IMP
2.0.0
The Integrative Modeling Platform
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Storage and access to force field.
#include <IMP/atom/ForceFieldParameters.h>
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. More... | |
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 | |
virtual void | clear_caches () |
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. More... | |
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 |
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) | |
Construct an object with the given name. More... | |
Protected Attributes | |
std::map< ResidueType, AtomTypeMap > | atom_res_type_2_force_field_atom_type_ |
std::map< String, FloatPair > | force_field_2_vdW_ |
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")) |
Related Functions inherited from IMP::base::Object | |
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
Definition at line 19 of file ForceFieldParameters.h.
void IMP::atom::ForceFieldParameters::add_radii | ( | Hierarchy | mhd, |
double | scale = 1.0 , |
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FloatKey | radius_key = FloatKey("radius") |
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) | const |
Each radius is scaled by the given scale.
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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.
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related |
Add vdW radius from given force field.