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/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/init_id_map.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/score.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/rna/util.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.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/legacy/modeler/rna/util.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <iostream>
#include <string>
#include <algorithm>
#include <cstdlib>
#include <ctime>
#include <cmath>
#include <core/scoring/rms_util.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_Classes.hh>
#include <core/io/silent/SilentFileData.hh>

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

Matrix

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

align_pdbs()

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, get_tag_from_pdb_filename(), create_a3b_hbs::ii, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), basic::options::OptionKeys::stepwise::rna::native_virtual_res, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, docking::s, 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().

align_pose_general()

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, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, superimpose_pose(), TR, and utility_exit_with_message.

Referenced by align_pdbs(), and calculate_pairwise_RMSD().

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(), create_a3b_hbs::ii, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, option, beta_nonlocal::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().

check_alignment_RMSD_cutoff()

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, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, average_rmsds::rmsd, and utility_exit_with_message.

Referenced by align_pdbs(), and calculate_pairwise_RMSD().

Convert_rebuild_residue_string_to_list()

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().

create_scorefxn()

core::scoring::ScoreFunctionOP create_scorefxn

(

)

References utility::io::oc::cout, pyrosetta::create_score_function, 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 o2prime_packer(), slice_ellipsoid_envelope(), and slice_sample_res_and_surrounding().

full_length_rmsd_over_reside_list_general()

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, utility::vector1< T, A >::has_value(), create_a3b_hbs::i, max(), average_rmsds::rmsd, ObjexxFCL::string_of(), TR, utility_exit_with_message, and basic::options::OptionKeys::sc::verbose.

Referenced by calculate_pairwise_RMSD().

get_one_letter_name()

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().

get_three_letter_name()

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().

import_and_dump_pdb()

void import_and_dump_pdb

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::matdes::dock::dump_pdb, utility::file::file_exists(), option, beta_nonlocal::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().

main()

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

References argv, basic::options::OptionKeys::magnesium::montecarlo::dump, test.T009_Exceptions::e, basic::init(), my_main(), basic::options::OptionKeys::stepwise::rna::native_virtual_res, NEW_OPT, basic::options::OptionKeys::full_model::sample_res, viewer_main(), and basic::options::OptionKeys::full_model::virtual_res.

mutate_residue()

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 beta_nonlocal::pose.

Referenced by mutate_residues_wrapper().

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(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, option, output_residue_struct(), beta_nonlocal::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().

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().

o2prime_packer()

void o2prime_packer

(

)

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

Referenced by my_main().

output_residue_struct()

void output_residue_struct

(

Residue_info const &

residue

)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, get_one_letter_name(), ObjexxFCL::lead_zero_string_of(), residue, and TR.

Referenced by mutate_residues_wrapper().

pdb_to_silent_file()

void pdb_to_silent_file

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, get_tag_from_pdb_filename(), create_a3b_hbs::ii, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, docking::s, 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().

slice_ellipsoid_envelope()

void slice_ellipsoid_envelope

(

)

References basic::options::OptionKeys::chemical::chemical, numeric::xyzMatrix< T >::cols(), utility::io::oc::cout, create_scorefxn(), measure_params::cross(), basic::options::OptionKeys::matdes::dock::dump_pdb, utility::vector1< T, A >::has_value(), create_a3b_hbs::i, create_a3b_hbs::ii, enumerate_junctions::int, numeric::inverse(), create_a3b_hbs::j, oop_conformations::length, basic::options::OptionKeys::legacy_sewing::max_loop_length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, natoms(), numeric::xyzVector< T >::normalize(), basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::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, oop_conformations::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< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by my_main().

slice_sample_res_and_surrounding()

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, utility::vector1< T, A >::has_value(), create_a3b_hbs::ii, enumerate_junctions::int, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::optimization::optimization, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::full_model::sample_res, oop_conformations::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

TR

basic::Tracer TR("swa_rna_util") ( "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().