NAME

       sc::IntCoorGen - IntCoorGen generates a set of simple internal coordinates for a molecule.

SYNOPSIS

       #include <coor.h>

       Inherits sc::SavableState.

   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

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 $2 (i-1) + 1$ 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.

Author

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