OOPSE/libmdtools/Molecule.hpp

#ifndef _MOLECULE_H_
#define _MOLECULE_H_

#include "Atom.hpp"
#include "SRI.hpp"
#include "MoleculeStamp.hpp"
#include "Exclude.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; // .. . . . .. . oriented 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 getNAtoms   ( void ) {return nAtoms;}
  int getNBonds   ( void ) {return nBonds;}
  int getNBends   ( void ) {return nBends;}
  int getNTorsions( void ) {return nTorsions;}
  int getNOriented( void ) {return nOriented;}
  int getNExcludes( void ) {return nExcludes;}
  int getNMembers ( void ) {return nMembers;}
  int getStampID  ( void ) {return stampID;}

  Atom**     getMyAtoms   ( void ) {return myAtoms;}
  Bond**     getMyBonds   ( void ) {return myBonds;}
  Bend**     getMyBends   ( void ) {return myBends;}
  Torsion**  getMyTorsions( void ) {return myTorsions;}
  Exclude**  getMyExcludes( void ) {return myExcludes;}
  
  void setStampID( int info ) {stampID = info;}

  void calcForces( void );
  double getPotential( void );
  

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; // .. . . . .. . oriented atoms . . . 
  int nMembers;  // .. . . . . . .atoms (legacy code) . . . 
  int nExcludes; // . . . . .. .. excludes .. . . 

  Atom** myAtoms;     // the array of atoms
  Bond** myBonds;     // arrays of all the short range interactions
  Bend** myBends;
  Torsion** myTorsions;
  Exclude** myExcludes; // array of the excluded pairs of long range forces
  
};

#endif
Revision:	424
Committed:	Thu Mar 27 20:36:16 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	2284 byte(s)
Log Message:	fixing some compile time bugs
#	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	gezelter	416	#include "Exclude.hpp"
8	mmeineke	377
9	mmeineke	407	typedef struct{
10
11			int stampID; // the ID in the BASS component stamp array
12			int nAtoms; // the number of atoms in the molecule
13			int nBonds; // ... .. .. . .bonds .. .. . . . .
14			int nBends; // . . . . .. . .bends . . . . .. .
15	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
16			int nOriented; // .. . . . .. . oriented atoms . . .
17	mmeineke	407
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	mmeineke	423
36			int getNAtoms ( void ) {return nAtoms;}
37			int getNBonds ( void ) {return nBonds;}
38			int getNBends ( void ) {return nBends;}
39			int getNTorsions( void ) {return nTorsions;}
40			int getNOriented( void ) {return nOriented;}
41			int getNExcludes( void ) {return nExcludes;}
42			int getNMembers ( void ) {return nMembers;}
43			int getStampID ( void ) {return stampID;}
44	mmeineke	407
45	mmeineke	423	Atom** getMyAtoms ( void ) {return myAtoms;}
46			Bond** getMyBonds ( void ) {return myBonds;}
47			Bend** getMyBends ( void ) {return myBends;}
48	mmeineke	424	Torsion** getMyTorsions( void ) {return myTorsions;}
49			Exclude** getMyExcludes( void ) {return myExcludes;}
50	mmeineke	377
51	mmeineke	423	void setStampID( int info ) {stampID = info;}
52
53			void calcForces( void );
54			double getPotential( void );
55	mmeineke	377
56
57			private:
58
59	mmeineke	407	int stampID; // the ID in the BASS component stamp array
60			int nAtoms; // the number of atoms in the molecule
61			int nBonds; // ... .. .. . .bonds .. .. . . . .
62			int nBends; // . . . . .. . .bends . . . . .. .
63	gezelter	416	int nTorsions; // .. . . .. . . torsions . . .. . .
64			int nOriented; // .. . . . .. . oriented atoms . . .
65	mmeineke	423	int nMembers; // .. . . . . . .atoms (legacy code) . . .
66			int nExcludes; // . . . . .. .. excludes .. . .
67	mmeineke	407
68			Atom** myAtoms; // the array of atoms
69	mmeineke	423	Bond** myBonds; // arrays of all the short range interactions
70	mmeineke	407	Bend** myBends;
71			Torsion** myTorsions;
72	mmeineke	423	Exclude** myExcludes; // array of the excluded pairs of long range forces
73	mmeineke	407
74	mmeineke	377	};
75
76			#endif