#include <core/types.hh>
#include <core/chemical/ChemicalManager.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 <core/pose/PDBInfo.hh>
#include <core/import_pose/import_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/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 <basic/options/option.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 <core/io/silent/BinarySilentStruct.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/evaluation/RmsdEvaluator.hh>
#include <protocols/comparative_modeling/ConstraintRemodelMover.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/ddg.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/casp.OptionKeys.gen.hh>
#include <sys/stat.h>

Functions
ScoreFunction &	reduce_fa_rep (float fraction_fa_rep, ScoreFunction &s)

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

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

void	optimize_pose (pose::Pose &p, ScoreFunctionOP scorefxn, std::string output_tag)

bool	already_minimized (std::string query, utility::vector1< std::string > check)

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

◆ already_minimized()

bool already_minimized	(	std::string	query,
		utility::vector1< std::string >	check
	)

References detail::check(), compare(), create_a3b_hbs::i, and cache_trajectory::query.

Referenced by main().

◆ main()

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

References already_minimized(), argv, begin, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, test.T009_Exceptions::e, create_a3b_hbs::f, utility::file::file_exists(), PREcst::fname, in::file::fullatom(), h, basic::init(), in::file::l(), basic::options::OptionKeys::in::file::list, optimize_pose(), basic::options::option, option, basic::options::OptionKeys::ddg::out_pdb_prefix, bin_torsions::output, score::patch(), pdbs, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::prefix, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), challenge::ss, predPRE::t, extract_by_sidechain_sasa_score::tags, and basic::options::OptionKeys::inout::dbms::user.

◆ minimize_with_constraints()

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

◆ optimize_pose()

void optimize_pose	(	pose::Pose &	p,
		ScoreFunctionOP	scorefxn,
		std::string	output_tag
	)

References basic::options::OptionKeys::ddg::harmonic_ca_tether, minimize_with_constraints(), basic::options::OptionKeys::ddg::no_constraints, basic::options::option, drrafter_rna::output_tag, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, oop_conformations::scorefxn, setup_ca_constraints(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ reduce_fa_rep()

ScoreFunction& reduce_fa_rep	(	float	fraction_fa_rep,
		ScoreFunction &	s
	)

References docking::s.

Referenced by minimize_with_constraints().

◆ setup_ca_constraints()

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

References local::constraint_weight, utility::io::oc::cout, basic::options::OptionKeys::templates::cst::cst, basic::options::OptionKeys::constraints::cst_file, create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, create_a3b_hbs::nres, basic::options::option, option, beta_nonlocal::pose, docking::s, basic::options::OptionKeys::ddg::sc_min_only, and basic::options::OptionKeys::inout::dbms::user.

Referenced by optimize_pose().

Functions