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IMP Reference Guide  develop.5de2a9ba5d,2024/02/25
The Integrative Modeling Platform
IMP::atom::CHARMMInternalCoordinate Class Reference

A geometric relationship between four atoms. More...

#include <IMP/atom/charmm_topology.h>

+ Inheritance diagram for IMP::atom::CHARMMInternalCoordinate:

Detailed Description

A geometric relationship between four atoms.

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 202 of file charmm_topology.h.

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 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 (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. More...
 
bool get_contains_atom (std::string name) const
 Return true if the bond contains the named atom. More...
 
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 >
Vector< CHARMMBondEndpointendpoints_
 

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