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Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::scoring::cryst::PhenixInterface Class Reference

#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

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

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(), and tempdir_.

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

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

core::Real core::scoring::cryst::PhenixInterface::getR ( )
core::Real core::scoring::cryst::PhenixInterface::getRfree ( )
core::Real core::scoring::cryst::PhenixInterface::getScore ( core::pose::Pose const &  pose)
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::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 core::scoring::cryst::TR().

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

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

explicitly recompute ksol/bsol

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

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

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().

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().

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().

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

set target function

References map_type_.

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

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().

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().

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

set sf calculation algorithm

References algo_.

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

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().

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

set twin law

References twin_law_.

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

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

update fcalc

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

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

Member Data Documentation

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

Referenced by set_cif_files().

std::string core::scoring::cryst::PhenixInterface::map_type_
private
std::string core::scoring::cryst::PhenixInterface::mtzfile_
private
std::string core::scoring::cryst::PhenixInterface::phenix_home_
private

Referenced by PhenixInterface().

core::pose::PoseOP core::scoring::cryst::PhenixInterface::ref_pose_
private
core::Real core::scoring::cryst::PhenixInterface::sharpen_b_
private
std::string core::scoring::cryst::PhenixInterface::target_function_
private
std::string core::scoring::cryst::PhenixInterface::tempdir_
private
std::string core::scoring::cryst::PhenixInterface::twin_law_
private

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