ensemble_generator_score12_sidechain_ver2.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.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/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/keys/OptionKeys.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.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 <basic/Tracer.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/func/Func.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.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/score.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/simple_moves/RotamerTrialsMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/excn/Exceptions.hh>
#include <time.h>
#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 output_tag, bool output_pdbs)
void	create_ensemble (pose::Pose &p, ScoreFunctionOP s, std::string 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

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

References out::nstruct(), basic::options::option, run_mc(), and basic::options::OptionKeys::abinitio::temperature.

Referenced by main().

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

References utility::io::oc::cerr, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, create_ensemble(), demo.D060_Folding::f, basic::options::OptionKeys::ddg::harmonic_ca_tether, devel::init(), in::file::l(), basic::options::OptionKeys::in::file::list, utility::excn::EXCN_Base::msg(), basic::options::option, option, options, basic::options::OptionKeys::cp::output, app.surface_docking.surface_docking::pose, in::file::s(), PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_ca_constraints(), and basic::options::OptionKeys::inout::dbms::user.

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

References app.delta_score_per_mutation::mm, basic::options::option, options, basic::options::OptionKeys::ddg::ramp_repulsive, reduce_fa_rep(), and basic::options::OptionKeys::ddg::sc_min_only.

Referenced by run_mc().

ScoreFunction& reduce_fa_rep	(	float	fraction_fa_rep,
		ScoreFunction &	s
	)

References basic::options::OptionKeys::in::file::s.

Referenced by minimize_with_constraints().

double run_mc	(	pose::Pose &	p,
		ScoreFunctionOP	s,
		core::Real	temperature,
		int	numstruct,
		std::string	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, basic::options::OptionKeys::ddg::last_accepted_pose_dir, basic::options::OptionKeys::mc::mc, basic::options::OptionKeys::ddg::min_with_cst, minimize_with_constraints(), app.delta_score_per_mutation::mm, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::mp::quickrelax::nmoves, basic::options::OptionKeys::ddg::no_bb_movement, basic::options::option, option, setup_ca_constraints(), setup_movers(), test.Workshop5test::shear_mover, out::file::silent(), test.Workshop5test::small_mover, and basic::options::OptionKeys::inout::dbms::user.

Referenced by create_ensemble().

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

References basic::options::OptionKeys::ddg::constraint_weight, basic::options::OptionKeys::templates::cst::cst, basic::options::OptionKeys::frags::j, make_symmdef_file_denovo::length, clean_pdb_keep_ligand::nres, and basic::options::option.

Referenced by main(), and run_mc().

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(), and zinc1_homodimer_design::setup().