swa_rna_analytical_closure.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>
#include <protocols/idealize/idealize.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <string>
#include <map>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_CombineLongLoopFilterer.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_CombineLongLoopFilterer.fwd.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_BaseCentroidScreener.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_BaseCentroidScreener.fwd.hh>
#include <protocols/stepwise/legacy/sampling/rna/StepWiseRNA_Minimizer.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_AnalyticalLoopCloseSampler.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_PoseSetup.fwd.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_PoseSetup.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_Clusterer.hh>
#include <protocols/stepwise/sampling/rna/StepWiseWorkingParametersSetup.hh>
#include <protocols/stepwise/sampling/rna/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/StepWiseLegacyClusterer.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_VDW_BinScreener.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_VDW_BinScreener.fwd.hh>
#include <protocols/rna/denovo/util.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <utility/excn/Exceptions.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <algorithm>
#include <cctype>
#include <iomanip>
#include <cstdlib>
#include <ctime>
#include <unistd.h>
#include <list>
#include <stdio.h>
#include <math.h>

Macros
#define	GetCurrentDir   getcwd

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
std::string	get_working_directory ()
utility::vector1< core::Size >	get_fixed_res (core::Size const nres)
bool	is_nonempty_input_silent_file (std::string const input_silent_file, std::string const exit_key_string)
utility::vector1< core::Size >	get_input_res (core::Size const nres, std::string const pose_num)
utility::vector1< std::string >	get_silent_file_tags ()
core::scoring::ScoreFunctionOP	create_scorefxn ()
protocols::stepwise::sampling::rna::working_parameters::StepWiseWorkingParametersOP	setup_rna_working_parameters (bool check_for_previously_closed_cutpoint_with_input_pose=false)
void	setup_copy_DOF_input (protocols::stepwise::sampling::rna::StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup)
protocols::stepwise::sampling::rna::StepWiseRNA_PoseSetupOP	setup_pose_setup_class (protocols::stepwise::sampling::rna::working_parameters::StepWiseWorkingParametersOP &working_parameters, bool const copy_DOF=true)
void	rna_resample_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Macro Definition Documentation

GetCurrentDir

#define GetCurrentDir   getcwd

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

create_scorefxn()

core::scoring::ScoreFunctionOP create_scorefxn

(

)

References utility::io::oc::cout, pyrosetta.io::create_score_function, basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar, option, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::score::weights.

Referenced by get_pose_energy_breakdown(), hermann_phase_two_minimize(), minimize_pdb(), post_rebuild_bulge_assembly(), rna_resample_test(), rna_sample_virtual_sugar(), and swa_rna_sample().

get_fixed_res()

utility::vector1< core::Size > get_fixed_res

(

core::Size const

nres

)

References basic::options::OptionKeys::rna::erraser::fixed_res, basic::options::OptionKeys::in::file::minimize_res, create_a3b_hbs::nres, option, basic::options::OptionKeys::full_model::rna::rna, and utility_exit_with_message.

Referenced by setup_rna_working_parameters().

get_input_res()

utility::vector1< core::Size > get_input_res	(	core::Size const	nres,
		std::string const	pose_num
	)

References utility::io::oc::cout, basic::options::OptionKeys::in::file::input_res, basic::options::OptionKeys::stepwise::input_res2, basic::options::OptionKeys::stepwise::rna::missing_res, basic::options::OptionKeys::stepwise::rna::missing_res2, create_a3b_hbs::nres, option, basic::options::OptionKeys::full_model::rna::rna, and utility_exit_with_message.

Referenced by setup_rna_working_parameters().

get_silent_file_tags()

utility::vector1< std::string > get_silent_file_tags

(

)

References utility::io::oc::cout, basic::options::OptionKeys::stepwise::rna::filter_output_filename, getline(), basic::options::OptionKeys::stepwise::rna::job_queue_ID, option, basic::options::OptionKeys::full_model::rna::rna, ObjexxFCL::string_of(), in::file::tags(), TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by rna_sample_virtual_sugar(), setup_copy_DOF_input(), and setup_rna_working_parameters().

get_working_directory()

std::string get_working_directory

(

)

References utility::io::oc::cout, GetCurrentDir, challenge::ss, and utility_exit_with_message.

Referenced by rna_resample_test(), rna_sample_virtual_sugar(), and swa_rna_sample().

is_nonempty_input_silent_file()

bool is_nonempty_input_silent_file	(	std::string const	input_silent_file,
		std::string const	exit_key_string
	)

References utility::io::oc::cout, getline(), line, and utility_exit_with_message.

