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

       Generated automatically by Doxygen for MPQC from the source code.

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

sc::IntCoorGen::IntCoorGen(constRef<Molecule>&,intnextra=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(constRef<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.

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

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

       #include <coor.h>

       Inherits sc::SavableState.

   PublicMemberFunctionsIntCoorGen (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.

   ProtectedMemberFunctions
       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)

   ProtectedAttributesRef< 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_AdditionalInheritedMembers