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Storage and access to force field.
Inheritance diagram for IMP::atom::ForceFieldParameters: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 or replace radii in 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 | |
| Public Member Functions inherited from IMP::base::Object | |
| std::size_t | __hash__ () const |
| virtual std::string | get_type_name () const =0 |
| Return a string identifying the type of the object. | |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Protected Types | |
|
typedef std::map< AtomType, ChargePair > | AtomTypeMap |
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typedef std::pair< std::string, double > | ChargePair |
Protected Member Functions | |
| void | add_bonds (Residue rd) const |
| void | add_bonds (Residue rd1, Residue rd2) 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 Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
Protected Attributes | |
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std::map< ResidueType, AtomTypeMap > | atom_res_type_2_force_field_atom_type_ |
| std::map< String, FloatPair > | force_field_2_vdW_ |
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std::map< ResidueType, base::Vector< Bond > > | residue_bonds_ |
Related Functions | |
(Note that these are not member functions.) | |
| void | add_bonds (Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters()) |
| void | add_radii (Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius")) |
| void IMP::atom::ForceFieldParameters::add_bonds | ( | Hierarchy | mhd | ) | const |
add bonds to the structure defined in the hierarchy
| void IMP::atom::ForceFieldParameters::add_radii | ( | Hierarchy | mhd, |
| double | scale = 1.0, |
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| FloatKey | radius_key = FloatKey("radius") |
||
| ) | const |
Add or replace radii in the structure defined in the hierarchy.
Each radius is scaled by the given scale.
| void IMP::atom::ForceFieldParameters::add_well_depths | ( | Hierarchy | mhd | ) | const |
Add LennardJones well depths to the structure.
get epsilon for non bonded vdW
|
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.
|
related |
Add vdW radius from given force field.
