utils.cc File Reference

util functions for peptide/glycopeptide sampling and refinement More...

#include <protocols/glycopeptide_docking/utils.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <numeric/xyzVector.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <protocols/carbohydrates/SimpleGlycosylateMover.hh>
#include <protocols/glycopeptide_docking/GlycopeptideDockingFlags.hh>
#include <protocols/docking/util.hh>
#include <protocols/docking/metrics.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/ScoreType.hh>
#include <core/select/residue_selector/ResidueIndexSelector.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <utility/stream_util.hh>

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

Functions
static basic::Tracer	TR ("protocols.glycopeptide_docking.utils")
core::Real	protocols::glycopeptide_docking::calculate_sampled_distance (core::pose::Pose const &pose, core::Size const glycosylation_residue, core::Size const donor_residue)
	Calculate distance between donor and substrate. More...
std::map< std::string, core::Real >	protocols::glycopeptide_docking::calculate_additional_glycosylation_metrics (core::pose::Pose const &pose, core::Size glycosylation_residue, core::Size const donor_residue)
	Calculate additional distance metrics for glycosylation. More...
void	protocols::glycopeptide_docking::write_debug_pdb (core::pose::Pose const &pose, core::Size const nstruct_max, core::Size const nstruct_index, std::string name)
	Write pdbs with output string with specified name and prefix, suffix and decoy number to match the fianl decoy. More...
void	protocols::glycopeptide_docking::glycosylate_residues (core::pose::Pose &pose, utility::vector1< core::Size > const &sugar_residues, utility::vector1< std::string > &sugar_names)
	Glycosylate residues (sugar_residues) with sugars specified in sugar_names. This feature is experimental. More...
void	protocols::glycopeptide_docking::setup_glycosylation_foldtree (core::pose::Pose &pose, protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, core::kinematics::FoldTreeOP ft_docking)
void	protocols::glycopeptide_docking::record_pose_metrics (core::pose::Pose &pose, protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, utility::vector1< int > const jumps, core::pose::PoseOP ref_pose)
	Record metrics such as important distances, rmsds and interaction energies (to match publication) More...

Detailed Description

util functions for peptide/glycopeptide sampling and refinement

Author

Sai Pooja Mahajan (saipo.nosp@m.oja@.nosp@m.gmail.nosp@m..com)

Function Documentation

TR()

static basic::Tracer TR ( "protocols.glycopeptide_docking.utils"  )

static