#include <PhenixInterface.hh>

Public Member Functions
	PhenixInterface ()
	constructor More...

core::Real	getScore (core::pose::Pose const &pose)
	score a structure More...

core::Real	getScoreAndDerivs (core::pose::Pose const &pose, utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &grads)
	score a structure with derivatives More...

void	fitBfactors (core::pose::Pose &pose)
	fit bfactors More...

std::string	getInfoLine ()
	dump r and rfree to a string for informational purposes More...

core::Real	getR ()
	dump r and rfree More...

core::Real	getRfree ()

void	updateFcalc ()
	update fcalc More...

void	updateSolventMask ()
	update mask More...

void	updateSolventMask (core::pose::Pose const &pose)
	update mask More...

void	optimizeSolventMask ()
	optimize fmask More...

void	optimizeSolvParams ()
	explicitly recompute ksol/bsol More...

void	optimizeSolvParamsAndMask ()
	explicitly recompute ksol/bsol and fmask More...

void	setResLimits (core::Real res_high=0.0, core::Real res_low=0.0)
	set the res limits More...

void	setTwinLaw (std::string twin_law)
	set twin law More...

void	setAlgorithm (std::string twin_law)
	set sf calculation algorithm More...

void	set_map_type (std::string map_type)
	set target function More...

void	set_adp_strategy (std::string adp_strat)
	set strategy for adp refinement More...

void	set_target_function (std::string tgt_val)
	set target function More...

void	set_cif_files (utility::vector1< std::string > cif_in)
	set cif files (ligand refinement) More...

void	set_sharpen_b (core::Real sharpen_b)
	set b sharpen value More...

std::string	calculateDensityMap (core::pose::Pose &pose, bool no_sidechain=false)
	use pose to rephase data; calculate a new density map; return map file name More...

Private Member Functions
void	stealBfactorsFromFile (core::pose::Pose &pose, std::string filename)

void	initialize_target_evaluator (core::pose::Pose const &pose, std::string eff_file="")

Private Attributes
core::Real	sharpen_b_

std::string	tempdir_

std::string	mtzfile_

std::string	phenix_home_

std::string	adp_strategy_

std::string	target_function_

std::string	twin_law_

std::string	algo_

std::string	map_type_

utility::vector1< std::string >	cif_files_

core::pose::PoseOP	ref_pose_

Constructor & Destructor Documentation

◆ PhenixInterface()

core::scoring::cryst::PhenixInterface::PhenixInterface ( )

constructor

References adp_strategy_, protocols::abinitio::filename(), map_type_, mtzfile_, protocols::hybridization::path, phenix_home_, sharpen_b_, target_function_, tempdir_, and twin_law_.

Member Function Documentation

◆ calculateDensityMap()

std::string core::scoring::cryst::PhenixInterface::calculateDensityMap	(	core::pose::Pose &	pose,
		bool	no_sidechain = `false`
	)

use pose to rephase data; calculate a new density map; return map file name

References initialize_target_evaluator(), and tempdir_.

Referenced by protocols::cryst::RecomputeDensityMapMover::apply().

◆ fitBfactors()

void core::scoring::cryst::PhenixInterface::fitBfactors ( core::pose::Pose & pose )

fit bfactors

References core::pose::Pose::dump_pdb(), core::pose::symmetry::extract_asymmetric_unit(), core::scoring::cryst::fix_bfactorsH(), core::scoring::cryst::fix_bfactorsMissing(), core::pose::initialize_disulfide_bonds(), and core::scoring::cryst::TR().

Referenced by protocols::cryst::FitBfactorsMover::apply().

◆ getInfoLine()

std::string core::scoring::cryst::PhenixInterface::getInfoLine ( )

dump r and rfree to a string for informational purposes

References getR(), and getRfree().

Referenced by protocols::cryst::TagPoseWithRefinementStatsMover::apply().

◆ getR()

core::Real core::scoring::cryst::PhenixInterface::getR ( )

dump r and rfree

Referenced by core::energy_methods::XtalMLEnergy::finalize_total_energy(), getInfoLine(), optimizeSolventMask(), optimizeSolvParams(), optimizeSolvParamsAndMask(), and updateSolventMask().

◆ getRfree()

core::Real core::scoring::cryst::PhenixInterface::getRfree ( )

Referenced by core::energy_methods::XtalMLEnergy::finalize_total_energy(), getInfoLine(), optimizeSolventMask(), optimizeSolvParams(), optimizeSolvParamsAndMask(), and updateSolventMask().

