pack_phosphates.cc File Reference

#include <core/types.hh>
#include <core/chemical/util.hh>
#include <core/chemical/rna/RNA_Info.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/id/NamedAtomID.hh>
#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/rna/RNA_ResidueLevelTask.hh>
#include <core/pack/rotamer_trials.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/monte_carlo/rna/StepWiseRNA_MonteCarlo.hh>
#include <protocols/stepwise/monte_carlo/rna/StepWiseRNA_MonteCarloOptions.hh>
#include <protocols/stepwise/monte_carlo/rna/util.hh>
#include <protocols/viewer/viewers.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <numeric/xyz.functions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <list>

Functions
void	fix_alpha_for_pack_phosphate (pose::Pose &pose, Size const res)
void	pack_phosphates ()
void	get_icoor ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.rhiju.pack_phosphates")

Function Documentation

fix_alpha_for_pack_phosphate()

void fix_alpha_for_pack_phosphate	(	pose::Pose &	pose,
		Size const	res
	)

References numeric::dihedral(), beta_nonlocal::pose, numeric::principal_angle_degrees(), res, and TR.

Referenced by pack_phosphates().

get_icoor()

void get_icoor

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::f, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

main()

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

References basic::options::OptionKeys::magnesium::montecarlo::add_delete_frequency, basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_hinge_moves, basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_local_moves, basic::options::OptionKeys::stepwise::monte_carlo::allow_skip_bulge, basic::options::OptionKeys::stepwise::monte_carlo::allow_variable_bond_geometry, argv, basic::options::OptionKeys::full_model::rna::bulge_res, basic::options::OptionKeys::rna::corrected_geo, utility::io::oc::cout, basic::options::OptionKeys::stepwise::monte_carlo::cycles, test.T009_Exceptions::e, basic::options::OptionKeys::rna::erraser::erraser, basic::options::OptionKeys::full_model::extra_min_res, in::file::fasta(), basic::options::OptionKeys::stepwise::rna::force_centroid_interaction, basic::options::OptionKeys::full_model::rna::force_syn_chi_res_list, icoor_test(), basic::init(), in::file::input_res(), basic::options::OptionKeys::stepwise::monte_carlo::just_min_after_mutation_frequency, basic::options::OptionKeys::stepwise::monte_carlo::minimize_single_res_frequency, my_main(), in::file::native(), NEW_OPT, out::nstruct(), basic::options::OptionKeys::stepwise::num_random_samples, option, basic::options::OptionKeys::full_model::sample_res, out::file::silent(), basic::options::OptionKeys::stepwise::monte_carlo::skip_deletions, basic::options::OptionKeys::stepwise::monte_carlo::switch_focus_frequency, local::temperature, basic::options::OptionKeys::full_model::rna::terminal_res, basic::options::OptionKeys::stepwise::monte_carlo::verbose_scores, viewer_main(), basic::options::OptionKeys::stepwise::rna::virtual_sugar_keep_base_fixed, and score::weights().

my_main()

void* my_main

(

void *

)

References utility::io::oc::cout, utility::options::OptionKeys::options::exit, get_icoor(), icoor_test(), option, and pack_phosphates().

Referenced by main().

pack_phosphates()

void pack_phosphates

(

)

References basic::options::OptionKeys::chemical::chemical, pyrosetta::create_score_function, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, fix_alpha_for_pack_phosphate(), utility::vector1< T, A >::has_value(), create_a3b_hbs::i, utility::keys::AutoKey< O, S, C >::index(), basic::options::OptionKeys::epr_deer::input_files, basic::options::OptionKeys::magnesium::monte_carlo, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, option, full_model::other_poses(), beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, test.T500_Packing::rotamer_trials, in::file::s(), basic::options::OptionKeys::full_model::sample_res, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::rna::denovo::minimize::skip_coord_constraints, basic::options::OptionKeys::rna::denovo::minimize::skip_o2prime_trials, basic::options::OptionKeys::stepwise::stepwise, TR, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::rna::vary_geometry, and score::weights().

Referenced by my_main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.rhiju.pack_phosphates") ( "apps.pilot.rhiju.pack_phosphates"  )

static

Referenced by fix_alpha_for_pack_phosphate(), and pack_phosphates().