SID_ERMS_prediction.cc File Reference

#include <basic/options/option.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/chains_util.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <utility/io/ozstream.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <utility/io/izstream.hh>
#include <numeric/random/random.hh>
#include <numeric/random/uniform.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/analysis/InterfaceAnalyzerMover.hh>
#include <cmath>
#include <core/pose/metrics/PoseMetricCalculatorBase.hh>
#include <protocols/pose_metric_calculators/SaltBridgeCalculator.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/metrics/PoseMetricContainer.hh>
#include <boost/config.hpp>
#include <iostream>
#include <vector>
#include <boost/graph/connected_components.hpp>
#include <boost/graph/adjacency_list.hpp>

Functions
core::Real	calc_prob (core::Real x, core::Real a, core::Real b)
void	read_complex_type (core::Size &n_chains, utility::vector1< char > &nodes, utility::vector1< utility::vector1< std::string >> &edges)
void	check_intensities (const utility::vector1< utility::vector1< core::Real >> &ERMS_data)
void	read_ERMS (utility::vector1< core::Real > &ACE, utility::vector1< utility::vector1< core::Real >> &ERMS_read, const core::Size n_chains)
void	read_B_vals (utility::vector1< core::Real > &B)
void	check_interface_symmetry (const core::pose::PoseOP &pose_check, const utility::vector1< std::string > &edges_check, core::Real &dSASA, core::Real &PRE)
void	calc_B_values (utility::vector1< core::Real > &B, const utility::vector1< utility::vector1< std::string >> &edges, core::Real &A, const core::Size n_chains)
void	simulate_ERMS (utility::vector1< utility::vector1< core::Real >> &ERMS_prediction, const utility::vector1< core::Real > &ACE, const utility::vector1< core::Real > &B, const core::Size n_chains, const utility::vector1< utility::vector1< std::string >> &edges, const core::Real A, const core::Real breakage_cut, const utility::vector1< char > &nodes)
void	calc_RMSE (const utility::vector1< utility::vector1< core::Real >> &ERMS_prediction, const utility::vector1< utility::vector1< core::Real >> &ERMS, const core::Size n_chains, const core::Size n_ACE)
void	output_results (const utility::vector1< core::Real > &ACE, const utility::vector1< utility::vector1< core::Real >> &ERMS_prediction)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.analysis.SID_ERMS_prediction")
basic::options::FileOptionKey const	complex_type ("complex_type")
basic::options::FileOptionKey const	ERMS ("ERMS")
basic::options::BooleanOptionKey const	RMSE ("RMSE")
basic::options::FileOptionKey const	B_vals ("B_vals")
basic::options::RealOptionKey const	steepness ("steepness")
basic::options::RealOptionKey const	breakage_cutoff ("breakage_cutoff")

Function Documentation

calc_B_values()

void calc_B_values	(	utility::vector1< core::Real > &	B,
		const utility::vector1< utility::vector1< std::string >> &	edges,
		core::Real &	A,
		const core::Size	n_chains
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, breakage_cutoff, chains, check_interface_symmetry(), utility::io::oc::cout, pyrosetta.io::create_score_function, detail::find(), create_a3b_hbs::i, interface, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), PREcst::PRE, basic::options::OptionKeys::in::file::s, steepness, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

calc_prob()

core::Real calc_prob	(	core::Real	x,
		core::Real	a,
		core::Real	b
	)

References a, compute_difference::b, and x.

Referenced by simulate_ERMS().

calc_RMSE()

void calc_RMSE	(	const utility::vector1< utility::vector1< core::Real >> &	ERMS_prediction,
		const utility::vector1< utility::vector1< core::Real >> &	ERMS,
		const core::Size	n_chains,
		const core::Size	n_ACE
	)

References count, ERMS, create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::pow(), and basic::options::TR.

Referenced by main().

check_intensities()

void check_intensities

(

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

ERMS_data

)

References create_a3b_hbs::i, create_a3b_hbs::j, sum(), and utility_exit_with_message.

Referenced by read_ERMS().

check_interface_symmetry()

void check_interface_symmetry	(	const core::pose::PoseOP &	pose_check,
		const utility::vector1< std::string > &	edges_check,
		core::Real &	dSASA,
		core::Real &	PRE
	)

References ObjexxFCL::abs(), pyrosetta.io::create_score_function, pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::j, PREcst::PRE, test.T120_core::sfxn, basic::options::TR, and basic::Tracer::Warning.

Referenced by calc_B_values().

main()

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

References utility::options::OptionCollection::add(), argv, B_vals, breakage_cutoff, calc_B_values(), calc_RMSE(), complex_type, utility::options::ScalarOption_T_< K, T >::def(), test.T009_Exceptions::e, ERMS, create_a3b_hbs::i, basic::init(), basic::options::option, output_results(), read_B_vals(), read_complex_type(), read_ERMS(), RMSE, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::frags::scoring::scoring, simulate_ERMS(), steepness, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::Tracer::Warning.

output_results()

void output_results	(	const utility::vector1< core::Real > &	ACE,
		const utility::vector1< utility::vector1< core::Real >> &	ERMS_prediction
	)

References create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::out::file::o, basic::options::option, erraser_single_res_analysis::out, lactamize::outfile, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

read_B_vals()

void read_B_vals

(

utility::vector1< core::Real > &

B

)

References B_vals, count, getline(), gaussian-sampling::input, line, basic::options::option, runtime_assert_string_msg, challenge::ss, and utility_exit_with_message.

Referenced by main().

read_complex_type()

void read_complex_type	(	core::Size &	n_chains,
		utility::vector1< char > &	nodes,
		utility::vector1< utility::vector1< std::string >> &	edges
	)

References complex_type, count, getline(), create_a3b_hbs::i, gaussian-sampling::input, create_a3b_hbs::j, create_a3b_hbs::k, line, basic::options::option, subloop_histogram::size, utility::split_whitespace(), challenge::ss, basic::options::TR, and utility_exit_with_message.

Referenced by main().

read_ERMS()

void read_ERMS	(	utility::vector1< core::Real > &	ACE,
		utility::vector1< utility::vector1< core::Real >> &	ERMS_read,
		const core::Size	n_chains
	)

References check_intensities(), ERMS, getline(), create_a3b_hbs::i, gaussian-sampling::input, line, basic::options::option, RMSE, runtime_assert_string_msg, challenge::ss, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::Tracer::Warning.

Referenced by main().

simulate_ERMS()

void simulate_ERMS	(	utility::vector1< utility::vector1< core::Real >> &	ERMS_prediction,
		const utility::vector1< core::Real > &	ACE,
		const utility::vector1< core::Real > &	B,
		const core::Size	n_chains,
		const utility::vector1< utility::vector1< std::string >> &	edges,
		const core::Real	A,
		const core::Real	breakage_cut,
		const utility::vector1< char > &	nodes
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, calc_prob(), count, pyrosetta.distributed.cluster.base::G, ObjexxFCL::get(), create_a3b_hbs::i, utility::vector1< T, A >::index(), create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, basic::options::TR, numeric::random::uniform(), and utility_exit_with_message.

Referenced by main().

Variable Documentation

B_vals

basic::options::FileOptionKey const B_vals("B_vals")

(

"B_vals"

)

Referenced by main(), and read_B_vals().

breakage_cutoff

basic::options::RealOptionKey const breakage_cutoff("breakage_cutoff")

(

"breakage_cutoff"

)

Referenced by calc_B_values(), and main().

complex_type

basic::options::FileOptionKey const complex_type("complex_type")

(

"complex_type"

)

Referenced by main(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_sequence_of_subelement_sets(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_choice_opt(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_choice_req(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_repeatable(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_single_instance_optional(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_single_instance_required(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::prepare_subelement_single_instance_required_ordered(), read_complex_type(), and utility::tag::XMLSchemaComplexTypeGeneratorImpl::write_complex_type_to_schema().

ERMS

basic::options::FileOptionKey const ERMS("ERMS")

(

"ERMS"

)

Referenced by calc_RMSE(), main(), and read_ERMS().

RMSE

basic::options::BooleanOptionKey const RMSE("RMSE")

(

"RMSE"

)

Referenced by main(), and read_ERMS().

steepness

basic::options::RealOptionKey const steepness("steepness")

(

"steepness"

)

Referenced by FindOptimalHydrophobicThk::apply(), calc_B_values(), and main().

TR

basic::Tracer TR("apps.public.analysis.SID_ERMS_prediction") ( "apps.public.analysis.SID_ERMS_prediction"  )

static