ddg_monomer.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <protocols/scoring/Interface.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.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/packing.OptionKeys.gen.hh>
#include <devel/init.hh>
#include <core/pack/task/ResfileReader.hh>
#include <fstream>
#include <ObjexxFCL/format.hh>
#include <cstdlib>
#include <string>
#include <protocols/ddg/ddGMover.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <core/pack/task/ResidueLevelTask.hh>

Typedefs
using	mutations = utility::vector1< core::chemical::AA >
using	ddgs = utility::vector1< double >

Functions
void	print_ddgs (std::string const &ddg_out, std::string const &label, ddgs const &delta_e_components, ddgs const &, double total_ddgs, protocols::ddg::ddGMover &mover, bool print_header, bool min_cst)
	print ddGs More...
void	read_in_mutations (utility::vector1< mutations > &res_to_mut, std::string filename, pose::Pose &pose)
	The input file is a list of mutation blocks. Usually, this will be a set of point mutations. where each "block" lists a single mutation. However, it is possible to specify multiple mutations together in a single block. More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.ddg.ddg_monomer")

Detailed Description

Author

Liz Kellogg ekell.nosp@m.ogg@.nosp@m.u.was.nosp@m.hing.nosp@m.ton.e.nosp@m.du comments by JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)

Typedef Documentation

ddgs

using ddgs = utility::vector1<double>

mutations

using mutations = utility::vector1<core::chemical::AA>

Function Documentation

main()

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

References argv, basic::options::OptionKeys::chemical::chemical, pyrosetta::create_score_function, extract_by_sidechain_sasa_score::cutoff, basic::Tracer::Debug, basic::options::OptionKeys::ddg::debug_output, ddg::debug_output(), basic::options::OptionKeys::ddg::dump_pdbs, ddg::dump_pdbs(), test.T009_Exceptions::e, score::fa_max_dis(), lactamize::filename, create_a3b_hbs::i, basic::init(), basic::options::OptionKeys::ddg::interface_ddg, ddg::interface_ddg(), autocorrelation::iterations, ddg::iterations(), create_a3b_hbs::j, basic::options::OptionKeys::ddg::local_opt_only, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::ddg::mean, min(), basic::options::OptionKeys::ddg::min_cst, basic::options::OptionKeys::ddg::minimization_patch, basic::options::OptionKeys::ddg::minimization_scorefunction, basic::options::OptionKeys::ddg::mut_file, local::num_iterations, OPT, basic::options::OptionKeys::casp::opt_radius, ddg::opt_radius(), basic::options::option, option, erraser_single_res_analysis::out, ddg::out(), parse_resfile(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, print_ddgs(), read_in_mutations(), packing::resfile(), runtime_assert, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), vancomycin::task, TR, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::ddg::weight_file, and ddg::weight_file().

print_ddgs()

void print_ddgs	(	std::string const &	ddg_out,
		std::string const &	label,
		ddgs const &	delta_e_components,
		ddgs const &	,
		double	total_ddgs,
		protocols::ddg::ddGMover &	mover,
		bool	print_header,
		bool	min_cst
	)

print ddGs

References job_manager::app, utility::exit(), ObjexxFCL::format::F(), create_a3b_hbs::i, predPRE::label, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::ddg::min_cst, print_header(), and TR.

Referenced by main().

read_in_mutations()

void read_in_mutations	(	utility::vector1< mutations > &	res_to_mut,
		std::string	filename,
		pose::Pose &	pose
	)

The input file is a list of mutation blocks. Usually, this will be a set of point mutations. where each "block" lists a single mutation. However, it is possible to specify multiple mutations together in a single block.

The file format is: "total N" followed by N blocks, where each block is "M" specifying followed by M lines of wt/resid/mutaa triples "wtaa resid mutaa" N, M and resid are all supposed to be integers. wtaa, and mutaa are supposed to be 1-letter amino acid codes.

References debug_assert, basic::Tracer::Error, lactamize::filename, analyze_ddG_stability::mutation, beta_nonlocal::pose, predPRE::resnum, runtime_assert, TR, and orn_macrocycle::wt.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.public.ddg.ddg_monomer") ( "apps.public.ddg.ddg_monomer"  )

static

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