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ScoreFunctionFactory.cc File Reference
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/DockingScoreFunction.hh>
#include <core/scoring/MinScoreScoreFunction.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/chemical/AA.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/options/OptionCollection.hh>
#include <utility/options/keys/OptionKeyList.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <basic/options/keys/mistakes.OptionKeys.gen.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/citation_manager/CitationManager.hh>
#include <sstream>
#include <utility/string_util.hh>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::scoring
 

Functions

static basic::Tracer TR ("core.scoring.ScoreFunctionFactory")
 
std::string const core::scoring::REF_2015 ("ref2015")
 
std::string const core::scoring::TALARIS_2014 ("talaris2014")
 
std::string const core::scoring::TALARIS_2013 ("talaris2013")
 
std::string const core::scoring::TALARIS_2013_CART ("talaris2013_cart")
 
std::string const core::scoring::PRE_TALARIS_2013_STANDARD_WTS ("pre_talaris_2013_standard")
 
std::string const core::scoring::CENTROID_WTS ("cen_std")
 
std::string const core::scoring::SOFT_REP_WTS ("soft_rep")
 
std::string const core::scoring::SOFT_REP_DESIGN_WTS ("soft_rep_design")
 
std::string const core::scoring::DNA_INT_WTS ("dna_no_gb")
 
std::string const core::scoring::DNA_INT_WTS_GB ("dna")
 
std::string const core::scoring::MM_STD_WTS ("mm_std")
 
std::string const core::scoring::RNA_LORES_WTS ("rna/denovo/rna_lores")
 
std::string const core::scoring::RNA_HIRES_WTS ("rna/denovo/rna_hires")
 
std::string const core::scoring::RNA_LORES_PLUS_HIRES_WTS ("rna/denovo/rna_lores_plus_hires")
 
std::string const core::scoring::MEMB_HIGHRES_WTS ("membrane_highres")
 
std::string const core::scoring::SCORE12_PATCH ("score12")
 
std::string const core::scoring::SCORE13 ("score13")
 
std::string const core::scoring::DOCK_PATCH ("docking")
 
std::string const core::scoring::DOCK_LOW_PATCH ("docking_cen")
 
std::string const core::scoring::SCORE4_SMOOTH_CART ("score4_smooth_cart")
 
std::string const core::scoring::BETA_GENPOT ("beta_genpot")
 
std::string const core::scoring::BETA_NOV16 ("beta_nov16")
 
std::string const core::scoring::BETA_NOV15 ("beta_nov15")
 
std::string const core::scoring::BETA_JULY15 ("beta_july15")
 
core::scoring::ScoreFunctionOP core::scoring::get_score_function (bool const is_fullatom=true)
 A helper function which returns a scoring function held in an owning pointer according to the user's command line parameters -score:weights and -score:patch By default it returns weights=talaris2013 for fullatom, and weights=cen_std and patch="" for centroid. More...
 
core::scoring::ScoreFunctionOP core::scoring::get_score_function (core::pose::Pose const &pose, bool const is_fullatom=true)
 Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose. More...
 
core::scoring::ScoreFunctionOP core::scoring::get_score_function (core::pose::Pose const &pose, utility::options::OptionCollection const &options, bool const is_fullatom=true)
 Get a ScoreFunction from cmd-line settings and dependant on the symmetrical state of the pose. Local Options collection. More...
 
core::scoring::ScoreFunctionOP core::scoring::get_score_function (utility::options::OptionCollection const &options, bool const is_fullatom=true)
 A helper function which creates a scoring function held in an owning pointer reading from the input OptionCollection. More...
 
void core::scoring::list_read_options_in_get_score_function (utility::options::OptionKeyList &opts)
 A documentation function which reports the set of options read by get_score_function. More...
 
core::scoring::ScoreFunctionOP core::scoring::get_score_function_legacy (std::string const &pre_talaris_2013_weight_set, std::string const &pre_talaris_2013_patch_file="")
 A helper function that either returns a ScoreFunctionOP created by get_score_function() or the one specified by the protocol which is activated by the -restore_pre_talaris_2013_behavior flag. The purpose of this function is to preserve legacy behavior for the sake of reproducibility and so that a record of the old behavior is still preserved in the code to ease the process of reverting the change to get_score_function if that were the wrong behavior. More...
 
core::scoring::ScoreFunctionOP core::scoring::get_score_function_legacy (utility::options::OptionCollection const &options, std::string const &pre_talaris_2013_weight_set, std::string const &pre_talaris_2013_patch_file)
 
void core::scoring::list_read_options_in_get_score_function_legacy (utility::options::OptionKeyList &opts)
 A documentation function which reports the set of options read by get_score_function_legacy. More...
 
std::string core::scoring::get_score_functionName (bool const is_fullatom=true)
 use the logic of get_score_function to get the name. The name format is <weights_tag>[_<patch_tag> ... ] More...
 
std::string core::scoring::basename_for_score_function (std::string const &sfxn_name)
 returns family name for a specific score function. For example, ref2015_cart returns ref2015 and beta_nov16_cst returns beta_nov16 Returns an empty string if no match is found More...
 
void core::scoring::apply_set_weights (ScoreFunctionOP scorefxn, utility::vector1< std::string > const &settings)
 

Function Documentation

static basic::Tracer TR ( "core.scoring.ScoreFunctionFactory"  )
static