Namespaces
	filters

	movers

Classes
class	DockDesignFilterFactory

class	FavorNativeResidue

class	FavorNonNativeResidue

class	ParserJobInputter

class	ParserJobInputterCreator

class	PatchdockReader

class	ReportPSSMDifferences

class	ReportSequenceDifferences

class	Revert

struct	Transformation

Typedefs
typedef utility::pointer::shared_ptr < DockDesignFilterFactory >	DockDesignFilterFactoryOP

typedef utility::pointer::shared_ptr < DockDesignFilterFactory const >	DockDesignFilterFactoryCOP

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

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

typedef utility::pointer::shared_ptr< DockDesignFilterFactory const > protocols::protein_interface_design::DockDesignFilterFactoryCOP

typedef utility::pointer::shared_ptr< DockDesignFilterFactory > protocols::protein_interface_design::DockDesignFilterFactoryOP

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

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

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

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

Function Documentation

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

Detailed: 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 backbone_stub_constraint.

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

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::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::Pose::secstruct(), and core::pose::Pose::total_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 backbone_stub_constraint, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::simple_filters::EnergyPerResidueFilter::compute(), core::pose::Pose::conformation(), and get_score_function().

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(), distance(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), runtime_assert, and core::conformation::Residue::xyz().

Referenced by make_hotspot_foldtree().

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

References backbone_stub_constraint, and end.

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::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(), find_nearest_residue(), core::conformation::Residue::name3(), core::conformation::Residue::nbr_atom(), core::pose::Pose::num_jump(), optimal_connection_point(), protocols::make_rot_lib::PEPTIDE, and core::pose::Pose::residue().

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

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 protocols::TR().

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

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(), end, 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().

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(), c, 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(), protocols::TR(), and core::pose::Pose::update_residue_neighbors().

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

core::Real protocols::protein_interface_design::sum_total_residue_energy	(	core::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().

Namespaces

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation