swa_rna_util.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.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 <core/pose/variant_util.hh>
#include <core/pose/util.tmpl.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/rna/util.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <core/import_pose/options/RNA_MinimizerOptions.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/stepwise/modeler/output_util.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/legacy/modeler/rna/util.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/rna/movers/RNA_LoopCloser.fwd.hh>
#include <core/pose/rna/RNA_BaseDoubletClasses.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <algorithm>
#include <cctype>
#include <iomanip>
#include <map>
#include <cstdlib>
#include <ctime>
#include <list>
#include <cstdio>
#include <cmath>

Typedefs
using	Matrix = numeric::xyzMatrix< Real >

Functions
core::scoring::ScoreFunctionOP	create_scorefxn ()
void	align_pose_general (core::pose::Pose const &static_pose, std::string const &static_tag, core::pose::Pose &moving_pose, std::string const &moving_tag, utility::vector1< std::pair< Size, Size > > const &alignment_res_pair_list, bool const base_only)
	Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh. More...
core::Real	check_alignment_RMSD_cutoff (core::pose::Pose const &static_pose, std::string const &static_tag, core::pose::Pose &moving_pose, std::string const &moving_tag, utility::vector1< std::pair< Size, Size > > const &alignment_res_pair_list, bool const base_only, core::Real const alignment_RMSD_cutoff)
Real	full_length_rmsd_over_reside_list_general (pose::Pose const &pose_one, pose::Pose const &pose_two, utility::vector1< std::pair< Size, Size > > const &rmsd_res_pair_list, bool const verbose, bool const ignore_virtual_atom)
	Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh. More...
void	align_pdbs ()
void	calculate_pairwise_RMSD ()
void	import_and_dump_pdb ()
void	o2prime_packer ()
void	mutate_residue (pose::Pose &pose, Size const seq_num, std::string const &res_name)
std::string	get_one_letter_name (std::string const &three_letter_name)
std::string	get_three_letter_name (std::string const &one_letter_name)
utility::vector1< Residue_info >	Convert_rebuild_residue_string_to_list (std::string const &rebuild_residue_string)
void	output_residue_struct (Residue_info const &residue)
void	mutate_residues_wrapper ()
void	slice_ellipsoid_envelope ()
void	slice_sample_res_and_surrounding ()
void	pdb_to_silent_file ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("swa_rna_util")

Typedef Documentation

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

void align_pdbs

(

)

References align_pose_general(), check_alignment_RMSD_cutoff(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T200_Scoring::ii, in::file::native(), basic::options::OptionKeys::stepwise::rna::native_virtual_res, option, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, TR, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::out::user_tag, and utility_exit_with_message.

Referenced by my_main().

void align_pose_general	(	core::pose::Pose const &	static_pose,
		std::string const &	static_tag,
		core::pose::Pose &	moving_pose,
		std::string const &	moving_tag,
		utility::vector1< std::pair< Size, Size > > const &	alignment_res_pair_list,
		bool const	base_only
	)

Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh.

References utility::io::oc::cout, TR, and utility_exit_with_message.

Referenced by align_pdbs(), and calculate_pairwise_RMSD().

void calculate_pairwise_RMSD

(

)

References align_pose_general(), check_alignment_RMSD_cutoff(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::magnesium::montecarlo::dump, basic::options::OptionKeys::matdes::dock::dump_pdb, full_length_rmsd_over_reside_list_general(), test.T200_Scoring::ii, in::file::native(), test.Workshop7test::native_pose, option, demo.D010_Pose_structure::pose, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, ObjexxFCL::string_of(), TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

core::Real check_alignment_RMSD_cutoff	(	core::pose::Pose const &	static_pose,
		std::string const &	static_tag,
		core::pose::Pose &	moving_pose,
		std::string const &	moving_tag,
		utility::vector1< std::pair< Size, Size > > const &	alignment_res_pair_list,
		bool const	base_only,
		core::Real const	alignment_RMSD_cutoff
	)

References utility::io::oc::cout, basic::options::OptionKeys::AnchoredDesign::rmsd, and utility_exit_with_message.

Referenced by align_pdbs(), and calculate_pairwise_RMSD().

utility::vector1< Residue_info > Convert_rebuild_residue_string_to_list

(

std::string const &

rebuild_residue_string

)

References get_three_letter_name().

Referenced by mutate_residues_wrapper().

core::scoring::ScoreFunctionOP create_scorefxn

(

)

References utility::io::oc::cout, pyrosetta::create_score_function, option, basic::options::OptionKeys::DisulfideInsertion::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 o2prime_packer(), post_rebuild_bulge_assembly(), rna_sample_virtual_sugar(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), and swa_rna_sample().

Real full_length_rmsd_over_reside_list_general	(	pose::Pose const &	pose_one,
		pose::Pose const &	pose_two,
		utility::vector1< std::pair< Size, Size > > const &	rmsd_res_pair_list,
		bool const	verbose,
		bool const	ignore_virtual_atom
	)

Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh.

References utility::io::oc::cout, max(), basic::options::OptionKeys::AnchoredDesign::rmsd, ObjexxFCL::string_of(), TR, and utility_exit_with_message.

Referenced by calculate_pairwise_RMSD().

std::string get_one_letter_name

(

std::string const &

three_letter_name

)

References utility::options::OptionKeys::options::exit, and TR.

Referenced by output_residue_struct().

std::string get_three_letter_name

(

std::string const &

one_letter_name

)

References utility::options::OptionKeys::options::exit, and TR.

Referenced by Convert_rebuild_residue_string_to_list().

void import_and_dump_pdb

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::matdes::dock::dump_pdb, utility::file::file_exists(), option, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

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

References utility::io::oc::cout, basic::options::OptionKeys::magnesium::montecarlo::dump, test.T009_Exceptions::e, devel::init(), utility::excn::Exception::msg(), my_main(), basic::options::OptionKeys::stepwise::rna::native_virtual_res, NEW_OPT, basic::options::OptionKeys::full_model::sample_res, and basic::options::OptionKeys::full_model::virtual_res.

void mutate_residue	(	pose::Pose &	pose,
		Size const	seq_num,
		std::string const &	res_name
	)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, and demo.D010_Pose_structure::pose.

Referenced by mutate_residues_wrapper().

void mutate_residues_wrapper

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, Convert_rebuild_residue_string_to_list(), utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::matdes::dock::dump_pdb, mutate_residue(), name, basic::options::OptionKeys::optimization::optimization, option, output_residue_struct(), demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::in::file::silent.

Referenced by my_main().

void* my_main

(

void *

)

References align_pdbs(), calculate_pairwise_RMSD(), utility::io::oc::cout, utility::options::OptionKeys::options::exit, import_and_dump_pdb(), mutate_residues_wrapper(), o2prime_packer(), option, pdb_to_silent_file(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), and utility_exit_with_message.

Referenced by main().

void o2prime_packer

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_scorefxn(), basic::options::OptionKeys::matdes::dock::dump_pdb, option, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), and basic::options::OptionKeys::DisulfideInsertion::scorefxn.

Referenced by my_main().

void output_residue_struct

(

Residue_info const &

residue

)

References ObjexxFCL::format::A(), pyrosetta.tests.distributed.test_dask::format, get_one_letter_name(), ObjexxFCL::lead_zero_string_of(), and TR.

Referenced by mutate_residues_wrapper().

void pdb_to_silent_file

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, test.T200_Scoring::ii, basic::options::OptionKeys::optimization::optimization, option, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, tag, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::full_model::virtual_res.

Referenced by my_main().

void slice_ellipsoid_envelope

(

)

References basic::options::OptionKeys::chemical::chemical, numeric::xyzMatrix< typename >::cols(), utility::io::oc::cout, create_scorefxn(), measure_params::cross(), basic::options::OptionKeys::matdes::dock::dump_pdb, test.T200_Scoring::ii, numeric::inverse(), basic::options::OptionKeys::frags::j, make_symmdef_file_denovo::length, basic::options::OptionKeys::legacy_sewing::max_loop_length, numeric::xyzVector< typename >::normalize(), basic::options::OptionKeys::optimization::optimization, option, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, numeric::rotation_matrix(), in::file::s(), basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, ObjexxFCL::string_of(), TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

Referenced by my_main().

void slice_sample_res_and_surrounding

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_scorefxn(), basic::options::OptionKeys::matdes::dock::dump_pdb, test.T200_Scoring::ii, make_symmdef_file_denovo::length, basic::options::OptionKeys::optimization::optimization, option, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, ObjexxFCL::string_of(), TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

Variable Documentation

basic::Tracer TR("swa_rna_util")

static

Referenced by align_pdbs(), align_pose_general(), calculate_pairwise_RMSD(), full_length_rmsd_over_reside_list_general(), get_one_letter_name(), get_three_letter_name(), output_residue_struct(), slice_ellipsoid_envelope(), and slice_sample_res_and_surrounding().