Namespaces
	filters

	movers

Classes
class	ReportSequenceDifferences

class	Revert

class	FavorNativeResidue

class	FavorNonNativeResidue

class	ParserJobInputter

class	ParserJobInputterCreator

struct	Transformation

class	PatchdockReader

class	ReportPSSMDifferences

Typedefs
using	Real = core::Real

using	Pose = core::pose::Pose

typedef utility::pointer::shared_ptr< ParserJobInputter >	PatchdockJobInputterOP

typedef utility::pointer::shared_ptr< ParserJobInputter const >	PatchdockJobInputterCOP

typedef utility::pointer::shared_ptr< PatchdockReader >	PatchdockReaderOP

typedef utility::pointer::shared_ptr< PatchdockReader const >	PatchdockReaderCOP

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

core::Real	sum_total_residue_energy (pose::Pose const &pose, core::Size const resid)

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 (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	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 (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 >	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...

core::kinematics::FoldTree	star_fold_tree (core::pose::Pose &pose)
	generate a star fold tree (originating at residue 1) More...

std::string	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	make_hotspot_foldtree (core::pose::Pose const &pose)

core::scoring::constraints::ConstraintCOPs	get_bbcsts (core::pose::Pose const &pose)

utility::vector1< core::Size >	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	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	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	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	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...

Typedef Documentation

◆ PatchdockJobInputterCOP

typedef utility::pointer::shared_ptr< ParserJobInputter const > protocols::protein_interface_design::PatchdockJobInputterCOP

◆ PatchdockJobInputterOP

typedef utility::pointer::shared_ptr< ParserJobInputter > protocols::protein_interface_design::PatchdockJobInputterOP

◆ PatchdockReaderCOP

typedef utility::pointer::shared_ptr< PatchdockReader const > protocols::protein_interface_design::PatchdockReaderCOP

◆ PatchdockReaderOP

typedef utility::pointer::shared_ptr< PatchdockReader > protocols::protein_interface_design::PatchdockReaderOP

◆ Pose

using protocols::protein_interface_design::Pose = typedef core::pose::Pose

◆ Real

using protocols::protein_interface_design::Real = typedef core::Real

Function Documentation

◆ best_bbcst_residues()

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

a utility function to 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

References core::scoring::backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::Energies::residue_total_energies(), and protocols::hybridization::score.

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

◆ best_cutpoint()

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.

utility function for stub_based_atom_tree. tries to find an optimal cutpoint in a pose given two different boundaries. First looks for a 3-res loop stretch on the downstream partner and returns the middle residue. Then, does the same for the upstream chain. Then, becomes desperate and tries to find any loop residue on downstream chain, and then on upstream chain. Finally, if no success, returns 0 which means that no break was found

References protocols::simple_filters::dssp(), core::pose::Pose::secstruct(), core::pose::Pose::size(), and protocols::hybridization::u.

◆ ddG_cycles()

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

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

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

◆ find_lowest_constraint_energy_residue()

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
	)

References core::scoring::backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::simple_filters::EnergyPerResidueFilter::compute(), core::pose::Pose::conformation(), and core::scoring::get_score_function().

◆ find_nearest_residue()

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
	)

find nearest residue on target_chain to res

find the nearest residue on the target chain to res

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::mpi_refinement::distance(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by make_hotspot_foldtree().

◆ get_bbcsts()

core::scoring::constraints::ConstraintCOPs protocols::protein_interface_design::get_bbcsts ( core::pose::Pose const & pose )

References core::scoring::backbone_stub_constraint, and core::pose::Pose::constraint_set().

◆ hbonded()

std::list< core::Size > protocols::protein_interface_design::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,
		core::scoring::ScoreFunctionOP	sfxn
	)

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

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

◆ hbonded_atom()

std::list< core::Size > protocols::protein_interface_design::hbonded_atom	(	Pose const &	in_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,
		core::scoring::ScoreFunctionOP	sfxn
	)

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

Referenced by protocols::protein_interface_design::filters::HbondsToAtomFilter::compute().

◆ make_hotspot_foldtree()

core::kinematics::FoldTree protocols::protein_interface_design::make_hotspot_foldtree ( core::pose::Pose const & pose )

generate a fold tree that connects each hotspot residue through its optimal connection point to the nearest atom on chain 1

References core::kinematics::FoldTree::add_edge(), core::conformation::Residue::atom_type(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::connect_to(), core::kinematics::FoldTree::delete_self_edges(), core::chemical::AtomType::element(), find_nearest_residue(), core::conformation::Residue::name3(), core::conformation::Residue::nbr_atom(), core::pose::Pose::num_jump(), optimal_connection_point(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), and core::kinematics::FoldTree::set_jump_atoms().

Referenced by protocols::protein_interface_design::movers::TryRotamers::apply(), and protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots().

◆ MinimizeInterface()

void protocols::protein_interface_design::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.

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(), 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::conformation::Residue::nbr_atom(), core::pose::Pose::num_jump(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::size(), 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().

◆ optimal_connection_point()

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

References protocols::protein_interface_design::movers::connect_to(), and TR().

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::splice::Splice::fold_tree(), and make_hotspot_foldtree().

◆ point_mutation()

void protocols::protein_interface_design::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::size().

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

◆ remove_coordinate_constraints_from_pose()

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

a utility function for removing ALL coordinate constraints from a pose. returns the constraints that were removed

References core::pose::Pose::constraint_set(), and core::pose::Pose::remove_constraints().

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), and protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints().

◆ star_fold_tree()

core::kinematics::FoldTree protocols::protein_interface_design::star_fold_tree ( core::pose::Pose & pose )

generate a star fold tree (originating at residue 1)

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::pose::Pose::fold_tree(), core::conformation::Residue::is_polymer(), core::conformation::Conformation::num_chains(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), TR(), and core::pose::Pose::update_residue_neighbors().

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

◆ sum_total_residue_energy()

core::Real protocols::protein_interface_design::sum_total_residue_energy	(	pose::Pose const &	pose,
		core::Size const	resid
	)

References core::pose::Pose::energies(), core::scoring::n_score_types, core::scoring::Energies::residue_total_energies(), and core::scoring::Energies::weights().

Referenced by protocols::protein_interface_design::ReportSequenceDifferences::calculate().

◆ SymMinimizeInterface()

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
	)

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::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::size(), TR(), and core::pose::Pose::update_residue_neighbors().

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

◆ TR()

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

static

Namespaces

Classes

Typedefs

Functions