util.cc File Reference

Utility functions for generalized kinematic closure. More...

#include <protocols/generalized_kinematic_closure/GeneralizedKIC.hh>
#include <protocols/generalized_kinematic_closure/GeneralizedKICCreator.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <basic/Tracer.hh>
#include <core/types.hh>
#include <utility/tag/Tag.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/pose/util.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <numeric/random/random.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzVector.io.hh>
#include <numeric/kinematic_closure/bridgeObjects.hh>
#include <numeric/kinematic_closure/kinematic_closure_helpers.hh>
#include <numeric/conversions.hh>
#include <boost/foreach.hpp>
#include <utility/excn/Exceptions.hh>
#include <core/pose/Pose.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::generalized_kinematic_closure

Functions
static thread_local basic::Tracer	protocols::generalized_kinematic_closure::TR ("protocols.generalized_kinematic_closure.util")
bool	protocols::generalized_kinematic_closure::is_in_list (core::Size const val, utility::vector1< core::Size > const &list)
	Function to determine whether a value is in a list. More...
bool	protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map (core::Size const residue_index, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
	function to determine whether a residue index from the original pose is in the residue_map list. More...
void	protocols::generalized_kinematic_closure::set_loop_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &t_ang, utility::vector1< core::Real > const &b_ang, utility::vector1< core::Real > const &b_len)
	Set the loop pose conformation based on a set of results from kinematic closure. More...
void	protocols::generalized_kinematic_closure::set_loop_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &t_ang)
	Set the loop pose conformation based on a set of results from kinematic closure. More...
void	protocols::generalized_kinematic_closure::copy_loop_pose_to_original (core::pose::Pose &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map)
	Copy the atom positions of the residues in the loop pose to the original pose. More...
void	protocols::generalized_kinematic_closure::general_set_phi (core::pose::Pose &pose, core::Size const residue_index, core::Real const &phi_value)
	Sets phi for an L-alpha amino acid, even if the nitrogen has a nonstandard connection. More...
void	protocols::generalized_kinematic_closure::general_set_psi (core::pose::Pose &pose, core::Size const residue_index, core::Real const &psi_value)
	Sets psi for an L-alpha amino acid, even if the carbonyl carbon has a nonstandard connection. More...
core::Size	protocols::generalized_kinematic_closure::get_original_pose_rsd (core::Size const perturbedloop_rsd, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
	Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the perturbed loop, return the corresponding residue index in the original pose. More...

Detailed Description

Utility functions for generalized kinematic closure.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)