#include <PoissonBoltzmannPotential.hh>

Inheritance diagram for core::scoring::PoissonBoltzmannPotential:

Collaboration diagram for core::scoring::PoissonBoltzmannPotential:

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_

Detailed Description

Definition at line 37 of file PoissonBoltzmannPotential.hh.

Constructor & Destructor Documentation

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

Definition at line 80 of file PoissonBoltzmannPotential.cc.

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

virtual

Definition at line 78 of file PoissonBoltzmannPotential.cc.

Member Function Documentation

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

inline

Definition at line 64 of file PoissonBoltzmannPotential.hh.

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

Definition at line 99 of file PoissonBoltzmannPotential.cc.

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

Definition at line 90 of file PoissonBoltzmannPotential.cc.

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

Definition at line 69 of file PoissonBoltzmannPotential.hh.

References i2c_, and lower_bound_.

Referenced by load_APBS_potential().

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

private

Read & load the APBS results.

Definition at line 281 of file PoissonBoltzmannPotential.cc.

References dx_filename_, i2c_, idx2cart(), lower_bound_, n_grid_, potential_, core::scoring::TR(), and upper_bound_.

Referenced by solve_pb().

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

inline

Definition at line 72 of file PoissonBoltzmannPotential.hh.

References lower_bound_.

Referenced by out_of_bounds().

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

inline

Definition at line 79 of file PoissonBoltzmannPotential.hh.

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.

Definition at line 240 of file PoissonBoltzmannPotential.cc.

References APBS_CONFIG_EXT, APBS_DX_EXT, apbs_path_, APBS_PQR_EXT, calcenergy_, config_filename_, dx_filename_, core::sequence::end, load_APBS_potential(), pqr_filename_, core::scoring::TR(), write_config(), and write_pqr().