Public Member Functions | |
| void | add_bonds (Hierarchy mhd) const |
| add bonds to the structure defined in the hierarchy | |
| void | add_radii (Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius")) const |
| add radii to the structure defined in the hierarchy | |
| void | add_well_depths (Hierarchy mhd) const |
| Add LennardJones well depths to the structure. | |
| Float | get_epsilon (Atom atom) const |
| get epsilon for non bonded vdW | |
| Float | get_radius (Atom atom) const |
| get radius | |
Protected Types | |
|
typedef std::map< AtomType, std::pair< std::string, float > > | AtomTypeMap |
Protected Member Functions | |
| void | add_bonds (Residue rd1, Residue rd2) const |
| void | add_bonds (Residue rd) const |
| Float | get_epsilon (const String &force_field_atom_type) const |
| virtual String | get_force_field_atom_type (Atom atom) const |
| Float | get_radius (const String &force_field_atom_type) const |
Protected Attributes | |
|
std::map< ResidueType, AtomTypeMap > | atom_res_type_2_force_field_atom_type_ |
|
std::map< String, std::pair < float, float > > | force_field_2_vdW_ |
|
std::map< ResidueType, std::vector< Bond > > | residue_bonds_ |
Friends | |
| template<class T > | |
| void | IMP::internal::unref (T *) |
Related Functions | |
| (Note that these are not member functions.) | |
| void | add_bonds (Hierarchy d, const ForceFieldParameters *ffp=default_force_field_parameters()) |
| void | add_radii (Hierarchy d, const ForceFieldParameters *ffp=default_force_field_parameters(), FloatKey radius_key=FloatKey("radius")) |
| void add_bonds | ( | Hierarchy | d, | |
| const ForceFieldParameters * | ffp = default_force_field_parameters() | |||
| ) | [related] |
Add bonds using definitions from given force field parameters. Note that, at the moment, all added bonds are reported as IMP::Bond::SINGLE, whether or not they actually are.
| void add_radii | ( | Hierarchy | d, | |
| const ForceFieldParameters * | ffp = default_force_field_parameters(), |
|||
| FloatKey | radius_key = FloatKey("radius") | |||
| ) | [related] |
Add vdW radius from given force field.
