#include <EnzdesFlexBBProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesFlexibleRegion:

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 () override

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, core::Size const threads_to_request) 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
	~Frame () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	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
	clone method, new frame with same alignment position, fragments are not copied! More...

virtual FrameOP	clone_with_frags () const
	clone method, new frame with same alignment position, fragments are not copied! More...

virtual FrameOP	clone_with_template ()
	clone method, new frame with same alignment position, one fragments is copied as template ( valid() == false ) More...

virtual std::string	type () const
	type() is specifying the output name of the Frame in FragmentIO ("FRAME", "JUMPFRAME", etc) More...

core::Size	add_fragment (FragDataCOP new_frag)
	add a fragment .. return new frag_nr More...

bool	add_fragment (FragDataCOPs new_frags)
	add all fragments in list More...

FragData const &	fragment (core::Size frag_num) const
	delete a fragment: Attention: all data in the FragCache is invalidated ( and deleted ) it would be complicated to change this behaviour. Thus, it is desirable to avoid using delete_fragment() altogether. Faster: Make a new Frame and add all fragments you are interested in. More...

FragDataCOP	fragment_ptr (core::Size frag_num) const
	accessor for underlying FragData More...

bool	is_valid () const
	accessor for underlying FragData as owning ptr More...

core::Size	apply (kinematics::MoveMap const &, core::Size frag_num, pose::Pose &pose) const
	insert fragment frag_num into pose More...

core::Size	apply (core::Size frag_num, pose::Pose &pose) const
	insert fragment frag_num into pose — ignore movemap More...

core::Size	apply_ss (kinematics::MoveMap const &, core::Size frag_num, std::string &ss) const
	change ss-string according to sec-struct info in fragments More...

bool	steal (pose::Pose const &pose)
	obtain fragment from pose at frame position More...

core::Size	is_applicable (kinematics::MoveMap const &) const
	is the Frame applicable to the pose with the given movemap? More...

virtual core::Size	seqpos (core::Size intra_pos) const
	translate intra-frame position into sequence position. (trivial for base-class) More...

core::Size	frag_id (core::Size frag_num) const
	a unique id for every fragment in the list. his is silly, but would enable later on to avoid cache_clearence on deletion of FragData entries in this case, we would require that the ID of a certain fragment never changes, even if the position in FragList changes More...

void	fragment_as_pose (core::Size frag_num, pose::Pose &pose, chemical::ResidueTypeSetCAP restype_set) const
	returns a (small) pose with fragment ( continous from seqpos 1 ... nr_res_affected() ) More...

virtual bool	is_continuous () const
	true if frame is continuous (always true for base class) More...

core::Size	nr_frags () const
	number of fragments attached to this frame More...

void	clear ()
	remove all valid fragments, a template fragment will be left over More...

bool	contains_seqpos (core::Size seqpos) const
	whether this fragment contains a certain position More...

core::Size	start () const
	first seqpos of this frame More...

virtual void	shift_to (core::Size setting)
	set start position More...

virtual void	shift_by (int offset)
	shift frame by offset relative to current start position ( change end accordingly ) More...

core::Size	end () const
	last sequence position affected by this frame More...

core::Size	stop () const
	/// More...

virtual bool	moves_residue (core::Size pos) const

core::Size	nr_res_affected (kinematics::MoveMap const &mm) const
	number of residues affected by this frame More...

core::Size	length () const
	number of residues in this frame ( for continuous frames it is the same as end()-start() + 1 ) More...

BaseCacheUnit &	cache (std::string tag, BaseCacheUnitOP const &new_cache) const
	return handle to cached data stored under "tag" shouldn't be called directly More...

void	clone_cache_data (Frame const &source, core::Size sid, core::Size nid)
	copies all entries in the Frame-Cache for fragment "sid" of Frame "source" to fragment "nid" of "this" frame More...

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)
	change frames residue numbers accoriding to map More...

FrameOP	generate_sub_frame (Size length, Size start=1) const
	generate_sub_frame of length from start ( internal numbers ) More...

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

Private Member Functions
	EnzdesFlexibleRegion ()
	Private default constructor – You must use the parameterized constructor to create! More...

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_

Additional Inherited Members
Protected Member Functions inherited from core::fragment::Frame
virtual void	show_fragments (std::ostream &out) const
	NOT IMPLEMENTED YET: generate_sub_frame according to mapping ( residue numbers ) returns NULL if mapping invalid. More...

bool	is_compatible (FragDataCOP new_frag) const
	is a FragData object compatible with the already stored ones ? @detail you can only add instances of FragData to the same Frame that are compatible, i.e., that contain the same class of FragData, e.g., based on BBTorsionSRFD, if you want to have different fragment for other dof's at the same sequence position create a new Frame. Users of the fragment-core are aware that multiple Frames for the same sequence position may exist. More...

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

Member Typedef Documentation

◆ SizeRealPair

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

private

◆ Super

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

private

Constructor & Destructor Documentation

◆ EnzdesFlexibleRegion() [1/2]

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(), frag_designabilities_, native_conf_, positions_, core::fragment::Frame::start(), and core::id::to_string().

◆ ~EnzdesFlexibleRegion()

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

overridedefault

◆ EnzdesFlexibleRegion() [2/2]

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

private

Private default constructor – You must use the parameterized constructor to create!

Member Function Documentation

◆ apply_ranked_fragment()

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

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

◆ assemble_enzdes_fragdata()

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

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

Referenced by EnzdesFlexibleRegion(), and remap_resid().

