functions which iterates over PDBs, chops out fragments and scores them, and then outputs residue energies More...

#include <devel/init.hh>
#include <core/chemical/AA.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperation.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/util.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunctionInfo.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <basic/options/option.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <basic/MetricValue.hh>
#include <basic/prof.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/format.hh>
#include <sstream>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <string>
#include <core/import_pose/import_pose.hh>

Namespaces
	rss_energy_calculator

Functions
void	init_usage_prompt (std::string exe)

void	repack_pose (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn)
	Takes the input Pose and runs a fast repack protocol on it. More...

void	create_and_score_fragments (std::string pdb_filename, scoring::ScoreFunctionOP scorefxn, std::map< std::string, std::vector< std::pair< std::string, scoring::EnergyMap > > > &aa_to_vector_pair_sequence_energymap)

void	score_folded_residues (std::string pdb_filename, scoring::ScoreFunctionOP scorefxn, std::map< std::string, std::vector< std::pair< std::string, scoring::EnergyMap > > > &aa_to_vector_pair_sequence_energymap)
	and stores them in the passed-in map More...

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

Variables
static basic::Tracer	TR ("rss_energy_calculator")

BooleanOptionKey const	rss_energy_calculator::no_repack_before_fragmenting ("rss_energy_calculator::no_repack_before_fragmenting")

BooleanOptionKey const	rss_energy_calculator::no_repack_before_scoring_fragment ("rss_energy_calculator::no_repack_before_scoring_fragment")

IntegerOptionKey const	rss_energy_calculator::fragment_length ("rss_energy_calculator::fragment_length")

std::string	usage_string

Detailed Description

functions which iterates over PDBs, chops out fragments and scores them, and then outputs residue energies

Author: Ron Jacak (ronj@.nosp@m.emai.nosp@m.l.unc.nosp@m..edu)

Function Documentation

◆ create_and_score_fragments()

void create_and_score_fragments	(	std::string	pdb_filename,
		scoring::ScoreFunctionOP	scorefxn,
		std::map< std::string, std::vector< std::pair< std::string, scoring::EnergyMap > > > &	aa_to_vector_pair_sequence_energymap
	)

References predPRE::chain, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, rss_energy_calculator::fragment_length, create_a3b_hbs::i, beta_nonlocal::jj, rss_energy_calculator::no_repack_before_fragmenting, rss_energy_calculator::no_repack_before_scoring_fragment, option, demo.D010_Pose_structure::pdb_filename, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), numeric::random::random_range(), repack_pose(), oop_conformations::scorefxn, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

◆ init_usage_prompt()

void init_usage_prompt ( std::string exe )

References usage_string.

Referenced by main().

◆ main()

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

References argv, utility::file::FileName::bare_name(), utility::io::oc::cerr, data, enumerate_junctions::default, test.T009_Exceptions::e, ObjexxFCL::format::F(), utility::file::file_exists(), file_exists(), rss_energy_calculator::fragment_length, pyrosetta.distributed.io::get_score_function(), getline(), create_a3b_hbs::i, basic::init(), init_usage_prompt(), subloop_histogram::iterator, beta_nonlocal::jj, kk, in::file::l(), line, utility::file::FileName::name(), rss_energy_calculator::no_repack_before_fragmenting, rss_energy_calculator::no_repack_before_scoring_fragment, basic::options::OptionKeys::AnchoredDesign::filters::omega, option, basic::options::OptionKeys::corrections::score::p_aa_pp, kic_runner::pdb, basic::options::OptionKeys::remodel::rama, in::file::s(), score_folded_residues(), oop_conformations::scorefxn, subloop_histogram::size, TR, usage_string, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and utility_exit_with_message_status.

◆ repack_pose()

void repack_pose	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	scorefxn
	)

Takes the input Pose and runs a fast repack protocol on it.

References beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by create_and_score_fragments(), and score_folded_residues().

◆ score_folded_residues()

void score_folded_residues	(	std::string	pdb_filename,
		scoring::ScoreFunctionOP	scorefxn,
		std::map< std::string, std::vector< std::pair< std::string, scoring::EnergyMap > > > &	aa_to_vector_pair_sequence_energymap
	)