make_retroinverso.cc File Reference

Generates a retroinverso version of a pose. More...

#include <devel/init.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <core/pose/Pose.hh>
#include <core/pose/init_id_map.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/id/AtomID.hh>
#include <core/types.hh>
#include <core/scoring/rms_util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/chemical/AA.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/select/residue_selector/NotResidueSelector.hh>
#include <core/select/residue_selector/ResidueIndexSelector.hh>
#include <core/pack/task/operation/OperateOnResidueSubset.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <protocols/relax/FastRelax.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>

Functions
void	register_options ()
void	build_inverso_sequence (core::pose::PoseCOP refpose, core::pose::PoseOP newpose)
	Given a reference pose, make a newpose where all of the L/D amino acids have been swapped and the sequence runs backwards. More...
void	update_atom_positions (core::pose::PoseOP newpose)
	Mirrors the pose so that the atom positions are correct. More...
void	set_inverso_conformation_main_chain (core::pose::PoseOP refpose, core::pose::PoseOP newpose)
	Sets pose conformation for the main chain. More...
void	set_inverso_conformation_side_chain (core::pose::PoseOP refpose, core::pose::PoseOP newpose)
	Sets pose conformation for the side chains. More...
void	align_conformations (core::pose::PoseOP refpose, core::pose::PoseOP newpose)
	Aligns the newpose and refpose. More...
void	fix_prolines (core::pose::PoseOP newpose)
	Fixes the prolines. More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("make_retroinverso")

Detailed Description

Generates a retroinverso version of a pose.

Author

Christine S. Kang (csyka.nosp@m.ng@u.nosp@m.w.edu)

Function Documentation

align_conformations()

void align_conformations	(	core::pose::PoseOP	refpose,
		core::pose::PoseOP	newpose
	)

Aligns the newpose and refpose.

References utility::exit(), kmeans_bb_dependent_rotlib::newN, create_a3b_hbs::r, and superimpose_pose().

Referenced by main().

build_inverso_sequence()

void build_inverso_sequence	(	core::pose::PoseCOP	refpose,
		core::pose::PoseOP	newpose
	)

Given a reference pose, make a newpose where all of the L/D amino acids have been swapped and the sequence runs backwards.

This changes the residue type, but does not fix the position of the atoms.

References create_a3b_hbs::i.

Referenced by main().

fix_prolines()

void fix_prolines

(

core::pose::PoseOP

newpose

)

Fixes the prolines.

References basic::options::OptionKeys::stepwise::move, create_a3b_hbs::r, and test.T120_core::sfxn.

Referenced by main().

main()

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

References align_conformations(), argv, build_inverso_sequence(), test.T009_Exceptions::e, fix_prolines(), basic::init(), basic::options::option, pyrosetta.distributed.io::pose_from_file, register_options(), basic::options::OptionKeys::in::file::s, set_inverso_conformation_main_chain(), set_inverso_conformation_side_chain(), update_atom_positions(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

register_options()

void register_options

(

)

References utility::options::OptionCollection::add_relevant(), basic::options::option, and basic::options::OptionKeys::in::file::s.

Referenced by main().

set_inverso_conformation_main_chain()

void set_inverso_conformation_main_chain	(	core::pose::PoseOP	refpose,
		core::pose::PoseOP	newpose
	)

Sets pose conformation for the main chain.

References utility::exit(), and create_a3b_hbs::r.

Referenced by main().

set_inverso_conformation_side_chain()

void set_inverso_conformation_side_chain	(	core::pose::PoseOP	refpose,
		core::pose::PoseOP	newpose
	)

Sets pose conformation for the side chains.

References a, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, utility::exit(), create_a3b_hbs::r, numeric::conversions::radians(), and runtime_assert_string_msg.

Referenced by main().

update_atom_positions()

void update_atom_positions

(

core::pose::PoseOP

newpose

)

Mirrors the pose so that the atom positions are correct.

Does not change the residue identities.

References a, create_a3b_hbs::r, and numeric::xyzVector< T >::x().

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("make_retroinverso") ( "make_retroinverso"  )

static