◆ getScore()

core::Real core::scoring::cryst::PhenixInterface::getScore ( core::pose::Pose const & pose )

score a structure

References protocols::hybridization::score.

Referenced by protocols::cryst::FitBfactorsMover::apply(), protocols::cryst::UpdateSolventMover::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), core::energy_methods::XtalMLEnergy::finalize_total_energy(), and core::energy_methods::XtalMLEnergy::setup_for_minimizing().

◆ getScoreAndDerivs()

core::Real core::scoring::cryst::PhenixInterface::getScoreAndDerivs	(	core::pose::Pose const &	pose,
		utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &	grads
	)

score a structure with derivatives

References protocols::hybridization::score.

Referenced by core::energy_methods::XtalMLEnergy::setup_for_derivatives().

◆ initialize_target_evaluator()

void core::scoring::cryst::PhenixInterface::initialize_target_evaluator	(	core::pose::Pose const &	pose,
		std::string	eff_file = `""`
	)

private

References algo_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::initialize_disulfide_bonds(), core::pose::symmetry::is_symmetric(), map_type_, mtzfile_, ref_pose_, core::scoring::Energies::scoring_end(), sharpen_b_, target_function_, tempdir_, core::scoring::cryst::TR(), and twin_law_.

Referenced by calculateDensityMap(), and updateSolventMask().

◆ optimizeSolventMask()

void core::scoring::cryst::PhenixInterface::optimizeSolventMask ( )

optimize fmask

explicitly recompute ksol/bsol

References getR(), getRfree(), and core::scoring::cryst::TR().

Referenced by protocols::cryst::UpdateSolventMover::apply().

◆ optimizeSolvParams()

void core::scoring::cryst::PhenixInterface::optimizeSolvParams ( )

explicitly recompute ksol/bsol

References getR(), getRfree(), and core::scoring::cryst::TR().

Referenced by protocols::cryst::UpdateSolventMover::apply().

◆ optimizeSolvParamsAndMask()

void core::scoring::cryst::PhenixInterface::optimizeSolvParamsAndMask ( )

explicitly recompute ksol/bsol and fmask

References getR(), getRfree(), and core::scoring::cryst::TR().

Referenced by protocols::cryst::UpdateSolventMover::apply().

◆ set_adp_strategy()

void core::scoring::cryst::PhenixInterface::set_adp_strategy ( std::string adp_strat )

inline

set strategy for adp refinement

References adp_strategy_.

Referenced by protocols::cryst::FitBfactorsMover::apply().

◆ set_cif_files()

void core::scoring::cryst::PhenixInterface::set_cif_files ( utility::vector1< std::string > cif_in )

inline

set cif files (ligand refinement)

References cif_files_.

Referenced by protocols::cryst::SetRefinementOptionsMover::apply().

◆ set_map_type()

void core::scoring::cryst::PhenixInterface::set_map_type ( std::string map_type )

set target function

References map_type_.

Referenced by protocols::cryst::SetRefinementOptionsMover::apply().

◆ set_sharpen_b()

void core::scoring::cryst::PhenixInterface::set_sharpen_b ( core::Real sharpen_b )

inline

set b sharpen value

References sharpen_b_.

Referenced by protocols::cryst::SetRefinementOptionsMover::apply().

◆ set_target_function()

void core::scoring::cryst::PhenixInterface::set_target_function ( std::string tgt_val )

inline

set target function

References target_function_.

Referenced by protocols::cryst::SetRefinementOptionsMover::apply().

◆ setAlgorithm()

void core::scoring::cryst::PhenixInterface::setAlgorithm ( std::string twin_law )

set sf calculation algorithm

References algo_.

Referenced by protocols::cryst::SetRefinementOptionsMover::apply().

◆ setResLimits()

void core::scoring::cryst::PhenixInterface::setResLimits	(	core::Real	res_high = `0.0`,
		core::Real	res_low = `0.0`
	)

set the res limits

update res limits

Referenced by protocols::cryst::SetRefinementOptionsMover::apply().

◆ setTwinLaw()

void core::scoring::cryst::PhenixInterface::setTwinLaw ( std::string twin_law )

set twin law

References twin_law_.

Referenced by protocols::cryst::SetRefinementOptionsMover::apply().

