analyze_ddG.cc File Reference

#include <devel/init.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/operation/TaskOperation.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/metrics/PoseMetricCalculatorBase.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionInfo.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/simple_moves/SetReturningPackRotamersMover.hh>
#include <protocols/minimization_packing/TaskAwareMinMover.hh>
#include <protocols/pose_metric_calculators/HPatchCalculator.hh>
#include <protocols/pose_metric_calculators/NeighborsByDistanceCalculator.hh>
#include <protocols/task_operations/RestrictToNeighborhoodOperation.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <basic/MetricValue.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/vector1.functions.hh>
#include <ObjexxFCL/format.hh>
#include <sstream>
#include <iostream>
#include <string>
#include <core/import_pose/import_pose.hh>

Namespaces
	analyze_ddG_stability

Functions
void	init_usage_prompt (std::string exe)
	the usage prompt that gets printed when the user doesn't enter all the required command line arguments More...
void	print_energies (scoring::EnergyMap e, scoring::ScoreFunctionOP scorefxn)
	Helper method for the main function. Takes in a pose, the scorefunction, hpatch energies and weights and prints everything out in a pretty format. More...
void	tokenize_string (const std::string &str, std::vector< std::string > &tokens, const std::string &delimiters=" ")
int	main (int argc, char *argv[])
	main method for the ddG protocol More...

Variables
static basic::Tracer	TR ("analyze_ddG_stability")
StringOptionKey const	analyze_ddG_stability::mutation ("analyze_ddG_stability::mutation")
std::string	usage_string

Function Documentation

init_usage_prompt()

void init_usage_prompt

(

std::string

exe

)

the usage prompt that gets printed when the user doesn't enter all the required command line arguments

References usage_string.

Referenced by main().

main()

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

main method for the ddG protocol

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, utility::arg_max(), argv, utility::file::FileName::base(), utility::io::oc::cerr, predPRE::chain, utility::io::oc::cout, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, ObjexxFCL::format::F(), utility::file::file_exists(), file_exists(), lactamize::filename, test.T110_numeric::I, create_a3b_hbs::ii, basic::init(), init_usage_prompt(), subloop_histogram::iterator, vancomycin::min_mover, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::in::file::movemap, analyze_ddG_stability::mutation, utility::file::FileName::name(), packing::ndruns(), basic::options::option, option, erraser_single_res_analysis::out, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, print_energies(), in::file::s(), create_a3b_hbs::score, oop_conformations::scorefxn, challenge::ss, basic::options::start_file(), vancomycin::task, tokenize_string(), TR, usage_string, utility_exit_with_message, utility_exit_with_message_status, basic::MetricValue< T >::value(), and value.

print_energies()

void print_energies	(	scoring::EnergyMap	e,
		scoring::ScoreFunctionOP	scorefxn
	)

Helper method for the main function. Takes in a pose, the scorefunction, hpatch energies and weights and prints everything out in a pretty format.

References utility::io::oc::cout, enumerate_junctions::default, test.T009_Exceptions::e, ObjexxFCL::format::F(), beta_nonlocal::jj, basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::OptionKeys::corrections::score::p_aa_pp, basic::options::OptionKeys::remodel::rama, oop_conformations::scorefxn, and basic::options::OptionKeys::sc::weight.

Referenced by main().

tokenize_string()

void tokenize_string	(	const std::string &	str,
		std::vector< std::string > &	tokens,
		const std::string &	delimiters = " "
	)

References make_symmdef_file_denovo::pos, and str().

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("analyze_ddG_stability") ( "analyze_ddG_stability"  )

static

Referenced by main().

usage_string

std::string usage_string

Referenced by init_usage_prompt(), and main().