IMP  2.3.1
The Integrative Modeling Platform
IMP::atom::ForceFieldParameters Class Reference

Storage and access to force field. More...

#include <IMP/atom/ForceFieldParameters.h>

+ Inheritance diagram for IMP::atom::ForceFieldParameters:

Detailed Description

Storage and access to force field.

Definition at line 19 of file ForceFieldParameters.h.

Classes

class  Bond
 

Public Member Functions

void add_bonds (Hierarchy mhd) const
 add bonds to the structure defined in the hierarchy More...
 
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. More...
 
Float get_epsilon (Atom atom) const
 get epsilon for non bonded vdW More...
 
Float get_radius (Atom atom) const
 get radius More...
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
CheckLevel get_check_level () const
 
LogLevel get_log_level () const
 
virtual VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
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)
 
virtual std::string get_type_name () const
 

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...
 
virtual void do_destroy ()
 

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_
 

Member Function Documentation

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,
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.

Float IMP::atom::ForceFieldParameters::get_epsilon ( Atom  atom) const

get epsilon for non bonded vdW

Float IMP::atom::ForceFieldParameters::get_radius ( Atom  atom) const

get radius


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