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 |