Functions
utility::vector1< core::Size >	initialize_ncbbs (Pose &pose)

utility::vector1< core::Size >	initialize_hbs (Pose &pose)

void	add_generic_hbs_constraint (core::pose::Pose &pose, core::Size hbs_pre_position, core::Real distance, core::Real std, std::string const &cy2name, std::string const &cy1name)

void	add_a3b_hbs_constraint (core::pose::Pose &pose, core::Size oop_seq_position)
	Add constraints to keep a3b hydrogen bond surrogate (hbs) macrocycle closed, default values (distance = 1.52, std = 0.05) More...

void	add_a3b_hbs_constraint (core::pose::Pose &pose, core::Size hbs_seq_position, core::Real distance, core::Real std)
	Add constraints to keep a3b hydrogen bond surrogate (hbs) ring closed. More...

void	add_hbs_constraint (core::pose::Pose &pose, core::Size oop_seq_position)
	Add constraints to keep hydrogen bond surrogate (hbs) macrocycle closed, default values (distance = 1.52, std = 0.05) More...

void	add_hbs_constraint (core::pose::Pose &pose, core::Size hbs_seq_position, core::Real distance, core::Real std)
	Add constraints to keep hydrogen bond surrogate (hbs) ring closed. More...

void	constrain_ring_atoms (core::pose::Pose &pose, utility::vector1< core::id::AtomID > ids)

void	add_triazole_constraint (core::pose::Pose &pose, core::Size triazole_seq_position)
	Add constraints to keep triazole closed. More...

utility::vector1< core::Size >	initialize_oops (Pose &pose)

void	add_oop_constraint (core::pose::Pose &pose, core::Size oop_seq_position)
	Add constraints to keep oligooxopiperazine (oop) ring closed, default values (distance = 1.5, std = 0.05) More...

void	add_oop_constraint (core::pose::Pose &pose, core::Size oop_seq_position, core::Real distance, core::Real std)
	Add constraints to keep oligooxopiperazine (oop) ring closed. More...

Function Documentation

◆ add_a3b_hbs_constraint() [1/2]

void core::pose::ncbb::add_a3b_hbs_constraint	(	core::pose::Pose &	pose,
		core::Size	hbs_pre_position,
		core::Real	distance,
		core::Real	std
	)

Add constraints to keep a3b hydrogen bond surrogate (hbs) ring closed.

References add_generic_hbs_constraint(), protocols::mpi_refinement::distance(), and core::pose::TR().

◆ add_a3b_hbs_constraint() [2/2]

void core::pose::ncbb::add_a3b_hbs_constraint	(	core::pose::Pose &	pose,
		core::Size	a3b_hbs_pre_position
	)

Add constraints to keep a3b hydrogen bond surrogate (hbs) macrocycle closed, default values (distance = 1.52, std = 0.05)

Referenced by protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply().

◆ add_generic_hbs_constraint()

void core::pose::ncbb::add_generic_hbs_constraint	(	core::pose::Pose &	pose,
		core::Size	hbs_pre_position,
		core::Real	distance,
		core::Real	std,
		std::string const &	cy2name,
		std::string const &	cy1name
	)

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), protocols::mpi_refinement::distance(), core::conformation::Residue::has_variant_type(), core::chemical::HBS_POST, core::chemical::HBS_PRE, core::conformation::Residue::name(), core::pose::Pose::residue(), and core::pose::TR().

Referenced by add_a3b_hbs_constraint(), and add_hbs_constraint().

◆ add_hbs_constraint() [1/2]

void core::pose::ncbb::add_hbs_constraint	(	core::pose::Pose &	pose,
		core::Size	hbs_pre_position,
		core::Real	distance,
		core::Real	std
	)

Add constraints to keep hydrogen bond surrogate (hbs) ring closed.

References add_generic_hbs_constraint(), protocols::mpi_refinement::distance(), and core::pose::TR().

◆ add_hbs_constraint() [2/2]

void core::pose::ncbb::add_hbs_constraint	(	core::pose::Pose &	pose,
		core::Size	hbs_pre_position
	)

Add constraints to keep hydrogen bond surrogate (hbs) macrocycle closed, default values (distance = 1.52, std = 0.05)

Referenced by protocols::simple_moves::hbs::HbsPatcher::apply(), and initialize_ncbbs().

◆ add_oop_constraint() [1/2]

void core::pose::ncbb::add_oop_constraint	(	core::pose::Pose &	pose,
		core::Size	oop_seq_position
	)

Add constraints to keep oligooxopiperazine (oop) ring closed, default values (distance = 1.5, std = 0.05)

Overloaded function which defines default values, calls more general add_oop_constraint function

Referenced by protocols::simple_moves::oop::OopPatcher::apply(), initialize_ncbbs(), and initialize_oops().

◆ add_oop_constraint() [2/2]

void core::pose::ncbb::add_oop_constraint	(	core::pose::Pose &	pose,
		core::Size	oop_seq_position,
		core::Real	distance,
		core::Real	std
	)

Add constraints to keep oligooxopiperazine (oop) ring closed.

General function to add atom pair constraints to CYP and CZP for given distance
Other constraints are setup to keep virtual atoms VYP fixed near CYP and VZP fixed near CZP

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), protocols::mpi_refinement::distance(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::name(), core::chemical::OOP_POST, core::chemical::OOP_PRE, core::pose::Pose::remove_constraint(), core::pose::Pose::residue(), and core::pose::TR().