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_

Additional Inherited Members¶

sc::IntCoorGen::IntCoorGen (const Ref< Molecule > &, int nextra = 0, int * extra = 0)¶

Create an IntCoorGen given a Molecule and, optionally, extra bonds. IntCoorGen keeps a reference to extra and deletes it when the destructor is called.

sc::IntCoorGen::IntCoorGen (const Ref< KeyVal > &)¶

The KeyVal constructor.

molecule

A Molecule object. There is no default.

radius_scale_factor

If the distance between two atoms is less than the radius scale factor times the sum of the atoms' atomic radii, then a bond is placed between the two atoms for the purpose of finding internal coordinates. The default is 1.1.

linear_bend_threshold

A bend angle in degress greater than 180 minus this keyword's floating point value is considered a linear bend. The default is 1.0.

linear_tors_threshold

The angles formed by atoms a-b-c and b-c-d are checked for near linearity. If an angle in degrees is greater than 180 minus this keyword's floating point value, then the torsion is classified as a linear torsion. The default is 1.0.

linear_bend

Generate BendSimpleCo objects to describe linear bends. The default is false.

linear_lbend

Generate pairs of LinIPSimpleCo and LinIPSimpleCo objects to describe linear bends. The default is true.

linear_tors

Generate TorsSimpleCo objects to described linear torsions. The default is false.

linear_stors

Generate ScaledTorsSimpleCo objects to described linear torsions. The default is true.

extra_bonds

This is a vector of atom numbers, where elements $2 (i-1) + 1$ and $2 i$ specify the atoms which are bound in extra bond $i$. The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found.