#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/sasa.hh>
#include <core/io/raw_data/ScoreMap.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <basic/options/util.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <devel/init.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <numeric/random/random.hh>
#include <protocols/ddg/ddGData.hh>
#include <utility/file/FileName.hh>
#include <utility/excn/Exceptions.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/database/open.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>
#include <sstream>
#include <algorithm>
#include <numeric>
#include <basic/Tracer.hh>

Functions
int	min_index (utility::vector1< double >scores)

utility::vector1< std::string >	header (pose::Pose p, ScoreFunctionOP sfxn)

utility::vector1< double >	weights (pose::Pose p, ScoreFunctionOP sfxn)

bool	sort_numerically_ascending (double a, double b)

utility::vector1< double >	calc_ddg (utility::vector1< pose::Pose > mut, utility::vector1< pose::Pose > wt, ScoreFunctionOP sfxn, bool mean, bool min)

std::string	mut_info (pose::Pose m, pose::Pose w)

void	print_header (pose::Pose p, ScoreFunctionOP sfxn, std::ostream &out)

void	print_ddgs (utility::vector1< double > ddg, utility::vector1< pose::Pose > mut, utility::vector1< pose::Pose > wt, core::Real experimental_value, std::ostream &out)

void	print_verbose_ddgs (utility::vector1< pose::Pose > mut, utility::vector1< pose::Pose > wt, ScoreFunctionOP sfxn, bool mean, bool min, core::Real experimental_value, std::ostream &outfile)

utility::vector1< int >	num_nbrs (pose::Pose p)

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

Detailed Description

Author: Liz Kellogg ekell.nosp@m.ogg@.nosp@m.u.was.nosp@m.hing.nosp@m.ton.e.nosp@m.du

Function Documentation

◆ calc_ddg()

utility::vector1<double> calc_ddg	(	utility::vector1< pose::Pose >	mut,
		utility::vector1< pose::Pose >	wt,
		ScoreFunctionOP	sfxn,
		bool	mean,
		bool	min
	)

◆ header()

utility::vector1<std::string> header	(	pose::Pose	p,
		ScoreFunctionOP	sfxn
	)

References create_a3b_hbs::i, create_a3b_hbs::ii, pyrosetta.bindings.energies::nonzero_weights(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, sm, and weights().

Referenced by utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::basic_mpi_ostream(), calc_ddg(), ui::task::NetworkCall::call(), Foldptn::Foldptn(), harvest_motifs_one(), main(), print_header(), utility::io::mpi_stream::basic_mpi_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::print_header(), utility::io::mpi_stream::basic_mpi_ostreambase< Elem, Tr, ElemA, ByteT, ByteAT >::print_header(), print_verbose_ddgs(), utility::io::TarParser::read(), sicdock_thread_num(), and transmit_silent_struct().

◆ main()

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

utility::vector1<core::Real> sasa(pose::Pose p){ const core::Real probe_radius = 1.2; id::AtomID_Map< Real > atom_sasa; utility::vector1< core::Real > rsd_sasa; core::scoring::calc_per_atom_sasa(p,atom_sasa,rsd_sasa,probe_radius); return rsd_sasa; }

double burial_weight(pose::Pose p, int position){ takes in a position in a pose and returns a weight based on some sort of metric for burial utility::vector1<core::Real> sa; sa = sasa(p); if(true){ if(sa[position] < 0.1){ return 1.0; }else if(sa[position] > 0.4){ return 0.5; }else{ return 0.75; } } }

References job_manager::app, argv, calc_ddg(), hist2d::dat, test.T009_Exceptions::e, basic::init(), basic::options::OptionKeys::ddg::mean, ddg::mean(), ddg::min(), min(), OPT, basic::options::option, lactamize::outfile, print_ddgs(), print_header(), basic::options::OptionKeys::ddg::print_per_res_diff, print_verbose_ddgs(), in::file::s(), out::file::scorefile(), test.T120_core::sfxn, basic::options::OptionKeys::inout::dbms::user, and orn_macrocycle::wt.

◆ min_index()

int min_index ( utility::vector1< double > scores )

References create_a3b_hbs::i, min(), and legacy_score_vs_rmsd::scores.

Referenced by MetalSiteFinderMover::apply(), assign_models(), calc_ddg(), numeric::find_nearest_value(), main(), and print_verbose_ddgs().

◆ mut_info()

std::string mut_info	(	pose::Pose	m,
		pose::Pose	w
	)

References create_a3b_hbs::ii, info(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, and w.

Referenced by print_ddgs(), and print_verbose_ddgs().

◆ num_nbrs()

utility::vector1<int> num_nbrs ( pose::Pose p )

References utility::graph::Node::const_edge_list_end(), utility::graph::Edge::get_node(), create_a3b_hbs::i, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

Referenced by calculate_distances(), and write_to_restype_file().

◆ print_ddgs()

void print_ddgs	(	utility::vector1< double >	ddg,
		utility::vector1< pose::Pose >	mut,
		utility::vector1< pose::Pose >	wt,
		core::Real	experimental_value,
		std::ostream &	out
	)

References utility::io::oc::cerr, compare(), utility::options::OptionKeys::options::exit, create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, mut_info(), basic::options::OptionKeys::relax::sequence, and orn_macrocycle::wt.

Referenced by main().

◆ print_header()

void print_header	(	pose::Pose	p,
		ScoreFunctionOP	sfxn,
		std::ostream &	out
	)

References h, header(), create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and test.T120_core::sfxn.

Referenced by main(), print_ddgs(), and sicdock_thread_num().

◆ print_verbose_ddgs()

void print_verbose_ddgs	(	utility::vector1< pose::Pose >	mut,
		utility::vector1< pose::Pose >	wt,
		ScoreFunctionOP	sfxn,
		bool	mean,
		bool	min,
		core::Real	experimental_value,
		std::ostream &	outfile
	)

◆ sort_numerically_ascending()

bool sort_numerically_ascending	(	double	a,
		double	b
	)

References a, and compute_difference::b.

Referenced by calc_ddg().

◆ weights()

utility::vector1<double> weights	(	pose::Pose	p,
		ScoreFunctionOP	sfxn
	)

Functions