design_utils.cc File Reference

various utilities for interface design. More...

#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>

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

Functions
static thread_local 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)
	utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein. More...
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)
	utility function for finding hbonding partners among a list of potential binder residues to a specific target More...
std::list< core::Size >	hbonded_atom (Pose const &in_pose, core::Size const target_residue, std::string target_atom, std::set< core::Size > const &binders, bool const bb, bool const sc, core::Real const energy_thres, bool const bb_bb)
	utility function for finding hbonding partners among a list of potential binder residues to a specific target More...

Detailed Description

various utilities for interface design.

Author

Sarel Fleishman (sarel.nosp@m.f@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Typedef Documentation

typedef core::pose::Pose Pose

typedef core::Real Real

typedef core::Size Size

Function Documentation

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

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
	)

utility function for finding hbonding partners among a list of potential binder residues to a specific target

References distance(), F, get_hbond_energies(), core::scoring::get_score_function(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, I, identify_hbonds_1way(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), and core::scoring::TR().

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

std::list< core::Size > hbonded_atom	(	Pose const &	in_pose,
		core::Size const	target_residue,
		std::string	target_atom,
		std::set< core::Size > const &	binders,
		bool const	bb,
		bool const	sc,
		core::Real const	energy_thres,
		bool const	bb_bb
	)

utility function for finding hbonding partners among a list of potential binder residues to a specific target

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_index(), distance(), F, get_hbond_energies(), core::scoring::get_score_function(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, I, identify_hbonds_1way(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), and core::scoring::TR().

Referenced by protocols::protein_interface_design::filters::HbondsToAtomFilter::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
	)

utility function for minimizing sidechain in rigid-body dof, the interface sc, and bb in the entire protein.

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.

References core::kinematics::FoldTree::add_edge(), begin, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), distance(), 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(), runtime_assert, core::kinematics::MoveMap::set_bb(), core::pose::Pose::total_residue(), core::scoring::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
	)

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
	)

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(), runtime_assert, core::kinematics::MoveMap::set_bb(), core::pose::Pose::total_residue(), core::scoring::TR(), and core::pose::Pose::update_residue_neighbors().

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

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

static