core::scoring::mm::MMLJLibrary Class Reference

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

#include <MMLJLibrary.hh>

Inheritance diagram for core::scoring::mm::MMLJLibrary:

Public Member Functions
virtual	~MMLJLibrary ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
	MMLJLibrary (core::chemical::MMAtomTypeSetCOP mm_atom_set)
	ctor More...
mm_lj_param_set	lookup_three_bond (Size atom) const
	blah More...
mm_lj_param_set	lookup_three_bond (std::string atom) const
	blah More...
mm_lj_param_set	lookup (Size atom) const
	blah More...
mm_lj_param_set	lookup (std::string atom) const
	blah More...
core::chemical::MMAtomTypeSetCAP	mm_atom_set () const
	blah More...
Real	nblist_dis2_cutoff_XX () const
	blah More...
Real	nblist_dis2_cutoff_XH () const
	blah More...
Real	nblist_dis2_cutoff_HH () const
	blah More...

Private Attributes
utility::vector1 < mm::mm_lj_param_set >	mm_lj_three_bond_library_
	library that contains lj params for sets in which atoms are seperated by 3 or bonds More...
utility::vector1 < mm::mm_lj_param_set >	mm_lj_library_
	library that contains lj params for sets in which atoms are seperated by 4 or more bonds More...
core::chemical::MMAtomTypeSetCAP	mm_atom_set_
	the MMAtomTypeSet associated with the library More...
Real	nblist_dis2_cutoff_XX_
	the cutoff distance at which the neighbor list will count two atoms as being neighbors given that those atom are both heavy, a heavy and a hydrogen, or a hydrogen and hydrogen respectivly More...
Real	nblist_dis2_cutoff_XH_
Real	nblist_dis2_cutoff_HH_

Detailed Description

A class to maintain a set of MM LJ paramaters.

blah

Constructor & Destructor Documentation

core::scoring::mm::MMLJLibrary::~MMLJLibrary ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

core::scoring::mm::MMLJLibrary::MMLJLibrary

(

core::chemical::MMAtomTypeSetCOP

mm_atom_set

)

ctor

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

References mm_atom_set_, mm_lj_library_, mm_lj_three_bond_library_, and core::scoring::mm::TR().

Member Function Documentation

mm_lj_param_set core::scoring::mm::MMLJLibrary::lookup ( Size  atom ) const

inline

blah

References mm_lj_library_.

Referenced by core::scoring::mm::MMLJScore::deriv_score(), core::scoring::mm::MMLJScore::min_dist(), and core::scoring::mm::MMLJScore::score().

mm_lj_param_set core::scoring::mm::MMLJLibrary::lookup ( std::string  atom ) const

inline

blah

References mm_atom_set_, and mm_lj_library_.

mm_lj_param_set core::scoring::mm::MMLJLibrary::lookup_three_bond ( Size  atom ) const

inline

blah

References mm_lj_three_bond_library_.

Referenced by core::scoring::mm::MMLJScore::deriv_score(), core::scoring::mm::MMLJScore::min_dist(), and core::scoring::mm::MMLJScore::score().

mm_lj_param_set core::scoring::mm::MMLJLibrary::lookup_three_bond ( std::string  atom ) const

inline

blah

References mm_atom_set_, and mm_lj_three_bond_library_.

core::chemical::MMAtomTypeSetCAP core::scoring::mm::MMLJLibrary::mm_atom_set ( ) const

inline

blah

References mm_atom_set_.

Real core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_HH ( ) const

inline

blah

References nblist_dis2_cutoff_HH_.

Referenced by core::scoring::methods::MMLJEnergyIntra::setup_for_minimizing_for_residue().

Real core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_XH ( ) const

inline

blah

References nblist_dis2_cutoff_XH_.

Referenced by core::scoring::methods::MMLJEnergyIntra::setup_for_minimizing_for_residue().

Real core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_XX ( ) const

inline

blah

References nblist_dis2_cutoff_XX_.

Referenced by core::scoring::methods::MMLJEnergyIntra::setup_for_minimizing_for_residue().

Member Data Documentation

core::chemical::MMAtomTypeSetCAP core::scoring::mm::MMLJLibrary::mm_atom_set_

private

the MMAtomTypeSet associated with the library

Referenced by lookup(), lookup_three_bond(), mm_atom_set(), and MMLJLibrary().

utility::vector1<mm::mm_lj_param_set> core::scoring::mm::MMLJLibrary::mm_lj_library_

private

library that contains lj params for sets in which atoms are seperated by 4 or more bonds

Referenced by lookup(), and MMLJLibrary().

utility::vector1<mm::mm_lj_param_set> core::scoring::mm::MMLJLibrary::mm_lj_three_bond_library_

private

library that contains lj params for sets in which atoms are seperated by 3 or bonds

Referenced by lookup_three_bond(), and MMLJLibrary().

Real core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_HH_

private

Referenced by nblist_dis2_cutoff_HH().

Real core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_XH_

private

Referenced by nblist_dis2_cutoff_XH().

Real core::scoring::mm::MMLJLibrary::nblist_dis2_cutoff_XX_

private

the cutoff distance at which the neighbor list will count two atoms as being neighbors given that those atom are both heavy, a heavy and a hydrogen, or a hydrogen and hydrogen respectivly

Referenced by nblist_dis2_cutoff_XX().

---

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

• src/core/scoring/mm/MMLJLibrary.hh
• src/core/scoring/mm/MMLJLibrary.cc