◆ stealBfactorsFromFile()

void core::scoring::cryst::PhenixInterface::stealBfactorsFromFile	(	core::pose::Pose &	pose,
		std::string	filename
	)

private

References core::chemical::ResidueType::atom_index(), core::chemical::element::B, core::chemical::ResidueTypeBase::canonical_atom_aliases(), core::pose::symmetry::extract_asymmetric_unit(), protocols::abinitio::filename(), core::scoring::cryst::fix_bfactorsH(), core::conformation::membrane::in, core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), and core::scoring::cryst::TR().

◆ updateFcalc()

void core::scoring::cryst::PhenixInterface::updateFcalc ( )

update fcalc

Referenced by protocols::cryst::UpdateSolventMover::apply().

◆ updateSolventMask() [1/2]

void core::scoring::cryst::PhenixInterface::updateSolventMask ( )

update mask

References getR(), getRfree(), and core::scoring::cryst::TR().

Referenced by protocols::cryst::UpdateSolventMover::apply(), core::energy_methods::XtalMLEnergy::setup_for_derivatives(), and core::energy_methods::XtalMLEnergy::setup_for_minimizing().

◆ updateSolventMask() [2/2]

void core::scoring::cryst::PhenixInterface::updateSolventMask ( core::pose::Pose const & pose )

update mask

References getR(), getRfree(), initialize_target_evaluator(), and core::scoring::cryst::TR().

Member Data Documentation

◆ adp_strategy_

std::string core::scoring::cryst::PhenixInterface::adp_strategy_

private

Referenced by PhenixInterface(), and set_adp_strategy().

◆ algo_

std::string core::scoring::cryst::PhenixInterface::algo_

private

Referenced by initialize_target_evaluator(), and setAlgorithm().

◆ cif_files_

utility::vector1<std::string> core::scoring::cryst::PhenixInterface::cif_files_

private

Referenced by set_cif_files().

◆ map_type_

std::string core::scoring::cryst::PhenixInterface::map_type_

private

Referenced by initialize_target_evaluator(), PhenixInterface(), and set_map_type().

◆ mtzfile_

std::string core::scoring::cryst::PhenixInterface::mtzfile_

private

Referenced by initialize_target_evaluator(), and PhenixInterface().

◆ phenix_home_

std::string core::scoring::cryst::PhenixInterface::phenix_home_

private

Referenced by PhenixInterface().

◆ ref_pose_

core::pose::PoseOP core::scoring::cryst::PhenixInterface::ref_pose_

private

Referenced by initialize_target_evaluator().

◆ sharpen_b_

core::Real core::scoring::cryst::PhenixInterface::sharpen_b_

private

Referenced by initialize_target_evaluator(), PhenixInterface(), and set_sharpen_b().

◆ target_function_

std::string core::scoring::cryst::PhenixInterface::target_function_

private

Referenced by initialize_target_evaluator(), PhenixInterface(), and set_target_function().

◆ tempdir_

std::string core::scoring::cryst::PhenixInterface::tempdir_

private

Referenced by calculateDensityMap(), initialize_target_evaluator(), and PhenixInterface().

◆ twin_law_

std::string core::scoring::cryst::PhenixInterface::twin_law_

private

Referenced by initialize_target_evaluator(), PhenixInterface(), and setTwinLaw().

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

src/core/scoring/cryst/PhenixInterface.hh
src/core/scoring/cryst/PhenixInterface.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ PhenixInterface()

Member Function Documentation

◆ calculateDensityMap()

◆ fitBfactors()

◆ getInfoLine()

◆ getR()

◆ getRfree()

◆ getScore()

◆ getScoreAndDerivs()

◆ initialize_target_evaluator()

◆ optimizeSolventMask()

◆ optimizeSolvParams()

◆ optimizeSolvParamsAndMask()

◆ set_adp_strategy()

◆ set_cif_files()

◆ set_map_type()

◆ set_sharpen_b()

◆ set_target_function()

◆ setAlgorithm()

◆ setResLimits()

◆ setTwinLaw()

◆ stealBfactorsFromFile()

◆ updateFcalc()

◆ updateSolventMask() [1/2]

◆ updateSolventMask() [2/2]

Member Data Documentation

◆ adp_strategy_

◆ algo_

◆ cif_files_

◆ map_type_

◆ mtzfile_

◆ phenix_home_

◆ ref_pose_

◆ sharpen_b_

◆ target_function_

◆ tempdir_

◆ twin_law_