util.cc File Reference

Utilities for DrugDesign. More...

#include <protocols/drug_design/util.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomRefMapping.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/ResidueLevelTask.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibrary.hh>
#include <utility/graph/Graph.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/xyz.functions.hh>
#include <basic/Tracer.hh>

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

Functions
static basic::Tracer	TR ("protocols.drug_design.util")
void	protocols::drug_design::align_residues (core::conformation::Residue &residue, core::conformation::Residue const &target, core::chemical::IndexIndexMapping const &map)
	Reassign the coordinates of residue to best match that of target using the provided mapping. More...
void	protocols::drug_design::place_new_restype (core::pose::Pose &pose, core::Size position, core::chemical::ResidueType const &new_restype, core::chemical::IndexIndexMapping const &map, std::string const &method="default")
	Replace the residue at the given position in the pose with the new residue type, using the atom correspondence in the mapping The method used can be specified ("default") being whatever is currently thought of as "best". More...
void	protocols::drug_design::place_new_restype_no_align (core::pose::Pose &pose, core::Size position, core::chemical::ResidueType const &new_restype)
	Replaces the residue at the given position in the pose with the new residue type. Does no alignment - assumes that the internal coordinates of the new restype are properly set. More...
void	protocols::drug_design::place_new_restype_rotamer_align (core::pose::Pose &pose, core::Size position, core::chemical::ResidueType const &new_restype, core::chemical::IndexIndexMapping const &map)
	Replaces the residue at the given position in the pose with the new residue type, using the rotamer with the best alignment of mapped atoms and a fixed rigid body position of the neighbor atom. More...

Detailed Description

Utilities for DrugDesign.

Author

Rocco Moretti (rmore.nosp@m.ttia.nosp@m.se@gm.nosp@m.ail..nosp@m.com)

Function Documentation

TR()

static basic::Tracer TR ( "protocols.drug_design.util"  )

static