#include <coor.h>
Inheritance diagram for sc::IntCoorGen:
Public Member Functions | |
IntCoorGen (const Ref< Molecule > &, int nextra=0, int *extra=0) | |
Create an IntCoorGen given a Molecule and, optionally, extra bonds. | |
IntCoorGen (const Ref< KeyVal > &) | |
The KeyVal constructor. | |
IntCoorGen (StateIn &) | |
void | save_data_state (StateOut &) |
Standard member. | |
virtual void | generate (const Ref< SetIntCoor > &) |
This generates a set of internal coordinates. | |
virtual void | print (std::ostream &out=ExEnv::out0()) const |
Print out information about this. | |
Protected Member Functions | |
void | init_constants () |
double | cos_ijk (Molecule &m, int i, int j, int k) |
int | hterminal (Molecule &m, BitArrayLTri &bonds, int i) |
int | nearest_contact (int i, Molecule &m) |
void | add_bonds (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m) |
void | add_bends (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m) |
void | add_tors (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m) |
void | add_out (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m) |
Protected Attributes | |
Ref< Molecule > | molecule_ |
int | linear_bends_ |
int | linear_lbends_ |
int | linear_tors_ |
int | linear_stors_ |
int | nextra_bonds_ |
int * | extra_bonds_ |
double | linear_bend_thres_ |
double | linear_tors_thres_ |
double | radius_scale_factor_ |
Create an IntCoorGen given a Molecule and, optionally, extra bonds.
IntCoorGen keeps a reference to extra and deletes it when the destructor is called.
The KeyVal constructor.
molecule
radius_scale_factor
linear_bend_threshold
linear_tors_threshold
linear_bend
linear_lbend
linear_tors
linear_stors
extra_bonds