ensemble_generator.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/chemical/ResidueTypeSelector.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/PackerTask.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 <utility/excn/Exceptions.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/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/ProteinSilentStruct.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/io/silent/silent.fwd.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.hh>
#include <protocols/evaluation/RmsdEvaluator.hh>
#include <protocols/comparative_modeling/ConstraintRemodelMover.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.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, std::string output_tag)
void	setup_ca_constraints (pose::Pose &pose, ScoreFunction &s, float const CA_cutoff, float const cst_tol)
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, ScoreFunction &s, core::Real temperature, int numstruct, std::string output_tag, bool output_pdbs)
core::Real	set_temp_based_on_ens_diversity (pose::Pose &p, ScoreFunction &s, core::Real avg_ca_rmsd_target)
void	create_ensemble (pose::Pose &p, ScoreFunction &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

create_ensemble()

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

References basic::options::OptionKeys::ddg::ens_variation, out::nstruct(), basic::options::option, drrafter_rna::output_tag, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, run_mc(), docking::s, set_temp_based_on_ens_diversity(), local::temperature, and basic::options::OptionKeys::inout::dbms::user.

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, 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, docking::s, 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,
		std::string	output_tag
	)

References beta_nonlocal::mm, basic::options::option, options, basic::options::OptionKeys::ddg::out_pdb_prefix, drrafter_rna::output_tag, 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,
		ScoreFunction &	s,
		core::Real	temperature,
		int	numstruct,
		std::string	output_tag,
		bool	output_pdbs
	)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, pyrosetta::create_score_function, lactamize::cs, basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::i, basic::options::OptionKeys::ddg::last_accepted_pose_dir, mc, basic::options::OptionKeys::ddg::min_cst_weights, 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::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, test.Workshop5test::small_mover, and local::temperature.

Referenced by create_ensemble(), and set_temp_based_on_ens_diversity().

set_temp_based_on_ens_diversity()

core::Real set_temp_based_on_ens_diversity	(	pose::Pose &	p,
		ScoreFunction &	s,
		core::Real	avg_ca_rmsd_target
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, run_mc(), docking::s, and local::temperature.

Referenced by create_ensemble().

setup_ca_constraints()

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

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(), and zinc1_homodimer_design::setup().