#include <EnzdesFlexBBProtocol.hh>

Public Member Functions
	EnzdesFlexibleRegion (core::Size index_in, core::Size start, core::Size end, core::Size nr_res, core::pose::Pose const &pose, EnzdesFlexBBProtocolCAP enz_prot)

	~EnzdesFlexibleRegion ()

core::Size	no_ranked_frags () const

bool	contains_catalytic_res () const

bool	remodelable () const

core::Size	remodel_min_length () const

core::Size	remodel_max_length () const

toolbox::match_enzdes_util::EnzdesLoopInfoCOP	enz_loop_info () const

core::Size	index () const

void	declare_remodelable (core::Size min_length, core::Size max_length)

core::Real	deltaE_best (core::Size const frag_rank) const

core::fragment::FragDataOP	assemble_enzdes_fragdata (core::pose::Pose const &pose)

utility::vector1< core::Size > const &	positions () const

core::Real	extract_lig_designability_score (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task, core::Real &backgroundE)

core::Real	get_region_mm_bend_score (core::pose::Pose const &pose) const

void	apply_ranked_fragment (core::pose::Pose &pose, core::Size frag_rank)

void	hack_fillup_frag_designabilities ()

void	sort_ensemble_by_designability (core::pose::Pose const &ref_pose, core::scoring::ScoreFunctionOP scorefxn, core::pack::task::PackerTaskCOP task)

core::Real	calculate_rotamer_set_design_targets_partition_sum (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, core::pack::task::PackerTaskCOP task) const

bool	examine_new_loopconf (core::pose::Pose const &pose, core::pose::Pose &template_pose, utility::vector1< core::pose::PoseOP > &compare_poses, utility::vector1< core::Real > &rmsd_to_native)

bool	minimize_region (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, std::set< core::Size > const &chi_to_move, bool const including_CA_angles, core::Real min_tolerance)

core::Real	get_region_total_score (core::pose::Pose const &pose) const

bool	remap_resid (core::pose::Pose const &pose, core::id::SequenceMapping const &smap)

void	scale_target_proximity_to_starting_conformation (core::Real factor)

void	set_target_proximity_to_starting_conformation (core::Real proximity)

void	scale_target_proximity_to_other_conformations (core::Real factor)

std::set< core::Size >	get_10A_neighbors (core::pose::Pose const &pose) const
	requires that the pose was scored More...

Public Member Functions inherited from core::fragment::Frame
virtual	~Frame ()

	Frame ()

	Frame (core::Size begin, core::Size end, core::Size nr_res)

	Frame (core::Size start, core::Size length)

	Frame (core::Size start)

	Frame (core::Size start, FragDataCOP const &frag1)

	Frame (core::Size start, core::Size length, SingleResidueFragDataOP srfd)

virtual FrameOP	clone () const

virtual FrameOP	clone_with_frags () const

virtual FrameOP	clone_with_template ()

virtual std::string	type () const

core::Size	add_fragment (FragDataCOP new_frag)

bool	add_fragment (FragDataCOPs new_frags)

FragData const &	fragment (core::Size frag_num) const

FragDataCOP	fragment_ptr (core::Size frag_num) const

bool	is_valid () const

core::Size	apply (kinematics::MoveMap const &, core::Size frag_num, pose::Pose &pose) const

core::Size	apply (core::Size frag_num, pose::Pose &pose) const

core::Size	apply_ss (kinematics::MoveMap const &, core::Size frag_num, std::string &ss) const

bool	steal (pose::Pose const &pose)

core::Size	is_applicable (kinematics::MoveMap const &) const

virtual core::Size	seqpos (core::Size intra_pos) const

core::Size	frag_id (core::Size frag_num) const

void	fragment_as_pose (core::Size frag_num, pose::Pose &pose, chemical::ResidueTypeSetCAP restype_set) const

virtual bool	is_continuous () const

core::Size	nr_frags () const

void	clear ()

bool	contains_seqpos (core::Size seqpos) const

core::Size	start () const

virtual void	shift_to (core::Size setting)

virtual void	shift_by (int offset)

core::Size	end () const

core::Size	stop () const

virtual bool	moves_residue (core::Size pos) const

core::Size	nr_res_affected (kinematics::MoveMap const &mm) const

core::Size	length () const

BaseCacheUnit &	cache (std::string tag, BaseCacheUnitOP const &new_cache) const

void	clone_cache_data (Frame const &source, core::Size sid, core::Size nid)

virtual void	show_classic (std::ostream &out) const

virtual void	show (std::ostream &out) const

virtual void	show_header (std::ostream &out) const

virtual void	read (std::istream &in)

bool	is_mergeable (Frame const &other) const

bool	merge (Frame const &other)

virtual bool	align (core::id::SequenceMapping const &map)

