14 |
|
int nBends; // . . . . .. . .bends . . . . .. . |
15 |
|
int nTorsions; // .. . . .. . . torsions . . .. . . |
16 |
|
int nOriented; // .. . . . .. . oriented atoms . . . |
17 |
+ |
int nExcludes; // . . .. . . . .exclude pairs.. . . . |
18 |
|
|
19 |
|
Atom** myAtoms; // the array of atoms |
20 |
|
Exclude** myExcludes;// the array of Excluded pairs |
33 |
|
~Molecule( void ); |
34 |
|
|
35 |
|
void initialize( molInit &theInit ); |
36 |
+ |
|
37 |
+ |
void setMyIndex( int theIndex ){ myIndex = theIndex;} |
38 |
|
|
39 |
|
int getNAtoms ( void ) {return nAtoms;} |
40 |
|
int getNBonds ( void ) {return nBonds;} |
56 |
|
void calcForces( void ); |
57 |
|
double getPotential( void ); |
58 |
|
|
59 |
+ |
void printMe( void ); |
60 |
+ |
|
61 |
|
|
62 |
|
private: |
63 |
|
|
70 |
|
int nMembers; // .. . . . . . .atoms (legacy code) . . . |
71 |
|
int nExcludes; // . . . . .. .. excludes .. . . |
72 |
|
|
73 |
+ |
int myIndex; // mostly just for debug |
74 |
+ |
|
75 |
|
Atom** myAtoms; // the array of atoms |
76 |
|
Bond** myBonds; // arrays of all the short range interactions |
77 |
|
Bend** myBends; |