#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_dm (bool dm)
	set target function More...

void	set_prime_and_switch (bool prime_and_switch)
	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 target function 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	res_low_

core::Real	res_high_

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_

utility::vector1< std::string >	cif_files_

bool	dm_

bool	prime_and_switch_

core::pose::PoseOP	ref_pose_

Constructor & Destructor Documentation

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

constructor

References adp_strategy_, dm_, filename(), basic::options::OptionKeys::cryst::mtzfile, mtzfile_, basic::options::option, path, phenix_home_, prime_and_switch_, res_high_, res_low_, target_function_, tempdir_, and twin_law_.

Member Function Documentation

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(), tempdir_, and utility_exit_with_message.

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(), utility_exit, and utility_exit_with_message.

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

dump r and rfree to a string for informational purposes

References getR(), getRfree(), and utility_exit_with_message.

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

dump r and rfree

References utility_exit_with_message.

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

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

References utility_exit_with_message.

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

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

score a structure

References score, and utility_exit_with_message.

Referenced by core::scoring::cryst::XtalMLEnergy::finalize_total_energy(), and core::scoring::cryst::XtalMLEnergy::setup_for_minimizing().

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 score, and utility_exit_with_message.

Referenced by core::scoring::cryst::XtalMLEnergy::setup_for_derivatives().

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

private

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

optimize fmask

explicitly recompute ksol/bsol

References getR(), getRfree(), and utility_exit_with_message.

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

explicitly recompute ksol/bsol

References getR(), getRfree(), and utility_exit_with_message.

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

explicitly recompute ksol/bsol and fmask

References getR(), getRfree(), and utility_exit_with_message.

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

inline

set strategy for adp refinement

References adp_strategy_.

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

inline

set target function

References cif_files_.

void core::scoring::cryst::PhenixInterface::set_dm ( bool dm )

set target function

References dm_, and utility_exit_with_message.

void core::scoring::cryst::PhenixInterface::set_prime_and_switch ( bool prime_and_switch )

set target function

References prime_and_switch_, and utility_exit_with_message.

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

inline

set target function

References target_function_.

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

set sf calculation algorithm

References algo_, and utility_exit_with_message.

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

References res_high_, res_low_, and utility_exit_with_message.

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

set twin law

References twin_law_, and utility_exit_with_message.

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

private

References core::chemical::ResidueType::atom_index(), core::pose::symmetry::extract_asymmetric_unit(), core::scoring::cryst::fix_bfactorsH(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), and utility_exit_with_message.

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

update fcalc

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

update mask

References getR(), getRfree(), and utility_exit_with_message.

Referenced by core::scoring::cryst::XtalMLEnergy::setup_for_derivatives(), and core::scoring::cryst::XtalMLEnergy::setup_for_minimizing().

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

update mask

References getR(), getRfree(), initialize_target_evaluator(), and utility_exit_with_message.

Member Data Documentation

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

private

Referenced by PhenixInterface(), and set_adp_strategy().

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

private

Referenced by initialize_target_evaluator(), and setAlgorithm().

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

private

Referenced by set_cif_files().

bool core::scoring::cryst::PhenixInterface::dm_

private

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

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

private

Referenced by initialize_target_evaluator(), and PhenixInterface().

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

private

Referenced by PhenixInterface().

bool core::scoring::cryst::PhenixInterface::prime_and_switch_

private

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

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

private

Referenced by initialize_target_evaluator().

core::Real core::scoring::cryst::PhenixInterface::res_high_

private

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

core::Real core::scoring::cryst::PhenixInterface::res_low_

private

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

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

private

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

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

private

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

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:

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

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation