#include <EnzdesFlexBBProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesFlexBBProtocol:

Collaboration diagram for protocols::enzdes::EnzdesFlexBBProtocol:

Public Member Functions
	EnzdesFlexBBProtocol ()

	~EnzdesFlexBBProtocol ()

void	apply (core::pose::Pose &pose)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

bool	is_flexible (core::Size seqpos) const

bool	is_remodelable (core::Size seqpos) const

void	get_tenA_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > &residue_positions)

core::pack::task::PackerTaskOP	modified_task (core::pose::Pose const &pose, core::pack::task::PackerTask const &orig_task)

void	test_flexbb_rotamer_sets (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task)

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

EnzdesFlexibleRegionCOP	enz_flexible_region (core::Size region) const

toolbox::match_enzdes_util::EnzdesLoopsFileCOP	enz_loops_file () const

void	generate_ensemble_for_region (core::pose::Pose &pose, core::Size region)

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

void	generate_alc_ensemble_for_region (core::pose::Pose &pose, core::Size region)

void	generate_backrub_ensemble_for_region (core::pose::Pose &pose, core::Size region)

void	determine_flexible_regions (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task)

Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
	EnzdesBaseProtocol ()

utility::vector1< Size >	catalytic_res (core::pose::Pose const &pose) const

std::set< Size > const &	design_targets (core::pose::Pose const &pose) const

bool	is_catalytic_position (core::pose::Pose const &pose, core::Size const seqpos) const

core::chemical::ResidueTypeSetCAP	restype_set () const

void	generate_explicit_ligand_rotamer_poses (core::pose::Pose const &orig_pose, utility::vector1< core::pose::PoseOP > &ligrot_poses, core::scoring::ScoreFunctionCOP scofx)

core::scoring::ScoreFunctionCOP	reduced_scorefxn () const

core::scoring::ScoreFunctionOP	reduced_scorefxn ()

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

void	remove_enzdes_constraints (core::pose::Pose &pose, bool keep_covalent) const

void	add_pregenerated_enzdes_constraints (core::pose::Pose &pose) const

void	cst_minimize (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool cst_opt=false) const

core::pack::task::PackerTaskOP	create_enzdes_pack_task (core::pose::Pose &pose, bool design=true)

void	setup_sequence_recovery_cache (core::pose::Pose &pose, core::pack::task::PackerTask const &task) const

void	set_all_jumps_minimizable (bool const &setting)

void	set_minimize_options (bool const &min_sc, bool const &min_bb, bool const &min_rb, bool const &min_lig, bool backrub=false)

void	set_fix_cataa (bool const &setting)

core::kinematics::MoveMapOP	create_enzdes_movemap (core::pose::Pose &pose, core::pack::task::PackerTaskCOP task, bool min_all_jumps=false) const

void	enzdes_pack (core::pose::Pose &pose, core::pack::task::PackerTaskCOP, core::scoring::ScoreFunctionCOP scorefxn, core::Size cycles, bool minimize_after_packing, bool pack_unconstrained, bool favor_native) const

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)

void	setup_bbmin_ft_and_csts (core::pose::Pose &pose, utility::vector1< bool > allow_move_bb, core::Size jump_id) const

Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
	LigandBaseProtocol ()

virtual	~LigandBaseProtocol ()

core::scoring::ScoreFunctionOP	get_scorefxn ()

core::scoring::ScoreFunctionCOP	get_scorefxn () const

core::Size	get_ligand_jump_id (core::pose::Pose const &pose) const

core::Size	get_ligand_id (core::pose::Pose const &pose) const
	Return the residue sequence number for our ligand. More...

core::Size	get_ligand_id (core::pose::Pose const &pose, core::Size jump_id) const
	Return the residue sequence number for our ligand. More...

void	restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::constraints::FuncOP restr_func) const

void	reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const
	reorders a fold tree such that movement in the mobile regions will More...

void	get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
static void	register_options ()

