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util.cc File Reference

Utility functions for helical bundle construction. More...

#include <cstdio>
#include <protocols/helical_bundle/util.hh>
#include <core/chemical/ResidueType.hh>
#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/string_util.hh>
#include <utility/io/izstream.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 <protocols/rosetta_scripts/util.hh>
#include <utility/excn/Exceptions.hh>
#include <core/pose/Pose.hh>
#include <utility/tag/XMLSchemaGeneration.hh>

Namespaces

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

Functions

static basic::Tracer protocols::helical_bundle::TR ("protocols.helical_bundle.util")
 
void protocols::helical_bundle::add_attributes_for_make_bundle_symmetry (AttributeList &attlist)
 
void protocols::helical_bundle::add_attributes_for_make_bundle_minorhelix_defaults (AttributeList &attlist)
 
void protocols::helical_bundle::add_attributes_for_make_bundle_other_defaults (AttributeList &attlist)
 
void protocols::helical_bundle::add_attributes_for_helix_params (AttributeList &attlist)
 
void protocols::helical_bundle::add_attributes_for_minor_helix_params (AttributeList &attlist)
 
void protocols::helical_bundle::add_attributes_for_other_helix_params (AttributeList &attlist)
 
void protocols::helical_bundle::write_crick_params_file_data (utility::io::ozstream &outfile, 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)
 Actual write of the crick_params file data. More...
 
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)
 Write out a crick_params file. More...
 
void protocols::helical_bundle::write_minor_helix_params (std::string const &filename, core::Size const &residues_per_repeat, utility::vector1< core::Size > const &atoms_per_residue, 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)
 Write out a crick_params file. More...
 
std::string protocols::helical_bundle::get_crick_params_filename_formatted (std::string const &basename)
 Given a Crick params filename stub (e.g. "alpha_helix_100"), get the string with the full path and extension (e.g. "protocol_data/crick_parameters/alpha_helix_100.crick_params"). More...
 
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, core::Size &residues_per_repeat, utility::vector1< core::Size > &atoms_per_residue)
 Read minor helix parameters from a crick_params file. More...
 
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, core::Real const &epsilon, 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, core::Size const residues_per_repeat, utility::vector1< core::Size > const &atoms_per_residue, core::Size const repeating_unit_offset, 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...
 
void protocols::helical_bundle::parse_resnames (std::string const &string_in, utility::vector1< std::string > &vect_out)
 Given a comma-separated list of residue names, separate these out into a vector of residue names. 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)