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.
#	User	Rev	Content
1	mmeineke	377	#ifndef _MOLECULE_H_
2			#define _MOLECULE_H_
3
4			#include "Atom.hpp"
5			#include "SRI.hpp"
6	mmeineke	407	#include "MoleculeStamp.hpp"
7	mmeineke	377
8	mmeineke	407	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	mmeineke	377	class Molecule{
27
28			public:
29
30	mmeineke	407	Molecule( void );
31			~Molecule( void );
32	mmeineke	377
33	mmeineke	407	void initialize( molInit &theInit );
34
35	mmeineke	377	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	mmeineke	407	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	mmeineke	377	int startAtom;
62			int endAtom;
63
64	mmeineke	407
65	mmeineke	377	};
66
67			#endif