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# sc::IntCoorGen Class Reference

IntCoorGen generates a set of simple internal coordinates for a molecule. More...

`#include <coor.h>`

Inheritance diagram for sc::IntCoorGen:

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Collaboration diagram for sc::IntCoorGen:

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List of all members.

## Public Methods

| IntCoorGen (const Ref< Molecule > &, int nextra=0, int *extra=0)
| Create an IntCoorGen given a Molecule and, optionally, extra bonds. More...
| IntCoorGen (const Ref< KeyVal > &)
| The KeyVal constructor. More...
| IntCoorGen (StateIn &)
| ~IntCoorGen ()
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 Methods

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_

## Detailed Description

IntCoorGen generates a set of simple internal coordinates for a molecule.

## Constructor & Destructor Documentation

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 and specify the atoms which are bound in extra bond . The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found.

The documentation for this class was generated from the following file:

- coor.h