IMP  2.0.0
The Integrative Modeling Platform
IMP::atom::ForceFieldParameters Class Reference

Storage and access to force field.

#include <IMP/atom/ForceFieldParameters.h>

+ 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. 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, FloatPairforce_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"))
 

Detailed Description

Definition at line 19 of file ForceFieldParameters.h.

Member Function Documentation

void IMP::atom::ForceFieldParameters::add_radii ( Hierarchy  mhd,
double  scale = 1.0,
FloatKey  radius_key = FloatKey("radius") 
) const

Each radius is scaled by the given scale.

Friends And Related Function Documentation

void add_bonds ( Hierarchy  d,
const ForceFieldParameters ffp = get_all_atom_CHARMM_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 = get_all_atom_CHARMM_parameters(),
FloatKey  radius_key = FloatKey("radius") 
)
related

Add vdW radius from given force field.


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