FrameOP	generate_sub_frame (Size length, Size start=1) const

Static Public Member Functions
static bool	compare_SizeRealPairs (SizeRealPair const &first, SizeRealPair const &second)

Static Public Member Functions inherited from core::fragment::Frame
static std::string	_static_type_name ()

Private Types
typedef std::pair< core::Size, core::Real >	SizeRealPair

typedef core::fragment::Frame	Super

Additional Inherited Members
Protected Member Functions inherited from core::fragment::Frame
virtual void	show_fragments (std::ostream &out) const

virtual bool	is_compatible (FragDataCOP new_frag) const

void	init_length (core::Size start, core::Size end, core::Size length)

Member Typedef Documentation

typedef std::pair< core::Size, core::Real > protocols::enzdes::EnzdesFlexibleRegion::SizeRealPair

private

typedef core::fragment::Frame protocols::enzdes::EnzdesFlexibleRegion::Super

private

Constructor & Destructor Documentation

protocols::enzdes::EnzdesFlexibleRegion::EnzdesFlexibleRegion	(	core::Size	index_in,
		core::Size	start,
		core::Size	end,
		core::Size	nr_res,
		core::pose::Pose const &	pose,
		EnzdesFlexBBProtocolCAP	enz_prot
	)

References core::fragment::Frame::add_fragment(), assemble_enzdes_fragdata(), core::fragment::Frame::end(), enzdes, frag_designabilities_, max_bb_deviation, max_bb_deviation_from_startstruct, native_conf_, option, options, positions_, utility::to_string(), user, and utility_exit_with_message.

protocols::enzdes::EnzdesFlexibleRegion::~EnzdesFlexibleRegion ( )

Member Function Documentation

void protocols::enzdes::EnzdesFlexibleRegion::apply_ranked_fragment	(	core::pose::Pose &	pose,
		core::Size	frag_rank
	)

References core::fragment::Frame::apply(), frag_designabilities_, and utility_exit_with_message.

core::fragment::FragDataOP protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata ( core::pose::Pose const & pose )

References angles, core::chemical::ResidueType::atom_index(), core::fragment::Frame::end(), enzdes_protocol_, core::pose::Pose::residue_type(), core::fragment::Frame::start(), and utility_exit_with_message.

Referenced by EnzdesFlexibleRegion(), and remap_resid().

core::Real protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::pack::task::PackerTaskCOP	task
	)		const

References core::pack::create_packer_graph(), core::graph::delete_all_intragroup_edges(), design_targets_, core::pack::interaction_graph::PDEdge::get_two_body_energy(), positions_, and core::pose::Pose::total_residue().

Referenced by sort_ensemble_by_designability().

static bool protocols::enzdes::EnzdesFlexibleRegion::compare_SizeRealPairs	(	SizeRealPair const &	first,
		SizeRealPair const &	second
	)

inlinestatic

Referenced by sort_ensemble_by_designability().

bool protocols::enzdes::EnzdesFlexibleRegion::contains_catalytic_res ( ) const

References core::fragment::Frame::contains_seqpos(), and design_targets_.

void protocols::enzdes::EnzdesFlexibleRegion::declare_remodelable	(	core::Size	min_length,
		core::Size	max_length
	)

References remodel_max_length_, remodel_min_length_, and remodelable_.

core::Real protocols::enzdes::EnzdesFlexibleRegion::deltaE_best ( core::Size const frag_rank ) const

References frag_designabilities_, and utility_exit_with_message.

toolbox::match_enzdes_util::EnzdesLoopInfoCOP protocols::enzdes::EnzdesFlexibleRegion::enz_loop_info ( ) const

References enzdes_protocol_, index_, loop_file, and utility_exit_with_message.

bool protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf	(	core::pose::Pose const &	pose,
		core::pose::Pose &	template_pose,
		utility::vector1< core::pose::PoseOP > &	compare_poses,
		utility::vector1< core::Real > &	rmsd_to_native
	)

