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Functions
core::pose::ncbb Namespace Reference

Functions

utility::vector1< core::Sizeinitialize_ncbbs (Pose &pose)
 
utility::vector1< core::Sizeinitialize_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::Sizeinitialize_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_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().

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(), and core::pose::TR().

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 
)
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().

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(), 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 protocols::simple_moves::oop::OopPatcher::apply(), 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::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), 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().

void core::pose::ncbb::add_triazole_constraint ( core::pose::Pose pose,
core::Size  i 
)
void core::pose::ncbb::constrain_ring_atoms ( core::pose::Pose pose,
utility::vector1< core::id::AtomID ids 
)
utility::vector1< core::Size > core::pose::ncbb::initialize_hbs ( Pose pose)
utility::vector1< core::Size > core::pose::ncbb::initialize_ncbbs ( Pose pose)
utility::vector1< core::Size > core::pose::ncbb::initialize_oops ( Pose pose)