mp_optimize_geometry_params.cc File Reference

#include <iostream>
#include <cmath>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <devel/init.hh>
#include <utility/vector1.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <utility/pointer/owning_ptr.hh>
#include <core/pose/variant_util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/EnergyMap.hh>
#include <numeric/xyzVector.hh>
#include <core/id/AtomID.hh>
#include <protocols/membrane/AddMembraneMover.hh>
#include <core/conformation/membrane/MembraneInfo.hh>
#include <core/conformation/membrane/MembraneGeometry.hh>
#include <core/conformation/membrane/membrane_geometry/Bicelle.hh>
#include <core/conformation/membrane/membrane_geometry/DoubleVesicle.hh>
#include <core/conformation/membrane/membrane_geometry/Vesicle.hh>
#include <protocols/membrane/OptimizeProteinEmbeddingMover.hh>
#include <protocols/membrane/OptimizeMembranePositionMover.hh>
#include <utility/io/ozstream.hh>

Functions
void	update_vesicle_radius (core::pose::Pose &pose, core::conformation::membrane::membrane_geometry::VesicleCOP vesicle, core::Real radius)
void	update_bicelle_radius (core::pose::Pose &pose, core::conformation::membrane::membrane_geometry::BicelleCOP bicelle, core::Real inner_radius)
void	update_double_vesicle (core::pose::Pose &pose, core::conformation::membrane::membrane_geometry::DoubleVesicleCOP dvesicle, core::Real distance, core::Real inner_r)
void	opt_vesicle_params (core::pose::Pose &pose, core::conformation::membrane::MembraneGeometryCOP mp_geometry, core::scoring::ScoreFunctionOP sfxn)
void	opt_double_vesicle_params (core::pose::Pose &pose, core::conformation::membrane::MembraneGeometryCOP mp_geometry, core::scoring::ScoreFunctionOP sfxn)
void	opt_bicelle_params (core::pose::Pose &pose, core::conformation::membrane::MembraneGeometryCOP mp_geometry, core::scoring::ScoreFunctionOP sfxn)
int	main (int argc, char **argv)

Function Documentation

main()

int main	(	int	argc,
		char **	argv
	)

References argv, utility::io::oc::cout, pyrosetta::create_score_function, enumerate_junctions::default, test.T009_Exceptions::e, basic::init(), opt_bicelle_params(), opt_double_vesicle_params(), opt_vesicle_params(), basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::s, test.T120_core::sfxn, basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::score::weights.

opt_bicelle_params()

void opt_bicelle_params	(	core::pose::Pose &	pose,
		core::conformation::membrane::MembraneGeometryCOP	mp_geometry,
		core::scoring::ScoreFunctionOP	sfxn
	)

References utility::io::oc::cout, lactamize::filename, test.Workshop4test::new_score, bin_torsions::output, beta_nonlocal::pose, create_a3b_hbs::r, test.T120_core::sfxn, utility::string_split(), erraser_analysis::temp, and update_bicelle_radius().

Referenced by main().

opt_double_vesicle_params()

void opt_double_vesicle_params	(	core::pose::Pose &	pose,
		core::conformation::membrane::MembraneGeometryCOP	mp_geometry,
		core::scoring::ScoreFunctionOP	sfxn
	)

References utility::io::oc::cout, lactamize::filename, test.Workshop4test::new_score, bin_torsions::output, beta_nonlocal::pose, create_a3b_hbs::r, test.T120_core::sfxn, utility::string_split(), erraser_analysis::temp, and update_double_vesicle().

Referenced by main().

opt_vesicle_params()

void opt_vesicle_params	(	core::pose::Pose &	pose,
		core::conformation::membrane::MembraneGeometryCOP	mp_geometry,
		core::scoring::ScoreFunctionOP	sfxn
	)

References utility::io::oc::cout, lactamize::filename, test.Workshop4test::new_score, bin_torsions::output, beta_nonlocal::pose, create_a3b_hbs::r, test.T120_core::sfxn, utility::string_split(), erraser_analysis::temp, and update_vesicle_radius().

Referenced by main().

update_bicelle_radius()

void update_bicelle_radius	(	core::pose::Pose &	pose,
		core::conformation::membrane::membrane_geometry::BicelleCOP	bicelle,
		core::Real	inner_radius
	)

References beta_nonlocal::pose.

Referenced by opt_bicelle_params().

update_double_vesicle()

void update_double_vesicle	(	core::pose::Pose &	pose,
		core::conformation::membrane::membrane_geometry::DoubleVesicleCOP	dvesicle,
		core::Real	distance,
		core::Real	inner_r
	)

References build_jacobian::distance, and beta_nonlocal::pose.

Referenced by opt_double_vesicle_params().

update_vesicle_radius()

void update_vesicle_radius	(	core::pose::Pose &	pose,
		core::conformation::membrane::membrane_geometry::VesicleCOP	vesicle,
		core::Real	radius
	)

References beta_nonlocal::pose, and basic::options::OptionKeys::cluster::radius.

Referenced by opt_vesicle_params().