◆ calculate_rotamer_set_design_targets_partition_sum()

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,
		core::Size const	threads_to_request
	)		const

References core::pack::create_packer_graph(), design_targets_, core::pack::interaction_graph::EdgeBase::get_other_ind(), protocols::mean_field::max(), protocols::mean_field::min(), positions_, and core::pose::Pose::size().

Referenced by sort_ensemble_by_designability().

◆ compare_SizeRealPairs()

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

inlinestatic

Referenced by sort_ensemble_by_designability().

◆ contains_catalytic_res()

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

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

◆ declare_remodelable()

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

References remodel_max_length_, remodel_min_length_, and remodelable_.

◆ deltaE_best()

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

References frag_designabilities_.

◆ enz_loop_info()

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

References enzdes_protocol_, and index_.

◆ examine_new_loopconf()

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
	)

◆ extract_lig_designability_score()

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().

◆ get_10A_neighbors()

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().

◆ get_region_mm_bend_score()

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().

◆ get_region_total_score()

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().

◆ hack_fillup_frag_designabilities()

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

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

◆ index()

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

inline

References index_.

◆ minimize_region()

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

References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueType::atom_index(), protocols::carbohydrates::backward, core::scoring::chainbreak, core::kinematics::FoldTree::check_fold_tree(), core::fragment::Frame::clear(), core::kinematics::FoldTree::clone(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_extra_vertices(), core::fragment::Frame::end(), core::pose::Pose::energies(), core::pose::Pose::fold_tree(), core::fragment::Frame::nr_frags(), core::kinematics::FoldTree::num_jump(), core::id::PHI, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), core::fragment::Frame::start(), core::fragment::Frame::steal(), core::scoring::Energies::total_energies(), and protocols::enzdes::tr().

◆ no_ranked_frags()

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

inline

References frag_designabilities_.

◆ positions()

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

inline

References positions_.

Referenced by sort_ensemble_by_designability().

◆ remap_resid()

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().

◆ remodel_max_length()

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

inline

References remodel_max_length_.

◆ remodel_min_length()

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

inline

References remodel_min_length_.

◆ remodelable()

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

inline

References remodelable_.

◆ scale_target_proximity_to_other_conformations()

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

inline

References target_proximity_to_other_conformations_.

◆ scale_target_proximity_to_starting_conformation()

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

inline

References target_proximity_to_native_conformation_.

◆ set_target_proximity_to_starting_conformation()

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

inline

References target_proximity_to_native_conformation_.

◆ sort_ensemble_by_designability()

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(), core::pack::pack_rotamers_loop(), core::pack::pack_scorefxn_pose_handshake(), positions(), protocols::enzdes::enzutil::recreate_task(), core::pose::Pose::size(), core::id::to_string(), protocols::enzdes::tr(), and core::pose::Pose::update_residue_neighbors().

Member Data Documentation

◆ design_targets_

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().

◆ desired_remodel_ss_strings_

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

private

◆ enzdes_protocol_

EnzdesFlexBBProtocolCAP protocols::enzdes::EnzdesFlexibleRegion::enzdes_protocol_

private

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

◆ frag_designabilities_

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().

◆ index_

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

private

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

◆ native_conf_

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

private

Referenced by EnzdesFlexibleRegion(), and remap_resid().

◆ positions_

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().

◆ remodel_max_length_

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

private

Referenced by declare_remodelable(), and remodel_max_length().

◆ remodel_min_length_

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

private

Referenced by declare_remodelable(), and remodel_min_length().

◆ remodelable_

bool protocols::enzdes::EnzdesFlexibleRegion::remodelable_

private

Referenced by declare_remodelable(), and remodelable().

◆ target_proximity_to_native_conformation_

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().

◆ target_proximity_to_other_conformations_

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

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ SizeRealPair

◆ Super

Constructor & Destructor Documentation

◆ EnzdesFlexibleRegion() [1/2]

◆ ~EnzdesFlexibleRegion()

◆ EnzdesFlexibleRegion() [2/2]

Member Function Documentation

◆ apply_ranked_fragment()

◆ assemble_enzdes_fragdata()

◆ calculate_rotamer_set_design_targets_partition_sum()

◆ compare_SizeRealPairs()

◆ contains_catalytic_res()

◆ declare_remodelable()

◆ deltaE_best()

◆ enz_loop_info()

◆ examine_new_loopconf()

◆ extract_lig_designability_score()

◆ get_10A_neighbors()

◆ get_region_mm_bend_score()

◆ get_region_total_score()

◆ hack_fillup_frag_designabilities()

◆ index()

◆ minimize_region()

◆ no_ranked_frags()

◆ positions()

◆ remap_resid()

◆ remodel_max_length()

◆ remodel_min_length()

◆ remodelable()

◆ scale_target_proximity_to_other_conformations()

◆ scale_target_proximity_to_starting_conformation()

◆ set_target_proximity_to_starting_conformation()

◆ sort_ensemble_by_designability()

Member Data Documentation

◆ design_targets_

◆ desired_remodel_ss_strings_

◆ enzdes_protocol_

◆ frag_designabilities_

◆ index_

◆ native_conf_

◆ positions_

◆ remodel_max_length_

◆ remodel_min_length_

◆ remodelable_

◆ target_proximity_to_native_conformation_

◆ target_proximity_to_other_conformations_