Protected Member Functions
bool	assemble_next_best_loop_combination (core::pose::Pose &pose)

bool	hack_assemble_next_loop_combination (core::pose::Pose &pose)

bool	recover_loops_from_file (core::pose::Pose const &pose)

void	setup_catalytic_residue_minimization_for_region (core::pose::Pose const &pose, core::Size region)

Protected Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
void	setup_enzdes_constraints (core::pose::Pose &pose, bool allow_missing_remark_blocks) const

void	enable_constraint_scoreterms ()

void	disable_constraint_scoreterms ()
	function to disable constraint scoring terms: : this will leave eventual covalent connections set up by EnzConstraintIO untouched. More...

bool	exchange_ligands_in_pose (core::pose::Pose &pose, bool check_bb_clashes, core::scoring::ScoreFunctionCOP scofx)

Protected Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
core::scoring::ScoreFunctionOP	make_tweaked_scorefxn (std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight)

core::Vector	choose_desired_centroid (core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >)

void	move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts)

void	move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid)

core::kinematics::MoveMapOP	make_movemap (core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const

core::pack::task::PackerTaskOP	make_packer_task (core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const
	Shared machinery for the next two. More...

core::pack::task::PackerTaskOP	make_packer_task (core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const
	Receptor (interface?) plus ligand. More...

core::pack::task::PackerTaskOP	make_packer_task_ligand_only (core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const
	Just ligand, not the receptor. More...

void	find_interface_rsds (core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const

void	find_interface_backbone (core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const

core::scoring::constraints::ConstraintOP	restrain_ligand_nbr_atom (core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const

void	setup_bbmin_foldtree (core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms)

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Protected Attributes
utility::vector1 < EnzdesFlexibleRegionOP >	flex_regions_

Protected Attributes inherited from protocols::enzdes::EnzdesBaseProtocol
core::scoring::ScoreFunctionOP	reduced_sfxn_

std::set< core::Size >	design_targets_

bool	include_all_design_targets_in_design_interface_

Protected Attributes inherited from protocols::ligand_docking::LigandBaseProtocol
bool	use_soft_rep_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	hard_scorefxn_

core::scoring::ScoreFunctionOP	soft_scorefxn_

core::Real	sc_interface_padding_

core::Real	bb_interface_cutoff_

core::pack::rotamer_set::UnboundRotamersOperationOP	unboundrot_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Detailed Description

Definition at line 50 of file EnzdesFlexBBProtocol.hh.

Constructor & Destructor Documentation

protocols::enzdes::EnzdesFlexBBProtocol::EnzdesFlexBBProtocol ( )

Definition at line 108 of file EnzdesFlexBBProtocol.cc.

References brub_mover_, brub_pivot_atoms_, flex_regions_, core::scoring::mm_bend, core::scoring::rama, protocols::enzdes::EnzdesBaseProtocol::reduced_sfxn_, and protocols::ligand_docking::LigandBaseProtocol::scorefxn_.

protocols::enzdes::EnzdesFlexBBProtocol::~EnzdesFlexBBProtocol ( )

Definition at line 106 of file EnzdesFlexBBProtocol.cc.

Member Function Documentation

void protocols::enzdes::EnzdesFlexBBProtocol::apply ( core::pose::Pose & pose)

virtual

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

Definition at line 157 of file EnzdesFlexBBProtocol.cc.

Referenced by generate_alc_ensemble_for_region(), and generate_backrub_ensemble_for_region().

bool protocols::enzdes::EnzdesFlexBBProtocol::assemble_next_best_loop_combination ( core::pose::Pose & pose)

protected

figure out which combination of loop conformations is the next most promising one

Definition at line 1152 of file EnzdesFlexBBProtocol.cc.

References flex_regions_, fragment_counters_, and protocols::enzdes::tr().

void protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTaskCOP	task
	)

Definition at line 510 of file EnzdesFlexBBProtocol.cc.

