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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: [legend]Collaboration diagram for sc::IntCoorGen: [legend]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