OOPSE/libmdtools/Molecule.hpp

#ifndef _MOLECULE_H_
#define _MOLECULE_H_

#include "Atom.hpp"
#include "SRI.hpp"
#include "MoleculeStamp.hpp"

typedef struct{
  
  int stampID;   // the ID in the BASS component stamp array
  int nAtoms;    // the number of atoms in the molecule
  int nBonds;    // ... .. ..  . .bonds .. .. . . . . 
  int nBends;    // . . . . .. . .bends . . . . .. . 
  int nTorsions  // .. . . .. . . torsions . . .. . . 
  int nOriented; // .. . . . .. . oreineted atoms . . . 
  
  
  Atom** myAtoms;      // the array of atoms
  Exclude** myExcludes;// the array of Excluded pairs 
  Bond** myBonds;      // arrays of all the short range interactions
  Bend** myBends;
  Torsion** myTorsions;


} molInit;

class Molecule{

public:
  
  Molecule( void );
  ~Molecule( void );

  void initialize( molInit &theInit );

  int   getNMembers( void )  { return nMembers; }
  int   getStartAtom( void ) { return startAtom; }
  int   getEndAtom( void )   { return endAtom; }
  int   getStampID( void )   { return stampID; }
  
  void   setNMembers( int info )  { nMembers = info; }
  void   setStartAtom( int info ) { startAtom = info; }
  void   setEndAtom( int info )   { endAtom = info; }
  void   setStampID( int info )   { stampID = info; }
  

private:

  int stampID;   // the ID in the BASS component stamp array
  int nAtoms;    // the number of atoms in the molecule
  int nBonds;    // ... .. ..  . .bonds .. .. . . . . 
  int nBends;    // . . . . .. . .bends . . . . .. . 
  int nTorsions  // .. . . .. . . torsions . . .. . . 
  int nOriented; // .. . . . .. . oreineted atoms . . . 
  

  Atom** myAtoms;     // the array of atoms
  Bond** myBonds;      // arrays of all the short range interactions
  Bend** myBends;
  Torsion** myTorsions;
  
  int startAtom;
  int endAtom;


};

#endif
Revision:	412
Committed:	Wed Mar 26 21:50:33 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	1790 byte(s)
Log Message:	still working on the SimSetup routine. also fixed some things in Exclude.hpp
#	Content
1	#ifndef _MOLECULE_H_
2	#define _MOLECULE_H_
3
4	#include "Atom.hpp"
5	#include "SRI.hpp"
6	#include "MoleculeStamp.hpp"
7
8	typedef struct{
9
10	int stampID; // the ID in the BASS component stamp array
11	int nAtoms; // the number of atoms in the molecule
12	int nBonds; // ... .. .. . .bonds .. .. . . . .
13	int nBends; // . . . . .. . .bends . . . . .. .
14	int nTorsions // .. . . .. . . torsions . . .. . .
15	int nOriented; // .. . . . .. . oreineted atoms . . .
16
17
18	Atom** myAtoms; // the array of atoms
19	Exclude** myExcludes;// the array of Excluded pairs
20	Bond** myBonds; // arrays of all the short range interactions
21	Bend** myBends;
22	Torsion** myTorsions;
23
24
25	} molInit;
26
27	class Molecule{
28
29	public:
30
31	Molecule( void );
32	~Molecule( void );
33
34	void initialize( molInit &theInit );
35
36	int getNMembers( void ) { return nMembers; }
37	int getStartAtom( void ) { return startAtom; }
38	int getEndAtom( void ) { return endAtom; }
39	int getStampID( void ) { return stampID; }
40
41	void setNMembers( int info ) { nMembers = info; }
42	void setStartAtom( int info ) { startAtom = info; }
43	void setEndAtom( int info ) { endAtom = info; }
44	void setStampID( int info ) { stampID = info; }
45
46
47	private:
48
49	int stampID; // the ID in the BASS component stamp array
50	int nAtoms; // the number of atoms in the molecule
51	int nBonds; // ... .. .. . .bonds .. .. . . . .
52	int nBends; // . . . . .. . .bends . . . . .. .
53	int nTorsions // .. . . .. . . torsions . . .. . .
54	int nOriented; // .. . . . .. . oreineted atoms . . .
55
56
57	Atom** myAtoms; // the array of atoms
58	Bond** myBonds; // arrays of all the short range interactions
59	Bend** myBends;
60	Torsion** myTorsions;
61
62	int startAtom;
63	int endAtom;
64
65
66	};
67
68	#endif