protocols::protein_interface_design Namespace Reference

Namespaces
	filters
	movers

Classes
class	ReportSequenceDifferences
class	Revert
class	FavorNativeResidue
class	FavorNonNativeResidue
class	DockDesignFilterFactory
class	ParserJobInputter
class	ParserJobInputterCreator
struct	Transformation
class	PatchdockReader
class	ReportPSSMDifferences

Typedefs
typedef utility::pointer::owning_ptr < DockDesignFilterFactory >	DockDesignFilterFactoryOP
typedef utility::pointer::owning_ptr < DockDesignFilterFactory const >	DockDesignFilterFactoryCOP
typedef utility::pointer::owning_ptr < ParserJobInputter >	PatchdockJobInputterOP
typedef utility::pointer::owning_ptr < ParserJobInputter const >	PatchdockJobInputterCOP

Functions
core::Real	sum_total_residue_energy (core::pose::Pose const &pose, core::Size const resid)
void	transform_pose (core::pose::Pose &pose, core::Size const chain, Transformation const &t)
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::owning_ptr< DockDesignFilterFactory const > protocols::protein_interface_design::DockDesignFilterFactoryCOP

Definition at line 25 of file DockDesignFilterFactory.fwd.hh.

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

Definition at line 22 of file DockDesignFilterFactory.fwd.hh.

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

Definition at line 25 of file ParserJobInputter.fwd.hh.

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

Definition at line 22 of file ParserJobInputter.fwd.hh.

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

Definition at line 179 of file util.cc.

References core::scoring::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

Definition at line 255 of file util.cc.

References 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
	)

Definition at line 212 of file util.cc.

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(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::SCORE12_PATCH, and core::scoring::STANDARD_WTS.

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

Definition at line 289 of file util.cc.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::kinematics::distance(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), 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)

Definition at line 148 of file util.cc.

References core::scoring::backbone_stub_constraint, and core::sequence::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

Definition at line 117 of file util.cc.

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(), 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

Definition at line 96 of file util.cc.

References protocols::protein_interface_design::movers::connect_to().

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::protein_interface_design::movers::Splice::fold_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

Definition at line 233 of file util.cc.

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

Referenced by protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), 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)

Definition at line 65 of file util.cc.

References core::kinematics::FoldTree::add_edge(), core::pack::dunbrack::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
	)

Definition at line 83 of file design_utils.cc.

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().

void protocols::protein_interface_design::transform_pose	(	core::pose::Pose &	pose,
		core::Size const	chain,
		Transformation const &	t
	)

Definition at line 136 of file read_patchdock.cc.

References protocols::protein_interface_design::Transformation::alpha, protocols::protein_interface_design::Transformation::beta, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), protocols::protein_interface_design::Transformation::gamma, core::pose::Pose::is_fullatom(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::scoring::sa, core::pose::Pose::set_xyz(), protocols::protein_interface_design::Transformation::translation, and core::pose::Pose::xyz().

Referenced by protocols::protein_interface_design::PatchdockReader::read_poses().