32 |
|
~Molecule( void ); |
33 |
|
|
34 |
|
void initialize( molInit &theInit ); |
35 |
+ |
|
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 |
|
|
45 |
< |
int getNMembers( void ) { return nMembers; } |
46 |
< |
int getStartAtom( void ) { return startAtom; } |
47 |
< |
int getEndAtom( void ) { return endAtom; } |
48 |
< |
int getStampID( void ) { return stampID; } |
45 |
> |
Atom** getMyAtoms ( void ) {return myAtoms;} |
46 |
> |
Bond** getMyBonds ( void ) {return myBonds;} |
47 |
> |
Bend** getMyBends ( void ) {return myBends;} |
48 |
> |
Torsions** getmyTorsions( void ) {return myTorsions;} |
49 |
> |
Exclude** getmyExcludes( void ) {return myExcludes;} |
50 |
|
|
51 |
< |
void setStampID( int info ) { stampID = info; } |
51 |
> |
void setStampID( int info ) {stampID = info;} |
52 |
> |
|
53 |
> |
void calcForces( void ); |
54 |
> |
double getPotential( void ); |
55 |
|
|
56 |
|
|
57 |
|
private: |
62 |
|
int nBends; // . . . . .. . .bends . . . . .. . |
63 |
|
int nTorsions; // .. . . .. . . torsions . . .. . . |
64 |
|
int nOriented; // .. . . . .. . oriented atoms . . . |
65 |
< |
int nMembers; |
65 |
> |
int nMembers; // .. . . . . . .atoms (legacy code) . . . |
66 |
> |
int nExcludes; // . . . . .. .. excludes .. . . |
67 |
|
|
68 |
|
Atom** myAtoms; // the array of atoms |
69 |
< |
Bond** myBonds; // arrays of all the short range interactions |
69 |
> |
Bond** myBonds; // arrays of all the short range interactions |
70 |
|
Bend** myBends; |
71 |
|
Torsion** myTorsions; |
72 |
+ |
Exclude** myExcludes; // array of the excluded pairs of long range forces |
73 |
|
|
59 |
– |
int startAtom; |
60 |
– |
int endAtom; |
61 |
– |
|
62 |
– |
|
74 |
|
}; |
75 |
|
|
76 |
|
#endif |