src/apps/public/ddg/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/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueSelector.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <basic/options/after_opts.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 <basic/database/open.hh>
#include <protocols/init.hh>
#include <core/io/pdb/pose_io.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <core/pack/task/ResfileReader.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <ios>
#include <utility/io/izstream.hh>
#include <ObjexxFCL/format.hh>
#include <cstdlib>
#include <string>
#include <protocols/moves/ddGMover.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/Tracer.hh>

Typedefs
typedef utility::vector1 < core::chemical::AA >	mutations
typedef utility::vector1< double >	ddgs
Functions
void	print_ddgs (std::string ddg_out, std::string label, ddgs delta_e_components, ddgs, double total_ddgs, protocols::moves::ddGMover &mover, bool print_header, bool min_cst)
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.
int	main (int argc, char *argv[])
Variables
static basic::Tracer	TR ("apps.public.ddg.ddg_monomer")

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Detailed Description

Author:

Liz Kellogg ekellogg@u.washington.edu

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Typedef Documentation

typedef utility::vector1< double > ddgs

typedef utility::vector1< core::chemical::AA > mutations

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Function Documentation

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

References basic::options::OptionKeys::chemical::chemical, basic::Tracer::Debug, basic::options::OptionKeys::ddg::debug_output, ddg::debug_output(), basic::options::OptionKeys::ddg::dump_pdbs, ddg::dump_pdbs(), basic::options::OptionKeys::score::fa_max_dis, score::fa_max_dis(), utility::filename(), basic::database::full_name(), color_pdb::i, src::init(), basic::options::OptionKeys::ddg::interface_ddg, ddg::interface_ddg(), basic::options::OptionKeys::ddg::iterations, ddg::iterations(), ddg::local_opt_only(), basic::options::OptionKeys::ddg::mean, basic::options::OptionKeys::ddg::min, basic::options::OptionKeys::ddg::min_cst, ddg::minimization_patch(), ddg::minimization_scorefunction(), basic::options::OptionKeys::nonlocal::moves, basic::options::OptionKeys::ddg::mut_file, ddg::mut_file(), basic::options::OptionKeys::casp::num_iterations, OPT, basic::options::OptionKeys::casp::opt_radius, ddg::opt_radius(), basic::options::option, option, options, basic::options::OptionKeys::canonical_sampling::out::out, ddg::out(), PyMOL_demo::pose, print_ddgs(), read_in_mutations(), packing::resfile(), runtime_assert, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), TR, basic::options::OptionKeys::mysql::user, basic::options::OptionKeys::casp::weight_file, and ddg::weight_file().

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

References utility::options::OptionKeys::options::exit, ObjexxFCL::fmt::F(), color_pdb::i, and TR.

Referenced by main().

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 basic::Tracer::Error, basic::options::OptionKeys::ddg::mut, get_pdb::resnum, runtime_assert, TR, and revert_app::wt.

Referenced by main().

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Variable Documentation

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