util.cc File Reference

Utility functions for helical bundle construction. More...

#include <stdio.h>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <basic/database/open.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/exit.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.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/id/TorsionID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/scoring/rms_util.hh>
#include <core/pose/util.tmpl.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.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/conversions.hh>
#include <numeric/crick_equations/BundleParams.hh>
#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::helical_bundle

Functions
static thread_local basic::Tracer	protocols::helical_bundle::TR ("protocols.helical_bundle.util")
void	protocols::helical_bundle::write_minor_helix_params (std::string const &filename, utility::vector1< core::Real > const &r1, core::Real const &omega1, core::Real const &z1, utility::vector1< core::Real > const &delta_omega1, utility::vector1< core::Real > const &delta_z1)
void	protocols::helical_bundle::read_minor_helix_params (std::string const &filename, utility::vector1< core::Real > &r1, core::Real &omega1, core::Real &z1, utility::vector1< core::Real > &delta_omega1, utility::vector1< core::Real > &delta_z1)
void	protocols::helical_bundle::generate_atom_positions (utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &outvector, core::pose::Pose const &helixpose, core::Size const helix_start, core::Size const helix_end, core::Real const &r0, core::Real const &omega0, core::Real const &delta_omega0, core::Real const &delta_t, core::Real const &z1_offset, core::Real const &z0_offset, bool const invert_helix, utility::vector1< core::Real > const &r1, core::Real const &omega1, core::Real const &z1, utility::vector1< core::Real > const &delta_omega1, core::Real const &delta_omega1_all, utility::vector1< core::Real > const &delta_z1, bool &failed)
	Generate the x,y,z coordinates of the mainchain atoms using the Crick equations. More...
void	protocols::helical_bundle::place_atom_positions (core::pose::Pose &pose, utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > const &atom_positions, core::Size const helix_start, core::Size const helix_end)
	Place the helix mainchain atoms based on the Crick equations. More...
void	protocols::helical_bundle::copy_helix_bondlengths (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone bond length values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	protocols::helical_bundle::copy_helix_bondangles (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone bond angle values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	protocols::helical_bundle::copy_helix_dihedrals (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Copy backbone dihedral values from one pose, where helix mainchain atom coordinates have been set with the Crick equations, to another with ideal geometry. More...
void	protocols::helical_bundle::align_mainchain_atoms (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Align mainchain atoms of pose to ref_pose mainchain atoms. More...
void	protocols::helical_bundle::align_mainchain_atoms_of_residue_range (core::pose::Pose &pose, core::pose::Pose const &ref_pose, core::Size const helix_start, core::Size const helix_end)
	Align mainchain atoms of pose to ref_pose mainchain atoms, moving ONLY the residues involved in the alignment. More...

Detailed Description

Utility functions for helical bundle construction.

Headers for utility functions for helical bundle construction.

Author

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