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IntCoorGen Class Reference

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

#include <coor.h>

Inheritance diagram for IntCoorGen

[legend]Collaboration diagram for 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::out()) 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_

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Detailed Description

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

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Constructor & Destructor Documentation

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.

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.

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

• coor.h

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