111	tim	66	vector<TFASAtom *> _atomList;
112			vector<TFASResidue *> _resList;
113			vector<TFASBond *> _bondList;
114			vector<TFASMolecule *> _molList;
115	tim	88
116	tim	86	TNameList _atomNames;
117			TNameList _atomTypes;
118			TNameList _resNames;
119			TNameList _resIds;
120			TNameList _chainNames;
121			TNameList _segNames;
122
123	tim	66	public:
124	tim	86
125	tim	66	TFASModel();
126			~TFASModel();
127	tim	86
128	tim	66	string GetModelName() { return _modelName;}
129			void SetModelName(string modelName) { _modelName = modelName;}
130	tim	86	void SetModelName(char * modelName) {_modelName = modelName;}
131	tim	88
132	tim	66	void FindMolecules();
133			};
134
135
136			#endif