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core::scoring::mm::MMTorsionLibrary Class Reference

A class to maintain a set of MM torsion paramaters. More...

#include <MMTorsionLibrary.hh>

Inheritance diagram for core::scoring::mm::MMTorsionLibrary:
Inheritance graph
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Public Member Functions

 MMTorsionLibrary (std::string filename, core::chemical::MMAtomTypeSetCOP mm_atom_set, utility::vector1< std::string > extra_mm_param_dirs=utility::vector1< std::string >())
 ctor More...
 
 ~MMTorsionLibrary () override
 
mm_torsion_library_citer_pair lookup (int atom1, int atom2, int atom3, int atom4) const
 lookup by atom type ints More...
 
mm_torsion_library_citer_pair lookup (std::string atom1, std::string atom2, std::string atom3, std::string atom4) const
 lookup by atom type strings More...
 

Private Attributes

mm_torsion_library fully_assigned_mm_torsion_library_
 library that contains torsion params for sets in which all mm atom types are specified for all 4 positions More...
 
mm_torsion_library wildcard_mm_torsion_library_
 library that contains torsion params for sets in which all mm atom types are NOT specified for all 4 positions More...
 
core::chemical::MMAtomTypeSetCAP mm_atom_set_
 the MMAtomTypeSet associated with the library More...
 

Detailed Description

A class to maintain a set of MM torsion paramaters.

The MMTorsionLibrary class contains functions and data structures to initialize, store, and provide lookups for molecular mechanics torsional paramaters. The sets of 4 atom types that make up a dihedral angle are stored in an mm_torsion_atom_quad . The sets 3 parameters that act as values for the actual MM torsion potential are stored in an mm_torsion_param_set . The class maintains 2 libraries; one for set of torsion parameter for which all 4 atom types in the dihedral at defined ( fully_assigned_mm_torsion_library_ ), and a library that is only dependant on the two central atom types ( wildcard_mm_torsion_library_ ). Wildcar atom types are designated by 'X'. Lookups are done with MMAtomType indicies or strings that are converted to MMAtomType indicies. Lookup functions return pairs of iterators to the map. The same set of 4 atom types can corespond to multiple paramter sets with different multiplicities to more accuratly define the potential and is the reason multimaps are used instead of just maps.

Constructor & Destructor Documentation

core::scoring::mm::MMTorsionLibrary::MMTorsionLibrary ( std::string  filename,
core::chemical::MMAtomTypeSetCOP  mm_atom_set,
utility::vector1< std::string >  extra_mm_param_dirs = utility::vector1< std::string > () 
)

ctor

Constructs a MMTorsionLibrary instance from a filename string and constant access pointer to an MMAtomTypeSet

References fully_assigned_mm_torsion_library_, mm_atom_set_, protocols::hybridization::score, core::scoring::mm::TR(), and wildcard_mm_torsion_library_.

core::scoring::mm::MMTorsionLibrary::~MMTorsionLibrary ( )
overridedefault

Member Function Documentation

mm_torsion_library_citer_pair core::scoring::mm::MMTorsionLibrary::lookup ( int  atom1,
int  atom2,
int  atom3,
int  atom4 
) const

lookup by atom type ints

The lookup function returns a pair of iterators to the first and last element in the multimap library that corespond to the set(s) of mm params that corespond to the 4 mm atom type indices. If non are found it exits.

References fully_assigned_mm_torsion_library_, mm_atom_set_, core::id::to_string(), core::scoring::mm::TR(), and wildcard_mm_torsion_library_.

Referenced by core::scoring::mm::MMTorsionScore::dscore(), core::scoring::mm::MMTorsionScore::score(), and protocols::simple_moves::CyclizationMover::setup_constraints().

mm_torsion_library_citer_pair core::scoring::mm::MMTorsionLibrary::lookup ( std::string  atom1,
std::string  atom2,
std::string  atom3,
std::string  atom4 
) const

lookup by atom type strings

References mm_atom_set_.

Member Data Documentation

mm_torsion_library core::scoring::mm::MMTorsionLibrary::fully_assigned_mm_torsion_library_
private

library that contains torsion params for sets in which all mm atom types are specified for all 4 positions

Referenced by lookup(), and MMTorsionLibrary().

core::chemical::MMAtomTypeSetCAP core::scoring::mm::MMTorsionLibrary::mm_atom_set_
private

the MMAtomTypeSet associated with the library

Referenced by lookup(), and MMTorsionLibrary().

mm_torsion_library core::scoring::mm::MMTorsionLibrary::wildcard_mm_torsion_library_
private

library that contains torsion params for sets in which all mm atom types are NOT specified for all 4 positions

Referenced by lookup(), and MMTorsionLibrary().


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