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_moves/ddG.hh>
#include <ObjexxFCL/format.hh>
#include <map>
#include <utility/vector0.hh>
#include <boost/lexical_cast.hpp>

Go to the source code of this file.

Typedefs
typedef core::Real	Real
typedef core::Size	Size
typedef core::pose::Pose	Pose

Functions
static basic::Tracer	TR ("protocols.protein_interface_design.design_utils")
core::Real	ddG_cycles (pose::Pose const &pose, core::scoring::ScoreFunctionOP scorefxn, core::Size const cycles)
void	point_mutation (pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, core::Size const seqpos, core::Size const mutation)
void	MinimizeInterface (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)
void	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 >	hbonded (Pose const &in_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)

Typedef Documentation

typedef core::pose::Pose Pose

Definition at line 79 of file design_utils.cc.

typedef core::Real Real

Definition at line 77 of file design_utils.cc.

typedef core::Size Size

Definition at line 78 of file design_utils.cc.

Function Documentation

core::Real ddG_cycles	(	pose::Pose const &	pose,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::Size const	cycles
	)

Definition at line 160 of file design_utils.cc.

References protocols::simple_moves::ddG::calculate(), and protocols::simple_moves::ddG::sum_ddG().

Referenced by protocols::protein_interface_design::Revert::apply().

std::list< core::Size > hbonded	(	Pose const &	in_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
	)

Definition at line 529 of file design_utils.cc.

References protocols::comparative_modeling::features::A, core::scoring::ScoreFunctionFactory::create_score_function(), core::kinematics::distance(), core::scoring::hbonds::get_hbond_energies(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::scoring::STANDARD_WTS, and core::TR().

Referenced by protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), and protocols::protein_interface_design::filters::HbondsToResidueFilter::compute().

void MinimizeInterface	(	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
	)

Detailed: minimize the interface between two partners. If target_residues is defined

the fold_tree for minimization is set up between the central residue in the target residues and the nearest residue on the partner. if simultaneous minimization is true, then all dofs are minimized at once.

Definition at line 353 of file design_utils.cc.

References core::kinematics::FoldTree::add_edge(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::kinematics::distance(), core::sequence::end, core::pose::Pose::fold_tree(), core::conformation::Residue::is_protein(), core::pose::Pose::num_jump(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::MoveMap::set_bb(), core::pose::Pose::total_residue(), core::TR(), core::pose::Pose::update_residue_neighbors(), and core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::movers::PlacementMinimizationMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_no_bb(), protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().

void point_mutation	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	seqpos,
		core::Size const	mutation
	)

Definition at line 175 of file design_utils.cc.

References core::pack::task::TaskFactory::create_packer_task(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), and core::pose::Pose::total_residue().

Referenced by protocols::protein_interface_design::Revert::apply(), and protocols::ddG_main().

void 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
	)

Definition at line 470 of file design_utils.cc.

References core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::pose::Pose::residue(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::kinematics::MoveMap::set_bb(), core::pose::Pose::total_residue(), core::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::protein_interface_design::movers::RepackMinimize::apply().

static basic::Tracer TR ( "protocols.protein_interface_design.design_utils"  )

static