| add_bends(const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m) (defined in IntCoorGen) | IntCoorGen | [protected] |
| add_bonds(const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m) (defined in IntCoorGen) | IntCoorGen | [protected] |
| add_out(const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m) (defined in IntCoorGen) | IntCoorGen | [protected] |
| add_tors(const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m) (defined in IntCoorGen) | IntCoorGen | [protected] |
| class_desc() const | DescribedClass | |
| class_name() const | DescribedClass | |
| class_version() const | DescribedClass | |
| cos_ijk(Molecule &m, int i, int j, int k) (defined in IntCoorGen) | IntCoorGen | [protected] |
| dereference() | RefCount | [inline] |
| DescribedClass() (defined in DescribedClass) | DescribedClass | |
| DescribedClass(const DescribedClass &) (defined in DescribedClass) | DescribedClass | |
| dir_restore_state(StateIn &si, const char *objectname, const char *keyword=0) (defined in SavableState) | SavableState | [static] |
| extra_bonds_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| generate(const Ref< SetIntCoor > &) | IntCoorGen | [virtual] |
| hterminal(Molecule &m, BitArrayLTri &bonds, int i) (defined in IntCoorGen) | IntCoorGen | [protected] |
| identifier() | Identity | [inline] |
| init_constants() (defined in IntCoorGen) | IntCoorGen | [protected] |
| IntCoorGen(const Ref< Molecule > &, int nextra=0, int *extra=0) | IntCoorGen | |
| IntCoorGen(const Ref< KeyVal > &) | IntCoorGen | |
| IntCoorGen(StateIn &) (defined in IntCoorGen) | IntCoorGen | |
| key_restore_state(StateIn &si, const char *keyword) | SavableState | [static] |
| linear_bend_thres_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| linear_bends_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| linear_lbends_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| linear_stors_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| linear_tors_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| linear_tors_thres_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| lock_ptr() const | RefCount | |
| managed() const (defined in RefCount) | RefCount | [inline] |
| managed() const | RefCount | [inline] |
| molecule_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| nearest_contact(int i, Molecule &m) (defined in IntCoorGen) | IntCoorGen | [protected] |
| nextra_bonds_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| nreference() const | RefCount | [inline] |
| operator=(const SavableState &) (defined in SavableState) | SavableState | |
| operator=(const DescribedClass &) (defined in DescribedClass) | DescribedClass | |
| operator=(const RefCount &) (defined in RefCount) | RefCount | [inline, protected] |
| print(std::ostream &out=ExEnv::out()) const | IntCoorGen | [virtual] |
| radius_scale_factor_ (defined in IntCoorGen) | IntCoorGen | [protected] |
| RefCount() (defined in RefCount) | RefCount | [inline, protected] |
| RefCount(const RefCount &) (defined in RefCount) | RefCount | [inline, protected] |
| reference() | RefCount | [inline] |
| restore_state(StateIn &si) | SavableState | [static] |
| SavableState() (defined in SavableState) | SavableState | [protected] |
| SavableState(const SavableState &) (defined in SavableState) | SavableState | [protected] |
| SavableState(StateIn &) | SavableState | [protected] |
| save_data_state(StateOut &) | IntCoorGen | [virtual] |
| save_object_state(StateOut &) | SavableState | |
| save_state(StateOut &) | SavableState | |
| save_state(SavableState *s, StateOut &) (defined in SavableState) | SavableState | [static] |
| save_vbase_state(StateOut &) | SavableState | [virtual] |
| unlock_ptr() const | RefCount | |
| unmanage() | RefCount | [inline] |
| use_locks(bool inVal) | RefCount | |
| ~DescribedClass() (defined in DescribedClass) | DescribedClass | [virtual] |
| ~Identity() (defined in Identity) | Identity | [virtual] |
| ~IntCoorGen() (defined in IntCoorGen) | IntCoorGen | |
| ~RefCount() (defined in RefCount) | RefCount | [virtual] |
| ~SavableState() (defined in SavableState) | SavableState | [virtual] |