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

       Generated automatically by Doxygen for MPQC from the source code.

Version 2.3.1                                    Sun Oct 4 2020                                sc::IntCoorGen(3)