#include <EnzdesBaseProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesBaseProtocol:

[legend]

Public Member Functions
	EnzdesBaseProtocol ()

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

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

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

utility::vector1< core::Size >	rb_min_jumps () const

void	rb_min_jumps (utility::vector1< core::Size > 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

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

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)

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)

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)

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)

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

	~LigandBaseProtocol () override

LigandBaseProtocolOP	shared_from_this ()

core::scoring::ScoreFunctionOP	get_scorefxn ()

core::scoring::ScoreFunctionCOP	get_scorefxn () const

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

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

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 MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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

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...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform 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
	Inform 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
	Generates a new Mover object freshly created with the default ctor. More...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol
static core::Size	get_ligand_jump_id (core::pose::Pose const &pose)

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

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

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions
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: @NOTE: 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)

bool	native_needs_load () const
	Do we need to (lazily) load the native pose? More...

void	set_native_needs_load (bool const setting)
	Set whether the native needs loading. More...

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)

core::pack::rotamer_set::UnboundRotamersOperationOP	unboundrot ()
	Nonconst access to the unboundrot_ object. More...

core::scoring::ScoreFunctionOP	scorefxn ()
	Access the scorefunction. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP const &sfxn_in)
	Set the scorefunction (cloning the input). More...

core::scoring::ScoreFunctionOP	hard_scorefxn ()
	Access the hard scorefunction. More...

core::scoring::ScoreFunctionOP	soft_scorefxn ()
	Access the soft scorefunction. More...

core::Real	sc_interface_padding () const
	Access the sc_interface_padding. More...

core::Real	bb_interface_cutoff () const
	Access the bb_interface_cutoff. More...

void	set_sc_interface_padding (core::Real const setting)
	Set the sc_interface_padding. More...

void	set_bb_interface_cutoff (core::Real const setting)
	Set the bb_interface_cutoff. More...

bool	use_soft_rep () const
	Are we using soft repulsion? More...

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
core::scoring::ScoreFunctionOP	reduced_sfxn_

std::set< core::Size >	design_targets_

bool	include_all_design_targets_in_design_interface_

Private Member Functions
void	read_ligand_superposition_file (std::string filename)

Private Attributes
core::chemical::ResidueTypeSetCAP	restype_set_

core::scoring::EnergyMap	constraint_weights_

core::Real	bb_min_allowed_dev_

core::Real	loop_bb_min_allowed_dev_

bool	lig_superposition_file_read_

std::pair< std::string, std::string >	res_to_superimpose_

utility::vector1< std::pair< std::string, std::string > >	atoms_to_superimpose_on_

bool	chi_min_

bool	bb_min_

bool	rb_min_

bool	minimize_ligand_torsions_

bool	bb_backrub_

bool	min_all_jumps_

bool	minimize_all_ligand_torsions_

core::Real	lig_min_stddev_

bool	native_needs_load_ = false
	Do we need to load a native pose? More...

bool	exclude_protein_protein_fa_elec_

bool	fix_catalytic_aa_

utility::vector1< core::Size >	rb_min_jumps_

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

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

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

Constructor & Destructor Documentation

◆ EnzdesBaseProtocol()

protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol ( )

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, atoms_to_superimpose_on_, bb_backrub_, bb_min_, bb_min_allowed_dev_, chi_min_, constraint_weights_, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::dihedral_constraint, enable_constraint_scoreterms(), core::scoring::ScoreFunction::energy_method_options(), core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec(), exclude_protein_protein_fa_elec_, core::chemical::FA_STANDARD, fix_catalytic_aa_, core::scoring::get_score_function(), core::scoring::ScoreFunction::has_zero_weight(), include_all_design_targets_in_design_interface_, lig_min_stddev_, loop_bb_min_allowed_dev_, min_all_jumps_, minimize_all_ligand_torsions_, minimize_ligand_torsions_, native_needs_load_, rb_min_jumps_, reduced_sfxn_, core::scoring::res_type_constraint, restype_set_, protocols::ligand_docking::LigandBaseProtocol::scorefxn(), core::scoring::ScoreFunction::set_energy_method_options(), set_scorefxn(), protocols::moves::Mover::type(), and core::scoring::ScoreFunction::weights().

Member Function Documentation

◆ add_pregenerated_enzdes_constraints()

void protocols::enzdes::EnzdesBaseProtocol::add_pregenerated_enzdes_constraints ( core::pose::Pose & pose ) const

References protocols::enzdes::ADD_PREGENERATED, protocols::enzdes::AddOrRemoveMatchCsts::apply(), and protocols::enzdes::AddOrRemoveMatchCsts::set_cst_action().

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply(), and enzdes_pack().

