A geometric relationship between four atoms. More...

Inheritance diagram for IMP::atom::CHARMMInternalCoordinate:

Public Member Functions
	CHARMMInternalCoordinate (const IMP::Strings &atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper)

	CHARMMInternalCoordinate (const base::Vector< CHARMMBondEndpoint > endpoints, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper)

float	get_dihedral () const

float	get_first_angle () const

float	get_first_distance () const

bool	get_improper () const

float	get_second_angle () const

float	get_second_distance () const

void	show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::atom::CHARMMConnection< 4 >
	CHARMMConnection (const IMP::Strings &atoms)

	CHARMMConnection (base::Vector< CHARMMBondEndpoint > endpoints)

Atoms	get_atoms (const CHARMMResidueTopology current_residue, const CHARMMResidueTopology previous_residue, const CHARMMResidueTopology next_residue, const std::map< const CHARMMResidueTopology , Hierarchy > &resmap) const
	Map the bond to a list of Atom particles.

bool	get_contains_atom (std::string name) const

const IMP::atom::CHARMMBondEndpoint &	get_endpoint (unsigned int i) const

void	show (std::ostream &out=std::cout) const

Additional Inherited Members
Protected Attributes inherited from IMP::atom::CHARMMConnection< 4 >
base::Vector< CHARMMBondEndpoint >	endpoints_

Detailed Description

The atoms (denoted i,j,k,l here) are uniquely positioned in 3D space relative to each other by means of two distances, two angles, and a dihedral.

A regular internal coordinate stores the distances between ij and kl respectively, and the angles between ijk and jkl.

An improper internal coordinate stores the distances between ik and kl respectively, and the angles between ikj and jkl.

In both cases the dihedral is the angle between the two planes formed by ijk and jkl.

Definition at line 193 of file charmm_topology.h.

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

Public Member Functions