chet_trp_to_gly.cc File Reference

#include <iostream>
#include <iomanip>
#include <devel/init.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/id/AtomID_Map.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/TwelveANeighborGraph.hh>
#include <core/scoring/Energies.hh>
#include <protocols/moves/RigidBodyMover.hh>
#include <protocols/moves/BackrubMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/KinematicMover.hh>
#include <protocols/loops/KinematicWrapper.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/loops_main.hh>
#include <basic/Tracer.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/after_opts.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>

Functions
void	do_minimization (core::pose::Pose &pose, utility::vector1< bool > &allow_moving, pack::task::PackerTaskCOP repack_task, scoring::ScoreFunctionCOP scorefxn, scoring::ScoreFunctionCOP repack_scorefxn)
void	do_KIC (core::pose::Pose &pose, utility::vector1< bool > &allow_moving, pack::task::PackerTaskCOP repack_task, scoring::ScoreFunctionCOP scorefxn, scoring::ScoreFunctionCOP repack_scorefxn)
void	do_backrub (core::pose::Pose &pose, utility::vector1< bool > &allow_moving, pack::task::PackerTaskCOP repack_task, scoring::ScoreFunctionCOP scorefxn, scoring::ScoreFunctionCOP repack_scorefxn)
int	main (int argc, char *argv[])
	General testing code. More...

Variables
static basic::Tracer	TR ("apps.pilot.chet_trp_to_gly.main")

Function Documentation

do_backrub()

void do_backrub	(	core::pose::Pose &	pose,
		utility::vector1< bool > &	allow_moving,
		pack::task::PackerTaskCOP	repack_task,
		scoring::ScoreFunctionCOP	scorefxn,
		scoring::ScoreFunctionCOP	repack_scorefxn
	)

References utility::vectorL< L, T, A >::at(), do_minimization(), indel::end_res, create_a3b_hbs::j, create_a3b_hbs::k, mc, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::backrub::ntrials, beta_nonlocal::pose, oop_conformations::scorefxn, indel::start_res, TR, and gaussian-sampling::trial.

do_KIC()

void do_KIC	(	core::pose::Pose &	pose,
		utility::vector1< bool > &	allow_moving,
		pack::task::PackerTaskCOP	repack_task,
		scoring::ScoreFunctionCOP	scorefxn,
		scoring::ScoreFunctionCOP	repack_scorefxn
	)

References utility::vectorL< L, T, A >::at(), create_a3b_hbs::j, create_a3b_hbs::k, demo.D080_Loop_modeling::loop_begin, pivot_selection::loop_end, mc, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::backrub::ntrials, beta_nonlocal::pose, oop_conformations::scorefxn, TR, and gaussian-sampling::trial.

Referenced by main().

do_minimization()

void do_minimization	(	core::pose::Pose &	pose,
		utility::vector1< bool > &	allow_moving,
		pack::task::PackerTaskCOP	repack_task,
		scoring::ScoreFunctionCOP	scorefxn,
		scoring::ScoreFunctionCOP	repack_scorefxn
	)

References utility::vectorL< L, T, A >::at(), create_a3b_hbs::j, beta_nonlocal::mm, beta_nonlocal::pose, oop_conformations::scorefxn, and TR.

Referenced by do_backrub(), and main().

main()

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

General testing code.

References argv, utility::vectorL< L, T, A >::at(), utility::graph::Node::const_edge_list_end(), do_KIC(), utility::options::OptionKeys::options::exit, utility::graph::Edge::get_node(), create_a3b_hbs::ii, basic::init(), create_a3b_hbs::j, NEW_OPT, local::nstruct, option, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::start_file(), and TR.

Variable Documentation

TR

basic::Tracer TR("apps.pilot.chet_trp_to_gly.main") ( "apps.pilot.chet_trp_to_gly.main"  )

static

Referenced by do_backrub(), do_KIC(), do_minimization(), and main().