src/brains/MoleculeCreator.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. 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
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
 /**
  * @file MoleculeCreator.hpp
  * @author tlin
  * @date 11/04/2004
  * @time 13:51am
  * @version 1.0
  */

#ifndef BRAINS_MOLECULECREATOR_HPP
#define BRAINS_MOLECULECREATOR_HPP

#include "brains/SimInfo.hpp"
#include "types/AtomStamp.hpp"
#include "types/BondStamp.hpp"
#include "types/BendStamp.hpp"
#include "types/CutoffGroupStamp.hpp"
#include "types/RigidBodyStamp.hpp"
#include "types/TorsionStamp.hpp"
#include "primitives/Molecule.hpp"
namespace oopse {

/**
 * @class MoleculeCreator MoleculeCreator.hpp "brains/MoleculeCreator.hpp"
 * @brief
 */
class MoleculeCreator {
    public:
        virtual Molecule* createMolecule(ForceField* ff, MoleculeStamp *molStamp,
            int stampId, int globalIndex,  LocalIndexManager* localIndexMan);

    protected:
        
        /** Create an atom by its stamp */
        virtual Atom* createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, 
            LocalIndexManager* localIndexMan);

        virtual RigidBody* createRigidBody(MoleculeStamp *molStamp, Molecule* mol, 
            RigidBodyStamp* rbStamp,  LocalIndexManager* localIndexMan); 

        virtual Bond* createBond(ForceField* ff, Molecule* mol, BondStamp* stamp);
        virtual Bend* createBend(ForceField* ff, Molecule* mol, BendStamp* stamp);
        virtual Torsion* createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp);
        virtual CutoffGroup* createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp);
        virtual CutoffGroup* createCutoffGroup(Molecule * mol, Atom* atom);
        virtual void createConstraintPair(Molecule* mol);     
        virtual void createConstraintElem(Molecule* mol);
};


}
#endif //BRAINS_MOLECULECREATOR_HPP
Revision:	246
Committed:	Wed Jan 12 22:41:40 2005 UTC (20 years, 9 months ago) by gezelter
File size:	3780 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	246	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file MoleculeCreator.hpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 13:51am
47			* @version 1.0
48			*/
49
50			#ifndef BRAINS_MOLECULECREATOR_HPP
51			#define BRAINS_MOLECULECREATOR_HPP
52
53			#include "brains/SimInfo.hpp"
54			#include "types/AtomStamp.hpp"
55			#include "types/BondStamp.hpp"
56			#include "types/BendStamp.hpp"
57			#include "types/CutoffGroupStamp.hpp"
58			#include "types/RigidBodyStamp.hpp"
59			#include "types/TorsionStamp.hpp"
60			#include "primitives/Molecule.hpp"
61			namespace oopse {
62
63			/**
64			* @class MoleculeCreator MoleculeCreator.hpp "brains/MoleculeCreator.hpp"
65			* @brief
66			*/
67			class MoleculeCreator {
68			public:
69			virtual Molecule* createMolecule(ForceField* ff, MoleculeStamp *molStamp,
70			int stampId, int globalIndex, LocalIndexManager* localIndexMan);
71
72			protected:
73
74			/** Create an atom by its stamp */
75			virtual Atom* createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
76			LocalIndexManager* localIndexMan);
77
78			virtual RigidBody* createRigidBody(MoleculeStamp molStamp, Molecule mol,
79			RigidBodyStamp* rbStamp, LocalIndexManager* localIndexMan);
80
81			virtual Bond* createBond(ForceField* ff, Molecule* mol, BondStamp* stamp);
82			virtual Bend* createBend(ForceField* ff, Molecule* mol, BendStamp* stamp);
83			virtual Torsion* createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp);
84			virtual CutoffGroup* createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp);
85			virtual CutoffGroup* createCutoffGroup(Molecule * mol, Atom* atom);
86			virtual void createConstraintPair(Molecule* mol);
87			virtual void createConstraintElem(Molecule* mol);
88			};
89
90
91			}
92			#endif //BRAINS_MOLECULECREATOR_HPP