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
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, 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...

Variables
static basic::Tracer	protocols::helical_bundle::TR ("protocols.helical_bundle.util")

Detailed Description

Utility functions for helical bundle construction.

Author

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