| 38 |
|
#include "math/Vector3.hpp" |
| 39 |
|
#include "primitives/Atom.hpp" |
| 40 |
|
#include "primitives/RigidBody.hpp" |
| 41 |
< |
#include "primitives/Bond.hpp" |
| 42 |
< |
#include "primitives/Bend.hpp" |
| 43 |
< |
#include "primitives/Torsion.hpp" |
| 41 |
> |
//#include "primitives/Bond.hpp" |
| 42 |
> |
//#include "primitives/Bend.hpp" |
| 43 |
> |
//#include "primitives/Torsion.hpp" |
| 44 |
> |
#include "primitives/SRI.hpp" |
| 45 |
|
#include "primitives/CutoffGroup.hpp" |
| 46 |
|
|
| 47 |
|
namespace oopse{ |
| 48 |
|
|
| 49 |
+ |
class Constraint; |
| 50 |
+ |
|
| 51 |
|
/** |
| 52 |
|
* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
| 53 |
|
* @brief |
| 55 |
|
class Molecule { |
| 56 |
|
public: |
| 57 |
|
|
| 58 |
< |
Molecule(); |
| 58 |
> |
Molecule(int stampId, int globalIndex); |
| 59 |
|
virtual ~Molecule(); |
| 60 |
|
|
| 61 |
|
/** |
| 142 |
|
unsigned int getNConstraints() { |
| 143 |
|
return constraints_.size(); |
| 144 |
|
} |
| 145 |
< |
|
| 145 |
> |
|
| 146 |
> |
Atom* getAtomAt(unsigned int i) { |
| 147 |
> |
assert(i < atoms_.size()); |
| 148 |
> |
return atoms_[i]; |
| 149 |
> |
} |
| 150 |
|
/** |
| 151 |
|
* Returns the first atom in this molecule and initialize the iterator. |
| 152 |
|
* @return the first atom, return NULL if there is not cut off group in this molecule |
| 254 |
|
std::vector<StuntDouble*> integrableObjects_; |
| 255 |
|
std::vector<CutoffGroup*> cutoffGroups_; |
| 256 |
|
std::vector<Constraint*> constraints_; |
| 257 |
+ |
|
| 258 |
+ |
int stampID; |
| 259 |
|
}; |
| 260 |
|
|
| 261 |
|
} //namespace oopse |