References core::fragment::Frame::add_fragment(), core::scoring::biggest_residue_deviation_no_super(), core::fragment::Frame::fragment_ptr(), core::scoring::is_protein_backbone(), core::scoring::is_protein_CA_or_CB(), core::fragment::Frame::length(), basic::options::OptionKeys::enzdes::max_bb_deviation, basic::options::OptionKeys::enzdes::min_cacb_deviation, core::pose::Pose::omega(), basic::options::option, core::pose::Pose::phi(), positions_, core::pose::Pose::psi(), core::pose::Pose::residue(), core::scoring::rmsd_no_super(), runtime_assert, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_xyz(), target_proximity_to_native_conformation_, target_proximity_to_other_conformations_, core::pose::Pose::total_residue(), user, utility_exit_with_message, and protocols::kinmatch::xyz().

core::Real protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTaskCOP	task,
		core::Real &	backgroundE
	)

function under heavy development, will prolly change a lot in the coming weeks/months

main idea: look at how the conformation of this region in the input pose interacts with

the ligand as well as the protein background, then combine the two numbers in some way

References core::fragment::Frame::contains_seqpos(), design_targets_, core::scoring::EnergyEdge::dot(), core::fragment::Frame::end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::fragment::Frame::length(), core::fragment::Frame::start(), and core::scoring::Energies::weights().

Referenced by sort_ensemble_by_designability().

std::set< core::Size > protocols::enzdes::EnzdesFlexibleRegion::get_10A_neighbors ( core::pose::Pose const & pose ) const

requires that the pose was scored

References core::fragment::Frame::contains_seqpos(), core::fragment::Frame::end(), core::pose::Pose::energies(), core::fragment::Frame::start(), and core::scoring::Energies::tenA_neighbor_graph().

Referenced by sort_ensemble_by_designability().

core::Real protocols::enzdes::EnzdesFlexibleRegion::get_region_mm_bend_score ( core::pose::Pose const & pose ) const

References core::fragment::Frame::end(), core::pose::Pose::energies(), core::scoring::mm_bend, core::scoring::Energies::residue_total_energies(), and core::fragment::Frame::start().

core::Real protocols::enzdes::EnzdesFlexibleRegion::get_region_total_score ( core::pose::Pose const & pose ) const

References core::fragment::Frame::end(), core::pose::Pose::energies(), core::scoring::Energies::residue_total_energy(), and core::fragment::Frame::start().

void protocols::enzdes::EnzdesFlexibleRegion::hack_fillup_frag_designabilities ( )

References frag_designabilities_, index_, and core::fragment::Frame::nr_frags().

core::Size protocols::enzdes::EnzdesFlexibleRegion::index ( ) const

inline

References index_.

bool protocols::enzdes::EnzdesFlexibleRegion::minimize_region	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn,
		std::set< core::Size > const &	chi_to_move,
		bool const	including_CA_angles,
		core::Real	min_tolerance
	)

minimize the backbone of this pose over the fragment residues, including the

bond angles around Calpha if desired. NOTE: CA ANGLE MINIMIZATION UNTESTED a chainbreak at the end of the region will be introduced. chainbreak weight will be set to 100 to make sure that it stays closed. in case the chainbreak score is higher after the min then before, function returns false. this might be the case when the input conformation has bad clashes, which is the case e.g. for some conformations that come out of remodel

core::Size protocols::enzdes::EnzdesFlexibleRegion::no_ranked_frags ( ) const

inline

References frag_designabilities_.

utility::vector1< core::Size > const& protocols::enzdes::EnzdesFlexibleRegion::positions ( ) const

inline

References positions_.

Referenced by sort_ensemble_by_designability().

bool protocols::enzdes::EnzdesFlexibleRegion::remap_resid	(	core::pose::Pose const &	pose,
		core::id::SequenceMapping const &	smap
	)

References core::fragment::Frame::add_fragment(), core::fragment::Frame::align(), assemble_enzdes_fragdata(), core::fragment::Frame::clear(), core::fragment::Frame::end(), frag_designabilities_, core::fragment::Frame::init_length(), core::fragment::Frame::is_continuous(), core::fragment::Frame::length(), native_conf_, positions_, and core::fragment::Frame::start().

core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_max_length ( ) const

inline

References remodel_max_length_.

core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_min_length ( ) const

inline

References remodel_min_length_.

bool protocols::enzdes::EnzdesFlexibleRegion::remodelable ( ) const

inline

References remodelable_.

void protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_other_conformations ( core::Real factor )

inline

References target_proximity_to_other_conformations_.

void protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_starting_conformation ( core::Real factor )

inline

References target_proximity_to_native_conformation_.

void protocols::enzdes::EnzdesFlexibleRegion::set_target_proximity_to_starting_conformation ( core::Real proximity )

inline

References target_proximity_to_native_conformation_.

void protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability	(	core::pose::Pose const &	ref_pose,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::pack::task::PackerTaskCOP	task
	)

this function assumes that the pose is a poly ala pose of the residues to redesign

and that the backbone is in the native conformation

References core::fragment::Frame::apply(), calculate_rotamer_set_design_targets_partition_sum(), compare_SizeRealPairs(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), core::fragment::Frame::contains_seqpos(), enzdes_protocol_, extract_lig_designability_score(), frag_designabilities_, get_10A_neighbors(), index_, core::fragment::Frame::length(), core::fragment::Frame::nr_frags(), pack_rotamers_loop(), core::pack::pack_scorefxn_pose_handshake(), positions(), protocols::enzdes::enzutil::recreate_task(), utility::to_string(), protocols::enzdes::tr, and utility_exit_with_message.

Member Data Documentation

std::set< core::Size > const& protocols::enzdes::EnzdesFlexibleRegion::design_targets_

private

Referenced by calculate_rotamer_set_design_targets_partition_sum(), contains_catalytic_res(), and extract_lig_designability_score().

utility::vector1< std::string > protocols::enzdes::EnzdesFlexibleRegion::desired_remodel_ss_strings_

private

EnzdesFlexBBProtocolCAP protocols::enzdes::EnzdesFlexibleRegion::enzdes_protocol_

private

Referenced by assemble_enzdes_fragdata(), enz_loop_info(), and sort_ensemble_by_designability().

utility::vector1< SizeRealPair > protocols::enzdes::EnzdesFlexibleRegion::frag_designabilities_

private

Referenced by apply_ranked_fragment(), deltaE_best(), EnzdesFlexibleRegion(), hack_fillup_frag_designabilities(), no_ranked_frags(), remap_resid(), and sort_ensemble_by_designability().

core::Size protocols::enzdes::EnzdesFlexibleRegion::index_

private

Referenced by enz_loop_info(), hack_fillup_frag_designabilities(), index(), and sort_ensemble_by_designability().

core::fragment::FragDataOP protocols::enzdes::EnzdesFlexibleRegion::native_conf_

private

Referenced by EnzdesFlexibleRegion(), and remap_resid().

utility::vector1< core::Size > protocols::enzdes::EnzdesFlexibleRegion::positions_

private

Referenced by calculate_rotamer_set_design_targets_partition_sum(), EnzdesFlexibleRegion(), examine_new_loopconf(), positions(), and remap_resid().

core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_max_length_

private

Referenced by declare_remodelable(), and remodel_max_length().

core::Size protocols::enzdes::EnzdesFlexibleRegion::remodel_min_length_

private

Referenced by declare_remodelable(), and remodel_min_length().

bool protocols::enzdes::EnzdesFlexibleRegion::remodelable_

private

Referenced by declare_remodelable(), and remodelable().

core::Real protocols::enzdes::EnzdesFlexibleRegion::target_proximity_to_native_conformation_

private

Referenced by examine_new_loopconf(), scale_target_proximity_to_starting_conformation(), and set_target_proximity_to_starting_conformation().

core::Real protocols::enzdes::EnzdesFlexibleRegion::target_proximity_to_other_conformations_

private

Referenced by examine_new_loopconf(), and scale_target_proximity_to_other_conformations().

The documentation for this class was generated from the following files:

src/protocols/enzdes/EnzdesFlexBBProtocol.hh
src/protocols/enzdes/EnzdesFlexBBProtocol.cc

Private Attributes
core::Size	index_

utility::vector1< core::Size >	positions_

core::fragment::FragDataOP	native_conf_

EnzdesFlexBBProtocolCAP	enzdes_protocol_

std::set< core::Size > const &	design_targets_

utility::vector1< SizeRealPair >	frag_designabilities_

core::Real	target_proximity_to_native_conformation_

core::Real	target_proximity_to_other_conformations_

bool	remodelable_

core::Size	remodel_min_length_

core::Size	remodel_max_length_

utility::vector1< std::string >	desired_remodel_ss_strings_

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation