design_utils.cc File Reference

#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/chemical/AA.hh>
#include <core/types.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <core/scoring/constraints/NonResidueTypeConstraint.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/kinematics/FoldTree.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <protocols/protein_interface_design/design_utils.hh>
#include <protocols/simple_ddg/ddG.hh>
#include <ObjexxFCL/format.hh>
#include <map>
#include <core/pack/task/ResidueLevelTask.hh>

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

Typedefs
using	protocols::protein_interface_design::Real = core::Real
using	protocols::protein_interface_design::Pose = core::pose::Pose

Functions
static basic::Tracer	protocols::protein_interface_design::TR ("protocols.protein_interface_design.design_utils")
core::Real	protocols::protein_interface_design::sum_total_residue_energy (pose::Pose const &pose, core::Size const resid)
core::Real	protocols::protein_interface_design::ddG_cycles (pose::Pose const &pose, core::scoring::ScoreFunctionOP scorefxn, core::Size const cycles)
void	protocols::protein_interface_design::point_mutation (pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const seqpos, core::Size const mutation)
void	protocols::protein_interface_design::MinimizeInterface (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, utility::vector1< bool > const &min_bb, utility::vector1< bool > const &min_sc, utility::vector1< bool > const &min_rb, bool const optimize_foldtree, utility::vector1< core::Size > const &target_residues, bool const simultaneous_minimization=false)
	utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein. More...
void	protocols::protein_interface_design::SymMinimizeInterface (pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, utility::vector1< bool > const &min_bb, utility::vector1< bool > const &min_sc, utility::vector1< bool > const &min_rb, bool const simultaneous_minimization)
std::list< core::Size >	protocols::protein_interface_design::hbonded (core::pose::Pose const &pose, core::Size const target_residue, std::set< core::Size > const &binders, bool const bb, bool const sc, core::Real const energy_thres, bool const bb_bb=false, core::scoring::ScoreFunctionOP sfxn=nullptr)
	utility function for finding hbonding partners among a list of potential binder residues to a specific target More...
std::list< core::Size >	protocols::protein_interface_design::hbonded_atom (core::pose::Pose const &pose, core::Size const target_residue, std::string const &target_atom, std::set< core::Size > const &binders, bool const bb, bool const sc, core::Real const energy_thres, bool const bb_bb=false, core::scoring::ScoreFunctionOP sfxn=nullptr)
	utility function for finding hbonding partners among a list of potential binder residues to a specific target More...