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/********************************************************************** |
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* Copyright (C) 2002-2003 by Gezelter's Group |
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*This program is free software; you can redistribute it and/or modify |
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*it under the terms of the GNU General Public License as published by |
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*the Free Software Foundation version 2 of the License. |
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* |
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*This program is distributed in the hope that it will be useful, |
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*but WITHOUT ANY WARRANTY; without even the implied warranty of |
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*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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*GNU General Public License for more details. |
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* |
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************************************************************************ |
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*Author: Teng Lin Email: tlin@nd.edu |
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*Date: 08/13/2002 Version: 1.0 |
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* |
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************************************************************************ |
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*Description: |
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* |
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***********************************************************************/ |
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#ifndef FASMOL_H |
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#define FASMOL_H |
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#include <iostream> |
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#include <vector> |
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#include <string> |
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#include "namelist.h" |
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#include "keylist.h" |
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#include "animation.h" |
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using namespace std; |
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class TFASAtom; |
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class TFASBond; |
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class TFASMolecule; |
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class TFASModel |
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/******************************************************************************* |
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In next version,I would like to declare TFASModel as template using class |
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partial specialization.So if you want to derived a class from TAnimation,( the |
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reason we want to do this is that if the trajectory file is too huge, we can |
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not load all the frames to memory at one time, we would like to load part of |
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it,and then we can doing the job of swapping as OS by ourself) and then we |
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can derive TFASmodel from the new Animation class easily. |
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declaration: |
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class TMyAnimation : public TAnimation |
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{ |
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public: |
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vector<TFrames *> _frames |
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int _activeFrame; |
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int _totalFrames; |
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int _numFrames; |
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void SwapFromDisk(); |
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void SwapToDisk(); |
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GetCoor(int frameIndex, int frameNum) |
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{ |
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if (frameNum = -1) |
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frameNum = _activeFrame; |
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if (framNum > frameNum && frameNum <totalNum) |
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{ |
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//here we know that the frame we want to acces is not now in memory |
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//so we trigger a exception, and the exception handler will swap some |
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//frames in and some out or we can just hard code here |
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throw exception |
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} |
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} |
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} |
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template<class T> class TFASModel : public T |
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{ |
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public: |
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vector<TFASAtom<T> *> _atomList; |
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}; |
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template<class T> class TFASAtom |
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{ |
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public: |
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TFASModel<T> _parent; |
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GetRX(int frameNum = -1) |
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{ |
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_parent.GetCoor(frameIndex, frameNum); |
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} |
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}; |
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so what we only need to do is |
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TFASModel<TMyAnimation> fasModel; |
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TFASAtom<TMyAnimation> fasAtom; |
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and then build up the structure of model |
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so if you want to get the coordinate of an atom,you can use below |
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fasAtom.GetRX(); |
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Actually, we can declare the TFASModel without deriving from TAnimation, just |
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delegate the operation about coordinate to TAnimation. |
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*******************************************************************************/ |
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class TFASModel : public TAnimation |
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{ |
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protected: |
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string _modelName; |
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unsigned int _nbonds; |
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unsigned int _nresidues; |
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unsigned int _nmols; |
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vector<TFASAtom *> _atomList; |
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vector<TFASResidue *> _resList; |
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vector<TFASBond *> _bondList; |
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vector<TFASMolecule *> _molList; |
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NameList<int> _atomNames; |
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NameList<int> _atomTypes; |
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NameList<int> _resNames; |
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NameList<int> _resIds; |
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NameList<int> _chainNames; |
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NameList<int> _segNames; |
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TNameList _atomNames; |
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TNameList _atomTypes; |
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TNameList _resNames; |
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TNameList _resIds; |
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TNameList _chainNames; |
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TNameList _segNames; |
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public: |
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TFASModel(); |
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~TFASModel(); |
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string GetModelName() { return _modelName;} |
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void SetModelName(string modelName) { _modelName = modelName;} |
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void SetModelName(char * modelName) {_modelName = new string(modelName);} |
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void SetModelName(char * modelName) {_modelName = modelName;} |
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void FindMolecules(); |
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}; |
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