rna_thread.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <utility/string_util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/PDBInfo.hh>
#include <protocols/farna/util.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/rna/util.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <utility/excn/Exceptions.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

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

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

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, remove_dashes(), runtime_assert, and utility_exit_with_message.

Referenced by rna_thread_test().

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

References utility::io::oc::cout, devel::init(), utility::excn::EXCN_Base::msg(), my_main(), NEW_OPT, options, and basic::options::OptionKeys::in::file::seq.

void* my_main

(

void *

)

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

Referenced by main().

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::farna::farna, utility::make_tag(), utility::make_tag_with_dashes(), basic::options::OptionKeys::rna::farna::offset, app.surface_docking.surface_docking::pose, runtime_assert, setup_alignment_map(), ObjexxFCL::FArray< typename >::size(), and basic::options::OptionKeys::full_model::working_res.

Referenced by rna_thread_test().

std::string remove_dashes

(

std::string const &

s

)

Referenced by figure_out_which_sequence_is_template().

void rna_thread_test

(

)

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

Referenced by my_main().

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

References clean_pdb_keep_ligand::count.

Referenced by prepare_threaded_model().

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

References utility::io::ozstream::close(), clean_pdb_keep_ligand::count, utility::io::oc::cout, basic::options::OptionKeys::rna::farna::offset, option, options, basic::options::OptionKeys::canonical_sampling::out::out, and basic::options::OptionKeys::inout::dbms::user.

Referenced by rna_thread_test().