core::scoring::PoissonBoltzmannPotential Class Reference

#include <PoissonBoltzmannPotential.hh>

Public Member Functions
	PoissonBoltzmannPotential ()
virtual	~PoissonBoltzmannPotential ()
core::Real	get_potential (ObjexxFCL::FArray3D< core::Real > const &potential, numeric::xyzVector< core::Real > const &cartX) const
void	eval_PB_energy_residue (core::conformation::Residue const &rsd, Real &PB_energy_residue, Real &PB_energy_backbone, Real &PB_energy_sidechain, Real const &PB_burial_weight) const
void	cart2idx (numeric::xyzVector< core::Real > const &cartX, numeric::xyzVector< core::Real > &idxX) const
template<class Q >
void	idx2cart (numeric::xyzVector< Q > const &idxX, numeric::xyzVector< core::Real > &cartX) const
numeric::xyzVector< core::Real >	lower_bound () const
numeric::xyzVector< core::Real >	upper_bound () const
bool	out_of_bounds (numeric::xyzVector< core::Real > const cartX) const
void	solve_pb (core::pose::Pose const &pose, std::string const &state_tag, std::map< std::string, bool > const &is_residue_charged_by_name)

Static Public Attributes
static const std::string	APBS_CONFIG_EXT = ".in"
static const std::string	APBS_PQR_EXT = ".pqr"
static const std::string	APBS_DX_EXT = ".dx"
static const std::string	DEFAULT_APBS_PATH = "apbs"

Private Member Functions
void	write_config (core::pose::Pose const &pose) const
	Prepare ABPS - generate .in and .pqr. More...
void	load_APBS_potential ()
	Read & load the APBS results. More...
void	write_pqr (core::pose::Pose const &pose, std::map< std::string, bool > const &is_residue_charged_by_name) const
	Write out .pqr. More...

Private Attributes
numeric::xyzMatrix< core::Real >	i2c_
numeric::xyzMatrix< core::Real >	c2i_
numeric::xyzVector< core::Real >	lower_bound_
numeric::xyzVector< core::Real >	upper_bound_
numeric::xyzVector< core::Real >	grid_spacing_
numeric::xyzVector< core::Size >	n_grid_
ObjexxFCL::FArray3D< core::Real >	potential_
std::string	config_filename_
std::string	pqr_filename_
std::string	dx_filename_
std::string	apbs_path_
bool	calcenergy_

Constructor & Destructor Documentation

core::scoring::PB::PoissonBoltzmannPotential

(

)

core::scoring::PB::~PoissonBoltzmannPotential ( )

virtual

Member Function Documentation

void core::scoring::PoissonBoltzmannPotential::cart2idx ( numeric::xyzVector< core::Real > const &  cartX, numeric::xyzVector< core::Real > &  idxX  ) const

inline

References c2i_, and lower_bound_.

Referenced by get_potential().

void core::scoring::PB::eval_PB_energy_residue	(	core::conformation::Residue const &	rsd,
		Real &	PB_energy_residue,
		Real &	PB_energy_backbone,
		Real &	PB_energy_sidechain,
		Real const &	PB_burial_weight
	)		const

References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atomic_charge(), get_potential(), core::conformation::Residue::natoms(), potential_, and core::conformation::Residue::xyz().

core::Real core::scoring::PB::get_potential	(	ObjexxFCL::FArray3D< core::Real > const &	potential,
		numeric::xyzVector< core::Real > const &	cartX
	)		const

References cart2idx(), core::scoring::electron_density::interp_linear(), and out_of_bounds().

Referenced by eval_PB_energy_residue().

template<class Q >

void core::scoring::PoissonBoltzmannPotential::idx2cart ( numeric::xyzVector< Q > const &  idxX, numeric::xyzVector< core::Real > &  cartX  ) const

inline

References i2c_, and lower_bound_.

Referenced by load_APBS_potential().

void core::scoring::PB::load_APBS_potential ( )

private

Read & load the APBS results.

References dx_filename_, utility::io::izstream::getline(), i2c_, idx2cart(), lower_bound_, n_grid_, basic::options::option, utility::io::izstream::peek(), potential_, basic::options::OptionKeys::pb_potential::potential_cap, runtime_assert, core::scoring::TR, and upper_bound_.

Referenced by solve_pb().

numeric::xyzVector< core::Real > core::scoring::PoissonBoltzmannPotential::lower_bound ( ) const

inline

References lower_bound_.

