ensemble_generator_score12_sidechain_ver2.cc File Reference

#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.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/keys/OptionKeys.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <numeric/xyzVector.hh>
#include <iostream>
#include <utility/io/izstream.hh>
#include <string>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/id/AtomID.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/pack/task/PackerTask.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <ctime>
#include <sys/stat.h>
#include <core/import_pose/import_pose.hh>

Functions
ScoreFunction &	reduce_fa_rep (float fraction_fa_rep, ScoreFunction &s)
void	minimize_with_constraints (pose::Pose &p, ScoreFunction &s)
void	setup_ca_constraints (pose::Pose &pose, ScoreFunction &s, float const CA_cutoff, float const)
void	setup_movers (simple_moves::SmallMoverOP small, simple_moves::ShearMoverOP shear, core::Real small_H_angle_max, core::Real small_E_angle_max, core::Real small_L_angle_max, core::Real shear_H_angle_max, core::Real shear_E_angle_max, core::Real shear_L_angle_max)
double	run_mc (pose::Pose &p, ScoreFunctionOP s, core::Real temperature, int numstruct, std::string const &output_tag, bool output_pdbs)
void	create_ensemble (pose::Pose &p, ScoreFunctionOP s, std::string const &output_tag)
int	main (int argc, char *argv[])

Detailed Description

Author

Liz Kellogg ekell.nosp@m.ogg@.nosp@m.u.was.nosp@m.hing.nosp@m.ton.e.nosp@m.du

Function Documentation

create_ensemble()

void create_ensemble	(	pose::Pose &	p,
		ScoreFunctionOP	s,
		std::string const &	output_tag
	)

References out::nstruct(), basic::options::option, drrafter_rna::output_tag, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, run_mc(), docking::s, and local::temperature.

Referenced by main().

main()

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

References argv, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, create_ensemble(), lactamize::cs, test.T009_Exceptions::e, create_a3b_hbs::f, PREcst::fname, pyrosetta.distributed.io::get_score_function(), h, basic::options::OptionKeys::ddg::harmonic_ca_tether, basic::init(), in::file::l(), basic::options::OptionKeys::in::file::list, basic::options::option, option, bin_torsions::output, pdbs, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_ca_constraints(), and basic::options::OptionKeys::inout::dbms::user.

minimize_with_constraints()

void minimize_with_constraints	(	pose::Pose &	p,
		ScoreFunction &	s
	)

References beta_nonlocal::mm, basic::options::option, options, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, basic::options::OptionKeys::ddg::ramp_repulsive, reduce_fa_rep(), docking::s, and basic::options::OptionKeys::ddg::sc_min_only.

Referenced by run_mc().

reduce_fa_rep()

ScoreFunction& reduce_fa_rep	(	float	fraction_fa_rep,
		ScoreFunction &	s
	)

References docking::s.

Referenced by minimize_with_constraints().

run_mc()

double run_mc	(	pose::Pose &	p,
		ScoreFunctionOP	s,
		core::Real	temperature,
		int	numstruct,
		std::string const &	output_tag,
		bool	output_pdbs
	)

References basic::options::OptionKeys::lh::bss, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, pyrosetta.distributed.io::get_score_function(), basic::options::OptionKeys::ddg::last_accepted_pose_dir, mc, basic::options::OptionKeys::ddg::min_with_cst, minimize_with_constraints(), beta_nonlocal::mm, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::mp::quickrelax::nmoves, basic::options::OptionKeys::ddg::no_bb_movement, basic::options::option, option, drrafter_rna::output_tag, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, docking::s, setup_ca_constraints(), setup_movers(), test.Workshop5test::shear_mover, out::file::silent(), test.Workshop5test::small_mover, local::temperature, and basic::options::OptionKeys::inout::dbms::user.

Referenced by create_ensemble().

setup_ca_constraints()

void setup_ca_constraints	(	pose::Pose &	pose,
		ScoreFunction &	s,
		float const	CA_cutoff,
		float const
	)

References local::constraint_weight, basic::options::OptionKeys::templates::cst::cst, create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, create_a3b_hbs::nres, basic::options::option, beta_nonlocal::pose, and docking::s.

Referenced by main(), and run_mc().

setup_movers()

void setup_movers	(	simple_moves::SmallMoverOP	small,
		simple_moves::ShearMoverOP	shear,
		core::Real	small_H_angle_max,
		core::Real	small_E_angle_max,
		core::Real	small_L_angle_max,
		core::Real	shear_H_angle_max,
		core::Real	shear_E_angle_max,
		core::Real	shear_L_angle_max
	)

Referenced by run_mc().