drrafter_error_estimation.cc File Reference

Calculate error estimates for a set of DRRAFTER models. More...

#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/rms_util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/init_id_map.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/init/init.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/pose/PDBInfo.hh>
#include <utility/vector1.hh>
#include <iostream>
#include <string>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/stream_util.hh>

Functions
core::Real	mean (utility::vector1< core::Real > const &real_vector)
core::Real	estimate_min_rmsd (core::Real const &mean_pairwise_rmsd)
core::Real	estimate_mean_rmsd (core::Real const &mean_pairwise_rmsd)
core::Real	estimate_rmsd_of_median_struct (core::Real const &mean_pairwise_rmsd)
std::string	get_median_structure (utility::vector1< std::string > all_pose_tags, std::map< std::string, std::map< std::string, core::Real > > pairwise_rmsds)
void	check_all_poses_have_the_same_sequence (utility::vector1< core::pose::Pose > const &all_poses)
core::id::AtomID_Map< core::id::AtomID >	setup_align_atom_map (core::pose::Pose const &pose)
std::map< core::id::AtomID, core::id::AtomID >	setup_rmsd_atom_map (core::pose::Pose const &pose, utility::vector1< core::Size > rmsd_residues)
utility::vector1< std::map< core::id::AtomID, core::id::AtomID > >	setup_per_residue_rmsd_atom_map (core::pose::Pose const &pose, utility::vector1< core::Size > rmsd_residues)
void	drrafter_error_estimation ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.DRRAFTER.drrafter_error_estimation")

Detailed Description

Calculate error estimates for a set of DRRAFTER models.

Author

Kalli Kappel

Function Documentation

check_all_poses_have_the_same_sequence()

void check_all_poses_have_the_same_sequence

(

utility::vector1< core::pose::Pose > const &

all_poses

)

References create_a3b_hbs::i, basic::options::OptionKeys::relax::sequence, and utility_exit_with_message.

Referenced by drrafter_error_estimation().

drrafter_error_estimation()

void drrafter_error_estimation

(

)

References check_all_poses_have_the_same_sequence(), basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, estimate_mean_rmsd(), estimate_min_rmsd(), estimate_rmsd_of_median_struct(), utility::options::OptionKeys::options::exit, get_median_structure(), create_a3b_hbs::i, gaussian-sampling::input, create_a3b_hbs::j, mean(), option, beta_nonlocal::pose, create_a3b_hbs::r, average_rmsds::rmsd, basic::options::OptionKeys::stepwise::rna::rmsd_res, basic::options::OptionKeys::abinitio::rmsd_residues, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, setup_align_atom_map(), setup_per_residue_rmsd_atom_map(), setup_rmsd_atom_map(), in::file::silent(), superimpose_pose(), tag, tag_from_pose(), in::file::tags(), TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

estimate_mean_rmsd()

core::Real estimate_mean_rmsd

(

core::Real const &

mean_pairwise_rmsd

)

Referenced by drrafter_error_estimation().

estimate_min_rmsd()

core::Real estimate_min_rmsd

(

core::Real const &

mean_pairwise_rmsd

)

Referenced by drrafter_error_estimation().

estimate_rmsd_of_median_struct()

core::Real estimate_rmsd_of_median_struct

(

core::Real const &

mean_pairwise_rmsd

)

Referenced by drrafter_error_estimation().

get_median_structure()

std::string get_median_structure	(	utility::vector1< std::string >	all_pose_tags,
		std::map< std::string, std::map< std::string, core::Real > >	pairwise_rmsds
	)

References basic::Tracer::Debug, create_a3b_hbs::i, create_a3b_hbs::j, mean(), and TR.

Referenced by drrafter_error_estimation().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), NEW_OPT, option, basic::options::OptionKeys::stepwise::rna::rmsd_res, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, in::file::silent(), in::file::tags(), and viewer_main().

mean()

core::Real mean

(

utility::vector1< core::Real > const &

real_vector

)

References create_a3b_hbs::i.

Referenced by drrafter_error_estimation(), and get_median_structure().

my_main()

void* my_main

(

void *

)

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

Referenced by main().

setup_align_atom_map()

core::id::AtomID_Map< core::id::AtomID > setup_align_atom_map

(

core::pose::Pose const &

pose

)

References create_a3b_hbs::i, option, and beta_nonlocal::pose.

Referenced by drrafter_error_estimation().

setup_per_residue_rmsd_atom_map()

utility::vector1< std::map< core::id::AtomID, core::id::AtomID > > setup_per_residue_rmsd_atom_map	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size >	rmsd_residues
	)

References create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, and basic::options::OptionKeys::abinitio::rmsd_residues.

Referenced by drrafter_error_estimation().

setup_rmsd_atom_map()

std::map<core::id::AtomID, core::id::AtomID> setup_rmsd_atom_map	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size >	rmsd_residues
	)

References create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, and basic::options::OptionKeys::abinitio::rmsd_residues.

Referenced by drrafter_error_estimation().

Variable Documentation

TR

basic::Tracer TR("apps.public.DRRAFTER.drrafter_error_estimation") ( "apps.public.DRRAFTER.drrafter_error_estimation"  )

static

Referenced by drrafter_error_estimation(), and get_median_structure().