core::scoring::PoissonBoltzmannPotential Class Reference

#include <PoissonBoltzmannPotential.hh>

Inheritance diagram for core::scoring::PoissonBoltzmannPotential:

Public Member Functions
	PoissonBoltzmannPotential ()
	~PoissonBoltzmannPotential () override
core::Real	get_potential (numeric::xyzVector< core::Real > const &cartX) const
Real	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, bool cleanup_files=false)
void	solve_pb (core::pose::Pose const &pose, std::string const &state_tag, id::AtomID_Map< bool > const &charged_atoms, id::AtomID_Map< bool > const &present_atoms, bool cleanup_files=false)
void	cleanup_files () const

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
std::string	fpath (std::string const &file) const
void	write_config (core::pose::Pose const &pose, id::AtomID_Map< bool > const &present_atoms) 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, id::AtomID_Map< bool > const &charged_atoms, id::AtomID_Map< bool > const &present_atoms) 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_
std::string	scratch_dir_
bool	calcenergy_

Constructor & Destructor Documentation

PoissonBoltzmannPotential()

core::scoring::PB::PoissonBoltzmannPotential

(

)

~PoissonBoltzmannPotential()

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

overridedefault

Member Function Documentation

cart2idx()

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().

cleanup_files()

void core::scoring::PB::cleanup_files

(

)

const

References config_filename_, dx_filename_, fpath(), and pqr_filename_.

Referenced by solve_pb().

eval_PB_energy_residue()

Real 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(), and core::conformation::Residue::xyz().

fpath()

std::string core::scoring::PB::fpath ( std::string const &  file ) const

private

References scratch_dir_.

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

get_potential()

core::Real core::scoring::PB::get_potential

(

numeric::xyzVector< core::Real > const &

cartX

)

const

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

Referenced by eval_PB_energy_residue(), core::scoring::sc::ElectrostaticComplementarityCalculator::prepare_correlation_lists(), and core::scoring::sc::ElectrostaticSimilarityCalculator::prepare_correlation_lists().

idx2cart()

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().

load_APBS_potential()

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

private

Read & load the APBS results.

References c2i_, dx_filename_, fpath(), grid_spacing_, i2c_, idx2cart(), lower_bound_, n_grid_, potential_, core::scoring::TR(), and upper_bound_.

Referenced by solve_pb().

lower_bound()

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

inline

References lower_bound_.

Referenced by out_of_bounds().

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().

solve_pb() [1/2]

void core::scoring::PB::solve_pb	(	core::pose::Pose const &	pose,
		std::string const &	state_tag,
		id::AtomID_Map< bool > const &	charged_atoms,
		id::AtomID_Map< bool > const &	present_atoms,
		bool	cleanup_files = false
	)

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

solve_pb() [2/2]

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,
		bool	cleanup_files = false
	)

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 cleanup_files(), core::id::AtomID_Map< T >::fill_with(), core::pose::initialize_atomid_map(), core::chemical::ResidueTypeBase::name(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::type().

Referenced by core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), and core::scoring::sc::ElectrostaticSimilarityCalculator::Calc().

upper_bound()

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

inline

References upper_bound_.

Referenced by out_of_bounds().

write_config()

void core::scoring::PB::write_config ( core::pose::Pose const &  pose, id::AtomID_Map< bool > const &  present_atoms  ) 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, fpath(), core::chemical::element::I, pqr_filename_, core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by solve_pb().

write_pqr()

void core::scoring::PB::write_pqr ( core::pose::Pose const &  pose, id::AtomID_Map< bool > const &  charged_atoms, id::AtomID_Map< bool > const &  present_atoms  ) const

private

Write out .pqr.

References core::conformation::Residue::atom(), core::chemical::ResidueType::atom_charge(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::chain(), chr_chains(), core::chemical::element::F, fpath(), core::chemical::element::I, core::chemical::AtomType::is_virtual(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), pqr_filename_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::seqpos(), core::pose::Pose::size(), core::scoring::TR(), and core::conformation::Atom::xyz().

Referenced by solve_pb().

Member Data Documentation

APBS_CONFIG_EXT

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

static

Referenced by solve_pb().

APBS_DX_EXT

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

static

Referenced by solve_pb(), and write_config().

apbs_path_

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

private

Referenced by solve_pb().

APBS_PQR_EXT

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

static

Referenced by solve_pb().

c2i_

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

private

Referenced by cart2idx(), and load_APBS_potential().

calcenergy_

bool core::scoring::PoissonBoltzmannPotential::calcenergy_

private

Referenced by solve_pb(), and write_config().

config_filename_

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

private

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

DEFAULT_APBS_PATH

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

static

dx_filename_

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

private

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

grid_spacing_

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

private

Referenced by load_APBS_potential().

i2c_

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

private

Referenced by idx2cart(), and load_APBS_potential().

lower_bound_

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

private

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

n_grid_

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

private

Referenced by load_APBS_potential().

potential_

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

private

Referenced by get_potential(), and load_APBS_potential().

pqr_filename_

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

private

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

scratch_dir_

std::string core::scoring::PoissonBoltzmannPotential::scratch_dir_

private

Referenced by fpath(), and solve_pb().

upper_bound_

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