#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <utility/file/FileName.hh>
#include <utility/string_util.hh>
#include <utility/excn/Exceptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/rms_util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <basic/options/option.hh>
#include <protocols/evaluation/RmsdEvaluator.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <core/chemical/ChemicalManager.hh>
#include <numeric/random/random.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/Tracer.hh>
#include <basic/options/keys/evolution.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>

Classes
struct	PoseAndData

struct	EnergyAndFilename

Functions
bool	compareEnergies (const PoseAndData &p1, const PoseAndData &p2)

void	readPoseAndData_PDB (PoseAndData &pad, const std::string &filename, core::scoring::ScoreFunctionOP scorefxn, pose::PoseOP native_pose, bool havenative)

void	readPoseAndData_SILENT (PoseAndData &pad, const std::string &filename, core::io::silent::SilentFileData::iterator &data, core::scoring::ScoreFunctionOP scorefxn, pose::PoseOP native_pose, bool havenative)

void	fillPoseAndDataList (std::vector< utility::file::FileName > &list, std::vector< PoseAndData > &poses, core::scoring::ScoreFunctionOP scorefxn)

void	processChild (PoseAndData &child, std::vector< PoseAndData > &parent_list, int size_limit)

void	processChildren (std::vector< utility::file::FileName > &list, core::scoring::ScoreFunctionOP scorefxn, std::vector< PoseAndData > &parent_list, int size_limit)

void	processChildrenIntensification (std::vector< utility::file::FileName > &list, core::scoring::ScoreFunctionOP scorefxn, std::vector< PoseAndData > &parent_list, int size_limit=200)
	Takes a list of filenames that yield input poses, scores the poses using the provided ScoreFunction,. More...

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

Function Documentation

◆ compareEnergies()

bool compareEnergies	(	const PoseAndData &	p1,
		const PoseAndData &	p2
	)

References PoseAndData::energy, and p2.

Referenced by processChildrenIntensification().

◆ fillPoseAndDataList()

void fillPoseAndDataList	(	std::vector< utility::file::FileName > &	list,
		std::vector< PoseAndData > &	poses,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References data, lactamize::filename, getline(), create_a3b_hbs::i, subloop_histogram::iterator, line, basic::options::OptionKeys::in::file::list, in::file::native(), docking::native_pose, basic::options::option, option, ObjexxFCL::pad(), pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, readPoseAndData_PDB(), oop_conformations::scorefxn, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

◆ main()

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

References evolution::action(), argv, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, evolution::childlist(), utility::io::oc::cout, test.T009_Exceptions::e, fillPoseAndDataList(), create_a3b_hbs::i, basic::init(), subloop_histogram::iterator, basic::options::option, option, lactamize::outfile, basic::options::OptionKeys::evolution::padding_score_filter, evolution::padding_score_filter(), basic::options::OptionKeys::evolution::padding_stage2_filter, evolution::padding_stage2_filter(), evolution::parentlist(), processChildren(), processChildrenIntensification(), ObjexxFCL::right_string_of(), extract_by_sidechain_sasa_score::scorefile, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::evolution::targetdir, evolution::targetdir(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

◆ processChild()

void processChild	(	PoseAndData &	child,
		std::vector< PoseAndData > &	parent_list,
		int	size_limit
	)

References PoseAndData::clusternumber, utility::io::oc::cout, PoseAndData::energy, PoseAndData::filename, subloop_histogram::iterator, basic::options::option, option, PoseAndData::pose, PoseAndData::rms, loops_kic::rms, basic::options::OptionKeys::lh::rms_limit, evolution::rms_threshold(), basic::options::OptionKeys::evolution::rms_topmargin, and evolution::rms_topmargin().

Referenced by processChildren().

◆ processChildren()

void processChildren	(	std::vector< utility::file::FileName > &	list,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::vector< PoseAndData > &	parent_list,
		int	size_limit
	)

◆ processChildrenIntensification()

void processChildrenIntensification	(	std::vector< utility::file::FileName > &	list,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::vector< PoseAndData > &	parent_list,
		int	size_limit = `200`
	)

Takes a list of filenames that yield input poses, scores the poses using the provided ScoreFunction,.

References compareEnergies(), count, demo.D060_Folding::counter, utility::io::oc::cout, data, end, PoseAndData::energy, lactamize::filename, getline(), create_a3b_hbs::i, subloop_histogram::iterator, line, basic::options::OptionKeys::in::file::list, in::file::native(), docking::native_pose, basic::options::option, option, PoseAndData::pose, pyrosetta.distributed.io::pose_from_file, readPoseAndData_PDB(), readPoseAndData_SILENT(), PoseAndData::rms, oop_conformations::scorefxn, sfd, PoseAndData::silent_index, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

◆ readPoseAndData_PDB()

void readPoseAndData_PDB	(	PoseAndData &	pad,
		const std::string &	filename,
		core::scoring::ScoreFunctionOP	scorefxn,
		pose::PoseOP	native_pose,
		bool	havenative
	)

References lactamize::filename, docking::native_pose, ObjexxFCL::pad(), and pyrosetta.distributed.io::pose_from_file.

Referenced by fillPoseAndDataList(), processChildren(), and processChildrenIntensification().

◆ readPoseAndData_SILENT()

void readPoseAndData_SILENT	(	PoseAndData &	pad,
		const std::string &	filename,
		core::io::silent::SilentFileData::iterator &	data,
		core::scoring::ScoreFunctionOP	scorefxn,
		pose::PoseOP	native_pose,
		bool	havenative
	)

References data, lactamize::filename, docking::native_pose, and ObjexxFCL::pad().

Referenced by processChildren(), and processChildrenIntensification().

Classes

Functions