References enz_loops_file_, flex_regions_, fragment_counters_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(), core::conformation::Residue::is_polymer(), protocols::loops::Loops::loop_file_name(), protocols::enzdes::enzutil::make_continuous_true_regions_in_bool_vector(), core::pose::Pose::observer_cache(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::datacache::CacheableObserverType::SPECIAL_SEGMENTS_OBSERVER, core::pose::Pose::total_residue(), protocols::enzdes::tr(), protocols::loops::Loops::v_begin(), and protocols::loops::Loops::v_end().

Referenced by apply().

EnzdesFlexibleRegionCOP protocols::enzdes::EnzdesFlexBBProtocol::enz_flexible_region ( core::Size region) const

inline

Definition at line 94 of file EnzdesFlexBBProtocol.hh.

References flex_regions_.

toolbox::match_enzdes_util::EnzdesLoopsFileCOP protocols::enzdes::EnzdesFlexBBProtocol::enz_loops_file ( ) const

inline

Definition at line 99 of file EnzdesFlexBBProtocol.hh.

References enz_loops_file_.

void protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region	(	core::pose::Pose &	pose,
		core::Size	region
	)

Definition at line 789 of file EnzdesFlexBBProtocol.cc.

References apply(), protocols::moves::MonteCarlo::boltzmann(), catmin_mover_, core::pose::Pose::energies(), flex_regions_, kinematic_mover_, protocols::moves::MonteCarlo::last_accepted_pose(), loop_ensemble_size_, loopgen_trials_, protocols::moves::MonteCarlo::lowest_score_pose(), mc_kt_high_, mc_kt_low_, minimize_cats_, protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::residue(), protocols::enzdes::EnzdesBaseProtocol::restype_set(), protocols::moves::MonteCarlo::set_temperature(), protocols::moves::MonteCarlo::show_counters(), core::io::serialization::size(), protocols::loops::start, protocols::loops::stop, core::scoring::Energies::total_energies(), core::scoring::total_score, and protocols::enzdes::tr().

Referenced by generate_ensemble_for_region().

void protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region	(	core::pose::Pose &	pose,
		core::Size	region
	)

void protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region	(	core::pose::Pose &	pose,
		core::Size	region
	)

std::string protocols::enzdes::EnzdesFlexBBProtocol::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Reimplemented from protocols::enzdes::EnzdesBaseProtocol.

Definition at line 316 of file EnzdesFlexBBProtocol.cc.

void protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues	(	core::pose::Pose const &	pose,
		utility::vector1< bool > &	residue_positions
	)

As output, residue_position[i] is true for all neighbor residues including orginal input residues. The function is used to find all neighboring residues of the loop residues in case they need to be repacked or minimized in fullatom refinement.

Definition at line 373 of file EnzdesFlexBBProtocol.cc.

References core::pose::Pose::energies(), is_flexible(), is_remodelable(), core::chemical::ResidueType::name(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by modified_task().

bool protocols::enzdes::EnzdesFlexBBProtocol::hack_assemble_next_loop_combination ( core::pose::Pose & pose)

protected

returns false if the last combination is reached, true otherwise

Definition at line 1193 of file EnzdesFlexBBProtocol.cc.

References flex_regions_, and fragment_counters_.

bool protocols::enzdes::EnzdesFlexBBProtocol::is_flexible ( core::Size seqpos) const

Definition at line 349 of file EnzdesFlexBBProtocol.cc.

References flex_regions_, and protocols::loops::start.

Referenced by get_tenA_neighbor_residues(), and modified_task().

bool protocols::enzdes::EnzdesFlexBBProtocol::is_remodelable ( core::Size seqpos) const

Definition at line 358 of file EnzdesFlexBBProtocol.cc.

References flex_regions_, and protocols::loops::start.

Referenced by get_tenA_neighbor_residues(), and modified_task().

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

Definition at line 776 of file EnzdesFlexBBProtocol.cc.

References flex_regions_.

core::pack::task::PackerTaskOP protocols::enzdes::EnzdesFlexBBProtocol::modified_task	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTask const &	orig_task
	)

Definition at line 395 of file EnzdesFlexBBProtocol.cc.

