sequence_tolerance_mf.cc File Reference

App for predicting the sequence tolerance of a structure or set of structures. More...

#include <protocols/genetic_algorithm/GeneticAlgorithm.hh>
#include <protocols/genetic_algorithm/FitnessFunction.hh>
#include <protocols/multistate_design/MultiStatePacker.hh>
#include <protocols/multistate_design/PackingState.hh>
#include <protocols/multistate_design/MetricCalculatorFitnessFunction.hh>
#include <protocols/multistate_design/MultiStateEntity.hh>
#include <protocols/pose_metric_calculators/DecomposeAndReweightEnergiesCalculator.hh>
#include <protocols/pose_metric_calculators/ResidueDecompositionByChainCalculator.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculatorLegacy.hh>
#include <protocols/simple_pose_metric_calculators/NumberHBondsCalculator.hh>
#include <protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <protocols/pose_metric_calculators/SurfaceCalculator.hh>
#include <protocols/pose_metric_calculators/MetricValueGetter.hh>
#include <protocols/mean_field/EnergiesByTaskCalculator.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.hh>
#include <protocols/toolbox/match_enzdes_util/EnzdesCstCache.hh>
#include <protocols/dna/PDBOutput.hh>
#include <protocols/dna/util.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/enzdes/AddorRemoveCsts.hh>
#include <devel/init.hh>
#include <protocols/mean_field/AAMatrix.hh>
#include <protocols/mean_field/AAProb.hh>
#include <core/types.hh>
#include <core/chemical/ResidueType.hh>
#include <basic/options/option.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/OperateOnCertainResidues.hh>
#include <core/pack/task/operation/ResFilters.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/task_operations/ProteinInterfaceDesignOperation.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/io/pdb/file_data.hh>
#include <core/pose/Pose.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <list>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/ms.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/mean_field.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/options/option_macros.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector0.hh>
#include <basic/MetricValue.hh>

Functions
void *	sequence_tolerance_mf_main (void *)
int	main (int argc, char *argv[])
template<typename A , typename B >
bool	cmpscnd (std::pair< A, B > const &a, std::pair< A, B > const &b)

Variables
static basic::Tracer	TR ("app.sequence_tolerance_mf")

Detailed Description

App for predicting the sequence tolerance of a structure or set of structures.

Function Documentation

cmpscnd()

template<typename A , typename B >

bool cmpscnd	(	std::pair< A, B > const &	a,
		std::pair< A, B > const &	b
	)

References a, and compute_difference::b.

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, test.T009_Exceptions::e, basic::init(), NEW_OPT, sequence_tolerance_mf_main(), surface, and viewer_main().

sequence_tolerance_mf_main()

void * sequence_tolerance_mf_main

(

void *

)

References aa, mean_field::biased_dist_all_gen(), run_backbone::choices, demo.D060_Folding::counter, end, ObjexxFCL::format::F(), evaluate_beta_mutants::file, lactamize::filename, ms::fraction_by_recombination(), func, mean_field::ga_pack_detect_interface(), ms::generations(), ms::checkpoint::gz(), create_a3b_hbs::i, basic::options::OptionKeys::mean_field::include_all_aa, basic::Tracer::Info, ms::checkpoint::interval(), ObjexxFCL::lead_zero_string_of(), ms::mutate_rate(), ms::num_packs(), ms::numresults(), basic::options::option, option, predPRE::pdbname, ms::pop_from_ss(), ms::pop_size(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.io::pose_from_pdb(), create_a3b_hbs::prefix, ms::checkpoint::prefix(), out::prefix(), basic::prof_reset(), basic::prof_show(), ms::checkpoint::rename(), packing::resfile(), mean_field::rf_peptide(), docking::s, in::file::s(), basic::options::OptionKeys::dna::specificity::score_function, subloop_histogram::size, utility::slurp(), basic::options::OptionKeys::mean_field::spec_profile, surface, predPRE::t, basic::t_debug, basic::t_info, tr, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("app.sequence_tolerance_mf") ( "app.sequence_tolerance_mf"  )

static

Referenced by sequence_tolerance_mf_main().