cs_rosetta_rna.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/pose/rna/BasePair.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.fwd.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <protocols/rna/denovo/RNA_DeNovoPoseInitializer.hh>
#include <core/import_pose/RNA_DeNovoParameters.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <iostream>
#include <string>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <protocols/viewer/viewers.hh>
#include <utility/vector1.hh>

Functions
ScoreFunctionOP	create_cs_rosetta_rna_scorefxn ()
utility::vector1< BasePair >	get_obligated_rna_pairings (RNA_DeNovoParameters const &rna_struct_params)
RNA_MinimizerOP	setup_rna_minimizer (ScoreFunctionOP scorefxn, RNA_DeNovoParameters const &rna_struct_params, core::pose::Pose &pose)
Real	compute_chem_shift_RMSD (Pose const &pose)
void	close_chain_breaks (Pose &pose)
void	cs_rosetta_rna_pdb (bool perform_minimize)
void *	my_main (void *)
int	main (int argc, char *argv[])

Function Documentation

close_chain_breaks()

void close_chain_breaks

(

Pose &

pose

)

References beta_nonlocal::pose.

Referenced by cs_rosetta_rna_pdb().

compute_chem_shift_RMSD()

Real compute_chem_shift_RMSD

(

Pose const &

pose

)

References pyrosetta::create_score_function, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::score::rna::rna_chemical_shift_exp_data, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by cs_rosetta_rna_pdb().

create_cs_rosetta_rna_scorefxn()

ScoreFunctionOP create_cs_rosetta_rna_scorefxn

(

)

References utility::io::oc::cout, pyrosetta::create_score_function, and oop_conformations::scorefxn.

Referenced by cs_rosetta_rna_pdb().

cs_rosetta_rna_pdb()

void cs_rosetta_rna_pdb

(

bool

perform_minimize

)

References basename, close_chain_breaks(), compute_chem_shift_RMSD(), utility::io::oc::cout, create_cs_rosetta_rna_scorefxn(), basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::option, basic::options::OptionKeys::flexPepDocking::params_file, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::score::rna::rna_chemical_shift_exp_data, oop_conformations::scorefxn, setup_rna_minimizer(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

get_obligated_rna_pairings()

utility::vector1< BasePair > get_obligated_rna_pairings

(

RNA_DeNovoParameters const &

rna_struct_params

)

References utility::io::oc::cout, create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by setup_rna_minimizer().

main()

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

References argv, utility::io::oc::cout, test.T009_Exceptions::e, basic::init(), SmotifHasher::mode, my_main(), NEW_OPT, basic::options::OptionKeys::flexPepDocking::params_file, kic_runner::pdb, and viewer_main().

my_main()

void* my_main

(

void *

)

References cs_rosetta_rna_pdb(), utility::options::OptionKeys::options::exit, SmotifHasher::mode, basic::options::option, and utility_exit_with_message.

Referenced by main().

setup_rna_minimizer()

RNA_MinimizerOP setup_rna_minimizer	(	ScoreFunctionOP	scorefxn,
		RNA_DeNovoParameters const &	rna_struct_params,
		core::pose::Pose &	pose
	)

References utility::io::oc::cout, get_obligated_rna_pairings(), beta_nonlocal::pose, erraser_analysis::res1, erraser_analysis::res2, cal_NBR_radius::res_num, and oop_conformations::scorefxn.

Referenced by cs_rosetta_rna_pdb().