Referenced by out_of_bounds().

bool core::scoring::PoissonBoltzmannPotential::out_of_bounds ( numeric::xyzVector< core::Real > const  cartX ) const

inline

References lower_bound(), and upper_bound().

Referenced by get_potential().

void core::scoring::PB::solve_pb	(	core::pose::Pose const &	pose,
		std::string const &	state_tag,
		std::map< std::string, bool > const &	is_residue_charged_by_name
	)

Execute ABPS to freshly compute the electrotatic field.

Parameters

pose	The pose
state_tag	Arbitrary string for generating APBS files. e.g. The current energy state.
is_residue_charged_by_name	Which residues are charged? The key is the residue name.

References APBS_CONFIG_EXT, APBS_DX_EXT, basic::options::OptionKeys::pb_potential::apbs_path, apbs_path_, APBS_PQR_EXT, begin, basic::options::OptionKeys::pb_potential::calcenergy, calcenergy_, config_filename_, dx_filename_, core::sequence::end, load_APBS_potential(), basic::options::option, pqr_filename_, runtime_assert, core::scoring::TR, user, write_config(), and write_pqr().

numeric::xyzVector< core::Real > core::scoring::PoissonBoltzmannPotential::upper_bound ( ) const

inline

References upper_bound_.

Referenced by out_of_bounds().

void core::scoring::PB::write_config ( core::pose::Pose const &  pose ) const

private

Prepare ABPS - generate .in and .pqr.

Write out the configurati

References APBS_DX_EXT, calcenergy_, core::conformation::membrane::center, config_filename_, dx_filename_, core::chemical::element::F, core::chemical::element::I, length, core::conformation::Residue::natoms(), pqr_filename_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::scoring::TR, numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by solve_pb().

void core::scoring::PB::write_pqr ( core::pose::Pose const &  pose, std::map< std::string, bool > const &  is_residue_charged_by_name  ) const

private

Write out .pqr.

References core::chemical::ResidueType::atom(), chain, core::chemical::Atom::charge(), charged_chains, chr_chains(), core::chemical::element::F, core::chemical::element::I, nres, pqr_filename_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::scoring::TR.

Referenced by solve_pb().

Member Data Documentation

const std::string core::scoring::PB::APBS_CONFIG_EXT = ".in"

static

Referenced by solve_pb().

const std::string core::scoring::PB::APBS_DX_EXT = ".dx"

static

Referenced by solve_pb(), and write_config().

std::string core::scoring::PoissonBoltzmannPotential::apbs_path_

private

Referenced by solve_pb().

const std::string core::scoring::PB::APBS_PQR_EXT = ".pqr"

static

Referenced by solve_pb().

numeric::xyzMatrix< core::Real > core::scoring::PoissonBoltzmannPotential::c2i_

private

Referenced by cart2idx().

bool core::scoring::PoissonBoltzmannPotential::calcenergy_

private

Referenced by solve_pb(), and write_config().

std::string core::scoring::PoissonBoltzmannPotential::config_filename_

private

Referenced by solve_pb(), and write_config().

const std::string core::scoring::PB::DEFAULT_APBS_PATH = "apbs"

static

std::string core::scoring::PoissonBoltzmannPotential::dx_filename_

private

Referenced by load_APBS_potential(), solve_pb(), and write_config().

numeric::xyzVector< core::Real > core::scoring::PoissonBoltzmannPotential::grid_spacing_

private

numeric::xyzMatrix< core::Real > core::scoring::PoissonBoltzmannPotential::i2c_

private

Referenced by idx2cart(), and load_APBS_potential().

numeric::xyzVector< core::Real > core::scoring::PoissonBoltzmannPotential::lower_bound_

private

Referenced by cart2idx(), idx2cart(), load_APBS_potential(), and lower_bound().

numeric::xyzVector< core::Size > core::scoring::PoissonBoltzmannPotential::n_grid_

private

Referenced by load_APBS_potential().

ObjexxFCL::FArray3D< core::Real > core::scoring::PoissonBoltzmannPotential::potential_

private

Referenced by eval_PB_energy_residue(), and load_APBS_potential().

std::string core::scoring::PoissonBoltzmannPotential::pqr_filename_

private

Referenced by solve_pb(), write_config(), and write_pqr().

numeric::xyzVector< core::Real > core::scoring::PoissonBoltzmannPotential::upper_bound_

private

Referenced by load_APBS_potential(), and upper_bound().

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

• src/core/scoring/PoissonBoltzmannPotential.hh
• src/core/scoring/PoissonBoltzmannPotential.cc