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

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

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...

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

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 initialize_ncbbs().

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 core::pose::Pose::add_constraint(), angle, core::conformation::Residue::atom_index(), dihedral(), core::pose::Pose::residue(), and core::pose::TR.

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 initialize_ncbbs(), and initialize_oops().

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::scoring::constraints::AtomPairConstraint::atom(), core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::conformation::Residue::has_variant_type(), core::chemical::OOP_PRE, core::pose::Pose::remove_constraint(), core::pose::Pose::residue(), runtime_assert_msg, and core::pose::TR.

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

References core::conformation::Residue::has_variant_type(), core::chemical::HBS_POST, core::chemical::HBS_PRE, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

References add_hbs_constraint(), add_oop_constraint(), core::conformation::Residue::has_variant_type(), core::chemical::HBS_POST, core::chemical::HBS_PRE, core::chemical::OOP_POST, core::chemical::OOP_PRE, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

loops through residues searching for oop variants and sets up constraints

References add_oop_constraint(), core::conformation::Residue::has_variant_type(), core::chemical::OOP_PRE, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by core::io::pdb::build_pose_as_is1().

Functions

Function Documentation