References core::chemical::aa_cys, core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), core::pack::task::PackerTask::design_residue(), core::chemical::DISULFIDE, get_tenA_neighbor_residues(), core::conformation::Residue::has_variant_type(), core::pack::task::PackerTask::IGEdgeReweights(), protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(), is_flexible(), is_remodelable(), core::conformation::Residue::name3(), core::chemical::num_canonical_aas, core::pack::task::PackerTask::pack_residue(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::rotamer_operations(), core::pack::task::ResidueLevelTask::rotamer_set_operation_begin(), core::pack::task::ResidueLevelTask::rotamer_set_operation_end(), core::pose::Pose::total_residue(), and protocols::enzdes::tr().

Referenced by apply().

bool protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file ( core::pose::Pose const & pose)

protected

Definition at line 1259 of file EnzdesFlexBBProtocol.cc.

References protocols::swa::rna::file_exists(), core::fragment::fill_template_frames_from_pdb(), flex_regions_, core::pose::Pose::pdb_info(), and protocols::enzdes::tr().

Referenced by apply().

void protocols::enzdes::EnzdesFlexBBProtocol::register_options ( )

static

Definition at line 321 of file EnzdesFlexBBProtocol.cc.

References protocols::moves::Mover::register_options().

void protocols::enzdes::EnzdesFlexBBProtocol::remap_resid	(	core::pose::Pose const &	pose,
		core::id::SequenceMapping const &	smap
	)

virtual

Reimplemented from protocols::enzdes::EnzdesBaseProtocol.

Definition at line 499 of file EnzdesFlexBBProtocol.cc.

References flex_regions_, and protocols::enzdes::EnzdesBaseProtocol::remap_resid().

void protocols::enzdes::EnzdesFlexBBProtocol::setup_catalytic_residue_minimization_for_region	(	core::pose::Pose const &	pose,
		core::Size	region
	)

protected

Definition at line 1306 of file EnzdesFlexBBProtocol.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, catmin_movemap_, catmin_mover_, catmin_sfxn_, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::fa_dun, core::scoring::fa_rep, flex_regions_, protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(), protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn(), protocols::loops::start, and protocols::enzdes::tr().

Referenced by generate_ensemble_for_region().

void protocols::enzdes::EnzdesFlexBBProtocol::test_flexbb_rotamer_sets	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTaskCOP	task
	)

Definition at line 2207 of file EnzdesFlexBBProtocol.cc.

Member Data Documentation

core::Size protocols::enzdes::EnzdesFlexBBProtocol::brub_max_atoms_

private

Definition at line 173 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_backrub_ensemble_for_region().

core::Size protocols::enzdes::EnzdesFlexBBProtocol::brub_min_atoms_

private

Definition at line 172 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_backrub_ensemble_for_region().

protocols::backrub::BackrubMoverOP protocols::enzdes::EnzdesFlexBBProtocol::brub_mover_

private

Definition at line 168 of file EnzdesFlexBBProtocol.hh.

Referenced by EnzdesFlexBBProtocol(), generate_backrub_ensemble_for_region(), and generate_ensemble_for_region().

utility::vector1< std::string > protocols::enzdes::EnzdesFlexBBProtocol::brub_pivot_atoms_

private

Definition at line 176 of file EnzdesFlexBBProtocol.hh.

Referenced by EnzdesFlexBBProtocol(), and generate_backrub_ensemble_for_region().

core::kinematics::MoveMapOP protocols::enzdes::EnzdesFlexBBProtocol::catmin_movemap_

private

Definition at line 182 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_ensemble_for_region(), and setup_catalytic_residue_minimization_for_region().

protocols::simple_moves::MinMoverOP protocols::enzdes::EnzdesFlexBBProtocol::catmin_mover_

private

Definition at line 183 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_alc_ensemble_for_region(), generate_backrub_ensemble_for_region(), generate_ensemble_for_region(), and setup_catalytic_residue_minimization_for_region().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesFlexBBProtocol::catmin_sfxn_

private

Definition at line 184 of file EnzdesFlexBBProtocol.hh.

Referenced by setup_catalytic_residue_minimization_for_region().

toolbox::match_enzdes_util::EnzdesLoopsFileCOP protocols::enzdes::EnzdesFlexBBProtocol::enz_loops_file_

private

Definition at line 161 of file EnzdesFlexBBProtocol.hh.

Referenced by determine_flexible_regions(), and enz_loops_file().

utility::vector1< EnzdesFlexibleRegionOP > protocols::enzdes::EnzdesFlexBBProtocol::flex_regions_

protected

Definition at line 157 of file EnzdesFlexBBProtocol.hh.

Referenced by apply(), assemble_next_best_loop_combination(), determine_flexible_regions(), enz_flexible_region(), EnzdesFlexBBProtocol(), generate_alc_ensemble_for_region(), generate_backrub_ensemble_for_region(), generate_ensemble_for_region(), hack_assemble_next_loop_combination(), is_flexible(), is_remodelable(), minimize_flexible_region(), recover_loops_from_file(), remap_resid(), and setup_catalytic_residue_minimization_for_region().

utility::vector1< core::Size > protocols::enzdes::EnzdesFlexBBProtocol::fragment_counters_

private

Definition at line 163 of file EnzdesFlexBBProtocol.hh.

Referenced by apply(), assemble_next_best_loop_combination(), determine_flexible_regions(), and hack_assemble_next_loop_combination().

protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP protocols::enzdes::EnzdesFlexBBProtocol::kinematic_mover_

private

Definition at line 169 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_alc_ensemble_for_region(), and generate_ensemble_for_region().

core::Size protocols::enzdes::EnzdesFlexBBProtocol::loop_ensemble_size_

private

Definition at line 174 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_alc_ensemble_for_region(), generate_backrub_ensemble_for_region(), and generate_ensemble_for_region().

core::Size protocols::enzdes::EnzdesFlexBBProtocol::loopgen_trials_

private

Definition at line 175 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_alc_ensemble_for_region(), generate_backrub_ensemble_for_region(), and generate_ensemble_for_region().

core::Real protocols::enzdes::EnzdesFlexBBProtocol::mc_kt_high_

private

Definition at line 171 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_alc_ensemble_for_region(), and generate_backrub_ensemble_for_region().

core::Real protocols::enzdes::EnzdesFlexBBProtocol::mc_kt_low_

private

Definition at line 171 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_alc_ensemble_for_region(), and generate_backrub_ensemble_for_region().

bool protocols::enzdes::EnzdesFlexBBProtocol::minimize_cats_

private

Definition at line 181 of file EnzdesFlexBBProtocol.hh.

Referenced by generate_alc_ensemble_for_region(), generate_backrub_ensemble_for_region(), and generate_ensemble_for_region().

utility::vector1< core::Real > protocols::enzdes::EnzdesFlexBBProtocol::native_fragment_bb_energies_

private

Definition at line 166 of file EnzdesFlexBBProtocol.hh.

core::pose::Pose protocols::enzdes::EnzdesFlexBBProtocol::pack_region_ala_pose_

private

Definition at line 165 of file EnzdesFlexBBProtocol.hh.

Referenced by apply().

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

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

Private Attributes
toolbox::match_enzdes_util::EnzdesLoopsFileCOP	enz_loops_file_

utility::vector1< core::Size >	fragment_counters_

core::pose::Pose	pack_region_ala_pose_

utility::vector1< core::Real >	native_fragment_bb_energies_

protocols::backrub::BackrubMoverOP	brub_mover_

protocols::loops::loop_closure::kinematic_closure::KinematicMoverOP	kinematic_mover_

core::Real	mc_kt_low_

core::Real	mc_kt_high_

core::Size	brub_min_atoms_

core::Size	brub_max_atoms_

core::Size	loop_ensemble_size_

core::Size	loopgen_trials_

utility::vector1< std::string >	brub_pivot_atoms_

bool	minimize_cats_

core::kinematics::MoveMapOP	catmin_movemap_

protocols::simple_moves::MinMoverOP	catmin_mover_

core::scoring::ScoreFunctionOP	catmin_sfxn_

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

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Member Data Documentation