minimize_with_cst.cc File Reference

#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.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/keys/OptionKeys.hh>
#include <devel/init.hh>
#include <numeric/xyzVector.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/excn/Exceptions.hh>
#include <cstdlib>
#include <string>
#include <core/chemical/ResidueTypeSet.fwd.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.hh>
#include <core/id/DOF_ID.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/SilentFileOptions.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/vector1.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/Tracer.hh>
#include <sys/stat.h>
#include <utility/vector0.hh>

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 const &output_tag)
void	optimize_pose (pose::Pose &pose, ScoreFunctionOP scorefxn, std::string const &output_tag)
bool	already_minimized (std::string query, utility::vector1< std::string > check)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.ddg.minimize_with_cst")

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

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

Referenced by main().

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

References already_minimized(), begin, basic::options::OptionKeys::constraints::constraints, test.T009_Exceptions::e, basic::options::OptionKeys::in::file::file, utility::file::file_exists(), in::file::fullatom(), devel::init(), in::file::l(), basic::options::OptionKeys::in::file::list, utility::excn::Exception::msg(), optimize_pose(), basic::options::option, option, options, erraser_single_res_analysis::out, basic::options::OptionKeys::ddg::out_pdb_prefix, basic::options::OptionKeys::cp::output, demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, erraser_single_res_analysis::prefix, in::file::s(), basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, in::file::silent(), basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::OptionKeys::mh::match::ss, utility::string_split(), tag, basic::options::OptionKeys::in::file::tags, TR, and basic::options::OptionKeys::inout::dbms::user.

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

References ObjexxFCL::abs(), pyrosetta::create_score_function, basic::options::OptionKeys::coupled_moves::initial_repack, loops_kic::mm, basic::options::option, options, basic::options::OptionKeys::ddg::out_pdb_prefix, basic::options::OptionKeys::ddg::output_dir, basic::options::OptionKeys::score::fiber_diffraction::p, basic::options::OptionKeys::ddg::ramp_repulsive, reduce_fa_rep(), basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::ddg::rna_all_prot_sc_min_only, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::ddg::sc_min_only, out::file::silent(), basic::options::OptionKeys::mh::match::ss, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by optimize_pose().

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

References basic::options::OptionKeys::ddg::cst_dist_cutoff, basic::options::OptionKeys::ddg::harmonic_ca_tether, minimize_with_constraints(), basic::options::OptionKeys::ddg::no_constraints, basic::options::option, setup_ca_constraints(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

ScoreFunction& reduce_fa_rep	(	float	fraction_fa_rep,
		ScoreFunction &	s
	)

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

Referenced by minimize_with_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, basic::options::OptionKeys::constraints::cst_file, basic::options::OptionKeys::frags::j, make_symmdef_file_denovo::length, clean_pdb_keep_ligand::nres, basic::options::option, option, basic::options::OptionKeys::ddg::sc_min_only, TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by optimize_pose().

Variable Documentation

basic::Tracer TR("apps.public.ddg.minimize_with_cst")

static

Referenced by main(), minimize_with_constraints(), and setup_ca_constraints().