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
  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:	407
Committed:	Wed Mar 26 20:22:02 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	1734 byte(s)
Log Message:	I'm overhauling the molecule class to contain it's own bonds, bends, and torsions. may god have mercy on my soul.
#	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	Bond** myBonds; // arrays of all the short range interactions
20	Bend** myBends;
21	Torsion** myTorsions;
22
23
24	} molInit;
25
26	class Molecule{
27
28	public:
29
30	Molecule( void );
31	~Molecule( void );
32
33	void initialize( molInit &theInit );
34
35	int getNMembers( void ) { return nMembers; }
36	int getStartAtom( void ) { return startAtom; }
37	int getEndAtom( void ) { return endAtom; }
38	int getStampID( void ) { return stampID; }
39
40	void setNMembers( int info ) { nMembers = info; }
41	void setStartAtom( int info ) { startAtom = info; }
42	void setEndAtom( int info ) { endAtom = info; }
43	void setStampID( int info ) { stampID = info; }
44
45
46	private:
47
48	int stampID; // the ID in the BASS component stamp array
49	int nAtoms; // the number of atoms in the molecule
50	int nBonds; // ... .. .. . .bonds .. .. . . . .
51	int nBends; // . . . . .. . .bends . . . . .. .
52	int nTorsions // .. . . .. . . torsions . . .. . .
53	int nOriented; // .. . . . .. . oreineted atoms . . .
54
55
56	Atom** myAtoms; // the array of atoms
57	Bond** myBonds; // arrays of all the short range interactions
58	Bend** myBends;
59	Torsion** myTorsions;
60
61	int startAtom;
62	int endAtom;
63
64
65	};
66
67	#endif