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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.
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 |
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const IMP::atom::CHARMMBondEndpoint & | get_endpoint (unsigned int i) const |
Additional Inherited Members | |
| Protected Attributes inherited from IMP::atom::CHARMMConnection< 4 > | |
| base::Vector< CHARMMBondEndpoint > | endpoints_ |
