util.cc File Reference

#include <protocols/protein_interface_design/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <boost/foreach.hpp>
#include <protocols/filters/Filter.hh>
#include <core/chemical/AtomType.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <protocols/simple_filters/EnergyPerResidueFilter.hh>

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

Functions
static thread_local basic::Tracer	TR ("protocols.protein_interface_design.util")
core::kinematics::FoldTree	protocols::protein_interface_design::star_fold_tree (core::pose::Pose &pose)
	generate a star fold tree (originating at residue 1) More...
std::string	protocols::protein_interface_design::optimal_connection_point (std::string const residue_type)
	what is the optimal connection point for an atom tree, given a residue type (puts the connection point at the beginning of a functional group More...
core::kinematics::FoldTree	protocols::protein_interface_design::make_hotspot_foldtree (core::pose::Pose const &pose)
core::scoring::constraints::ConstraintCOPs	protocols::protein_interface_design::get_bbcsts (core::pose::Pose const &pose)
utility::vector1< core::Size >	protocols::protein_interface_design::best_bbcst_residues (core::pose::Pose const &pose, core::Size const chain, core::Size const n_return)
	evaluate backbone_stub_constraints for each residue in a chain and return a vector with the top n_return residue numbers by cst score note that this function is NOT guaranteed to return n_return residues! It will return the best n<=n_return More...
void	protocols::protein_interface_design::find_lowest_constraint_energy_residue (core::pose::Pose const &pose, core::Size const chain, core::Size &resi, core::Real &lowest_energy)
core::scoring::constraints::ConstraintCOPs	protocols::protein_interface_design::remove_coordinate_constraints_from_pose (core::pose::Pose &pose)
	removes ALL coordinate constraints from a pose. returns the constraints that were removed More...
core::Size	protocols::protein_interface_design::best_cutpoint (core::pose::Pose &pose, core::Size const prev_u, core::Size const prev_d, core::Size const u, core::Size const d)
	utility function for stub_based_atom_tree. tries to find an optimal cutpoint in a pose given two different boundaries. More...
core::Size	protocols::protein_interface_design::find_nearest_residue (core::pose::Pose const &pose, core::Size const target_chain, core::Size const res, std::string const atom="CA")
	find nearest residue on target_chain to res More...

Detailed Description

Author

Sarel Fleishman (sarel.nosp@m.f@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), Jacob Corn (jecor.nosp@m.n@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Function Documentation

static thread_local basic::Tracer TR ( "protocols.protein_interface_design.util"  )

static