5 #ifndef BALL_KERNEL_MOLECULE_H
6 #define BALL_KERNEL_MOLECULE_H
8 #ifndef BALL_KERNEL_ATOMCONTAINER_H
12 #ifndef BALL_KERNEL_FRAGMENT_H
16 #ifndef BALL_KERNEL_FRAGMENTITERATOR_H
97 void set(
const Molecule& molecule,
bool deep =
true);
108 void get(
Molecule& molecule,
bool deep =
true)
const;
128 const System* getSystem()
const;
133 void prepend(
Atom& atom);
138 void append(
Atom& atom);
143 void insert(
Atom& atom);
160 bool remove(
Atom& atom);
215 virtual bool isMolecule()
const {
return true; }
229 virtual void dump(std::ostream& s = std::cout,
Size depth = 0)
const;
251 Molecule* getMolecule();
253 const Molecule* getMolecule()
const;
255 AtomContainer* getSuperAtomContainer();
257 const AtomContainer* getSuperAtomContainer()
const;
259 void prepend(Molecule& molecule);
261 void append(Molecule& molecule);
263 void insert(Molecule& molecule);
265 void insertBefore(Molecule& molecule, Composite& composite);
267 void insertAfter(Molecule& molecule, Composite& composite);
269 bool remove(Molecule& molecule);
271 bool isSubAtomContainerOf(
const AtomContainer& atom_container)
const;
275 #endif // BALL_KERNEL_MOLECULE_H