rna_thread.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <utility/string_util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/PDBInfo.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/rna/util.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <utility/excn/Exceptions.hh>

Typedefs
using	Matrix = numeric::xyzMatrix< Real >

Functions
void	setup_mask (ObjexxFCL::FArray1D_bool &sequence_mask, utility::vector1< sequence::SequenceOP > const &sequences_from_alignment)
void	setup_alignment_map (std::map< Size, Size > &mapping, std::string const &sequence_from_alignment)
std::string	remove_dashes (std::string const &s)
void	prepare_threaded_model (pose::Pose &pose, std::string const &target_sequence_from_alignment, std::string const &template_sequence_from_alignment, ObjexxFCL::FArray1D_bool &sequence_mask, Size offset=0)
Size	figure_out_which_sequence_is_template (utility::vector1< sequence::SequenceOP > const &sequences_from_alignment, pose::Pose const &template_pose, std::string const &template_file_name)
void	rna_thread_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

figure_out_which_sequence_is_template()

Size figure_out_which_sequence_is_template	(	utility::vector1< sequence::SequenceOP > const &	sequences_from_alignment,
		pose::Pose const &	template_pose,
		std::string const &	template_file_name
	)

References utility::io::oc::cout, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, remove_dashes(), runtime_assert, and utility_exit_with_message.

Referenced by rna_thread_test().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), NEW_OPT, beta_sc_scan::seq, and viewer_main().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and rna_thread_test().

Referenced by main().

prepare_threaded_model()

void prepare_threaded_model	(	pose::Pose &	pose,
		std::string const &	target_sequence_from_alignment,
		std::string const &	template_sequence_from_alignment,
		ObjexxFCL::FArray1D_bool &	sequence_mask,
		Size	offset = 0
	)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, create_a3b_hbs::i, DRRAFTER_util::make_tag(), DRRAFTER_util::make_tag_with_dashes(), offset, create_a3b_hbs::pdb_info, beta_nonlocal::pose, runtime_assert, setup_alignment_map(), and basic::options::OptionKeys::full_model::working_res.

Referenced by rna_thread_test().

remove_dashes()

std::string remove_dashes

(

std::string const &

s

)

References create_a3b_hbs::i, and docking::s.

Referenced by figure_out_which_sequence_is_template().

rna_thread_test()

void rna_thread_test

(

)

References utility::io::oc::cout, in::file::fasta(), figure_out_which_sequence_is_template(), out::file::o(), option, lactamize::outfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, prepare_threaded_model(), runtime_assert, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, setup_mask(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

setup_alignment_map()

void setup_alignment_map	(	std::map< Size, Size > &	mapping,
		std::string const &	sequence_from_alignment
	)

References count, and create_a3b_hbs::i.

Referenced by prepare_threaded_model().

setup_mask()

void setup_mask	(	ObjexxFCL::FArray1D_bool &	sequence_mask,
		utility::vector1< sequence::SequenceOP > const &	sequences_from_alignment
	)

References count, utility::io::oc::cout, create_a3b_hbs::i, enumerate_junctions::int, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, offset, option, erraser_single_res_analysis::out, and basic::options::OptionKeys::inout::dbms::user.

Referenced by rna_thread_test().