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
#	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	mmeineke	412	Atom** myAtoms; // the array of atoms
19			Exclude** myExcludes;// the array of Excluded pairs
20	mmeineke	407	Bond** myBonds; // arrays of all the short range interactions
21			Bend** myBends;
22			Torsion** myTorsions;
23
24
25			} molInit;
26
27	mmeineke	377	class Molecule{
28
29			public:
30
31	mmeineke	407	Molecule( void );
32			~Molecule( void );
33	mmeineke	377
34	mmeineke	407	void initialize( molInit &theInit );
35
36	mmeineke	377	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	mmeineke	407	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	mmeineke	377	int startAtom;
63			int endAtom;
64
65	mmeineke	407
66	mmeineke	377	};
67
68			#endif