#include <AtomVDW.hh>

Public Member Functions
	AtomVDW (std::string const &atom_type_set_name)
	ctor, reads data file More...

utility::vector1< Real > const &	operator() (Size const atom_type_index) const

Real	approximate_vdw_radius (Size const atom_type_index) const

std::string	atom_type_set_name () const

Private Member Functions
void	setup_approximate_vdw_radii (utility::vector1< int > const &atom_type_index, chemical::AtomTypeSet const &atom_type_set)

void	get_atom_type_set_name (std::string ats_suff)

Private Attributes
std::string	atom_type_set_name_

std::string	vdw_suffix_

utility::vector1 < utility::vector1< Real > >	atom_vdw_

utility::vector1< Real >	approximate_vdw_radii_
	Approximation to per-atom radii, derived from atom_vdw_ data. More...

Constructor & Destructor Documentation

core::scoring::AtomVDW::AtomVDW ( std::string const & atom_type_set_name_with_suffix )

ctor, reads data file

ctor, reads data file. Need to configure to allow alternate tables/atom_sets

References core::chemical::AtomTypeSet::atom_type_index(), atom_type_set_name(), atom_type_set_name_, atom_vdw_, core::chemical::CENTROID, utility::io::izstream::clear(), core::chemical::AtomTypeSet::directory(), get_atom_type_set_name(), core::chemical::ChemicalManager::get_instance(), getline(), utility::io::izstream::good(), l, core::chemical::AtomTypeSet::n_atomtypes(), basic::database::open(), utility::io::izstream::open(), setup_approximate_vdw_radii(), core::scoring::TR, utility_exit_with_message, and vdw_suffix_.

Member Function Documentation

Real core::scoring::AtomVDW::approximate_vdw_radius ( Size const atom_type_index ) const

inline

References approximate_vdw_radii_.

Referenced by core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), and core::scoring::methods::HybridVDW_Energy::residue_pair_energy().

std::string core::scoring::AtomVDW::atom_type_set_name ( ) const

References atom_type_set_name_.

Referenced by AtomVDW(), and core::scoring::vdwaals::VDW_Energy::calculate_hydrogen_interaction_cutoff().

void core::scoring::AtomVDW::get_atom_type_set_name ( std::string ats_suff )

private

References atom_type_set_name_, ss, utility_exit_with_message, and vdw_suffix_.

Referenced by AtomVDW().

utility::vector1< Real > const& core::scoring::AtomVDW::operator() ( Size const atom_type_index ) const

inline

References atom_vdw_.

void core::scoring::AtomVDW::setup_approximate_vdw_radii	(	utility::vector1< int > const &	atom_type_index,
		chemical::AtomTypeSet const &	atom_type_set
	)

private

Calculates approximation to a single per-atom radius using the pairwise data from the file For atoms not present in the file uses the lj_radius from atom_type_set

References approximate_vdw_radii_, atom_vdw_, and core::chemical::AtomTypeSet::n_atomtypes().

Referenced by AtomVDW().