Referenced by filter_combine_long_loop(), and swa_rna_cluster().

main()

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

References basic::options::OptionKeys::stepwise::rna::add_virt_root, basic::options::OptionKeys::stepwise::rna::alignment_res, basic::options::OptionKeys::stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP, basic::options::OptionKeys::stepwise::rna::allow_fixed_res_at_moving_res, argv, basic::options::OptionKeys::cluster::auto_tune, basic::options::OptionKeys::full_model::rna::bulge_res, basic::options::OptionKeys::stepwise::rna::centroid_screen, basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::full_model::cutpoint_open, basic::options::OptionKeys::stepwise::rna::distinguish_pucker, test.T009_Exceptions::e, basic::options::OptionKeys::dna::specificity::fast, basic::options::OptionKeys::stepwise::rna::filter_output_filename, basic::options::OptionKeys::stepwise::rna::finer_sampling_at_chain_closure, basic::options::OptionKeys::rna::erraser::fixed_res, basic::init(), basic::options::OptionKeys::in::file::input_res, basic::options::OptionKeys::stepwise::input_res2, basic::options::OptionKeys::stepwise::rna::job_queue_ID, basic::options::OptionKeys::stepwise::rna::jump_point_pairs, basic::options::OptionKeys::stepwise::rna::minimize_and_score_native_pose, basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar, basic::options::OptionKeys::in::file::minimize_res, basic::options::OptionKeys::stepwise::rna::missing_res, basic::options::OptionKeys::stepwise::rna::missing_res2, my_main(), basic::options::OptionKeys::stepwise::rna::native_alignment_res, basic::options::OptionKeys::stepwise::rna::native_edensity_score_cutoff, basic::options::OptionKeys::stepwise::rna::native_virtual_res, NEW_OPT, basic::options::OptionKeys::stepwise::num_pose_minimize, output_pdb(), basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure, basic::options::OptionKeys::stepwise::rna::rmsd_res, basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::stepwise::rna::sampler_num_pose_kept, basic::options::OptionKeys::cluster::score_diff_cut, basic::options::OptionKeys::rna::erraser::skip_minimize, basic::options::OptionKeys::full_model::rna::terminal_res, basic::options::OptionKeys::stepwise::rna::VDW_atr_rep_screen, basic::options::OptionKeys::stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF, basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_info, basic::options::OptionKeys::stepwise::VERBOSE, viewer_main(), and basic::options::OptionKeys::full_model::virtual_res.

my_main()

void* my_main

(

void *

)

References utility::io::oc::cout, utility::options::OptionKeys::options::exit, and rna_resample_test().

Referenced by main().

rna_resample_test()

void rna_resample_test

(

)

References basic::options::OptionKeys::stepwise::rna::centroid_screen, basic::options::OptionKeys::chemical::chemical, create_scorefxn(), basic::options::OptionKeys::stepwise::rna::distinguish_pucker, basic::options::OptionKeys::dna::specificity::fast, basic::options::OptionKeys::stepwise::rna::finer_sampling_at_chain_closure, get_working_directory(), basic::options::OptionKeys::stepwise::rna::minimize_and_score_native_pose, basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar, in::file::native(), basic::options::OptionKeys::stepwise::rna::native_edensity_score_cutoff, docking::native_pose, basic::options::OptionKeys::stepwise::num_pose_minimize, option, output_pdb(), basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::stepwise::rna::sampler_num_pose_kept, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_pose_setup_class(), setup_rna_working_parameters(), out::file::silent(), basic::options::OptionKeys::rna::erraser::skip_minimize, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, basic::options::OptionKeys::stepwise::rna::VDW_atr_rep_screen, basic::options::OptionKeys::stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF, basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_info, and basic::options::OptionKeys::stepwise::VERBOSE.

Referenced by my_main().

setup_copy_DOF_input()

void setup_copy_DOF_input

(

protocols::stepwise::sampling::rna::StepWiseRNA_PoseSetupOP &

stepwise_rna_pose_setup

)

References utility::io::oc::cout, get_silent_file_tags(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, in::file::s(), in::file::silent(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by setup_pose_setup_class().

setup_pose_setup_class()

protocols::stepwise::sampling::rna::StepWiseRNA_PoseSetupOP setup_pose_setup_class	(	protocols::stepwise::sampling::rna::working_parameters::StepWiseWorkingParametersOP &	working_parameters,
		bool const	copy_DOF = true
	)

References basic::options::OptionKeys::full_model::rna::bulge_res, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, in::file::native(), docking::native_pose, basic::options::OptionKeys::stepwise::rna::native_virtual_res, option, output_pdb(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, setup_copy_DOF_input(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::full_model::virtual_res.

Referenced by rna_resample_test(), rna_sample_virtual_sugar(), swa_rna_cluster(), and swa_rna_sample().

setup_rna_working_parameters()

protocols::stepwise::sampling::rna::working_parameters::StepWiseWorkingParametersOP setup_rna_working_parameters

(

bool

check_for_previously_closed_cutpoint_with_input_pose = false

)

References basic::options::OptionKeys::stepwise::rna::add_virt_root, basic::options::OptionKeys::stepwise::rna::alignment_res, basic::options::OptionKeys::stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP, basic::options::OptionKeys::stepwise::rna::allow_fixed_res_at_moving_res, basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::full_model::cutpoint_open, in::file::fasta(), get_fixed_res(), get_input_res(), get_silent_file_tags(), basic::options::OptionKeys::stepwise::rna::jump_point_pairs, basic::options::OptionKeys::stepwise::rna::native_alignment_res, create_a3b_hbs::nres, option, basic::options::OptionKeys::stepwise::rna::rmsd_res, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::full_model::sample_res, in::file::silent(), ObjexxFCL::string_of(), basic::options::OptionKeys::full_model::rna::terminal_res, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by filter_combine_long_loop(), rna_resample_test(), rna_sample_virtual_sugar(), swa_rna_cluster(), and swa_rna_sample().