◆ catalytic_res()

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

References protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::chemical::ResidueType::is_ligand(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

◆ create_enzdes_movemap()

core::kinematics::MoveMapOP protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap	(	core::pose::Pose &	pose,
		core::pack::task::PackerTaskCOP	task,
		bool	min_all_jumps = `false`
	)

This function will modify the fold tree and add constraints to the pose if used with the bb_min and minimize_ligand_torsions options. Be WARNED!

References bb_backrub_, bb_min_, chi_min_, protocols::ligand_docking::constrain_ligand_torsions(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_polymer(), lig_min_stddev_, protocols::enzdes::enzutil::make_continuous_true_regions_in_bool_vector(), minimize_all_ligand_torsions_, minimize_ligand_torsions_, core::pose::Pose::num_jump(), rb_min_, rb_min_jumps(), core::pose::Pose::residue(), setup_bbmin_ft_and_csts(), core::pose::Pose::size(), protocols::enzdes::tr(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by cst_minimize().

◆ create_enzdes_pack_task()

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

References core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), design_targets(), design_targets_, fix_catalytic_aa_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), include_all_design_targets_in_design_interface_, core::pack::task::TaskFactory::push_back(), setup_sequence_recovery_cache(), and protocols::ligand_docking::LigandBaseProtocol::unboundrot().

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply(), and protocols::enzdes::EnzdesFlexBBProtocol::apply().

◆ cst_minimize()

void protocols::enzdes::EnzdesBaseProtocol::cst_minimize	(	core::pose::Pose &	pose,
		core::pack::task::PackerTaskCOP	task,
		bool	cst_opt = `false`
	)

References core::pose::add_variant_type_to_pose_residue(), core::scoring::angle_constraint, core::scoring::atom_pair_constraint, bb_min_, core::scoring::chainbreak, core::pose::Pose::constraint_set(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), core::scoring::coordinate_constraint, create_enzdes_movemap(), core::scoring::dihedral_constraint, core::pose::Pose::dump_scored_pdb(), core::pose::Pose::fold_tree(), core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueProperties::get_variant_from_string(), core::chemical::ResidueTypeBase::has_variant_type(), is_catalytic_position(), min_all_jumps_, minimize_ligand_torsions_, core::scoring::omega, core::chemical::ResidueTypeBase::properties(), reduced_sfxn_, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::ligand_docking::LigandBaseProtocol::scorefxn(), core::pose::Pose::size(), and core::chemical::variants_match().

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), and enzdes_pack().

◆ design_targets()

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

References design_targets_, protocols::enzdes::enzutil::is_catalytic_seqpos(), core::chemical::ResidueType::is_ligand(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by create_enzdes_pack_task(), and remap_resid().

◆ design_targets_score()

core::Real protocols::enzdes::EnzdesBaseProtocol::design_targets_score ( core::pose::Pose const & pose ) const

References design_targets_, core::pose::Pose::energies(), and core::scoring::Energies::residue_total_energy().

◆ disable_constraint_scoreterms()

void protocols::enzdes::EnzdesBaseProtocol::disable_constraint_scoreterms ( )

protected

function to disable constraint scoring terms: @NOTE: this will leave eventual covalent connections set up by EnzConstraintIO untouched.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::EMapVector::clear(), constraint_weights_, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::res_type_constraint, protocols::ligand_docking::LigandBaseProtocol::scorefxn(), core::scoring::ScoreFunction::set_weight(), and core::scoring::ScoreFunction::weights().

◆ enable_constraint_scoreterms()

void protocols::enzdes::EnzdesBaseProtocol::enable_constraint_scoreterms ( )

protected

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, constraint_weights_, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::scoring::res_type_constraint, protocols::ligand_docking::LigandBaseProtocol::scorefxn(), and core::scoring::ScoreFunction::set_weight().

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::enzdes::SecondaryMatchProtocol::apply(), and EnzdesBaseProtocol().

◆ enzdes_pack()

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

References add_pregenerated_enzdes_constraints(), cst_minimize(), protocols::enzdes::enzutil::get_enzcst_io(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::moves::Mover::get_native_pose(), protocols::enzdes::enzutil::recreate_task(), remove_enzdes_constraints(), protocols::ligand_docking::LigandBaseProtocol::scorefxn(), and protocols::ligand_docking::LigandBaseProtocol::soft_scorefxn().

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply(), and protocols::enzdes::EnzdesFlexBBProtocol::apply().

◆ exchange_ligands_in_pose()

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

protected

References protocols::toolbox::match_enzdes_util::assemble_remark_line(), atoms_to_superimpose_on_, protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), lig_superposition_file_read_, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), read_ligand_superposition_file(), core::pose::Pose::replace_residue(), res_to_superimpose_, core::pose::Pose::residue(), restype_set(), restype_set_, core::pose::Pose::size(), protocols::toolbox::match_enzdes_util::split_up_remark_line(), protocols::enzdes::tr(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::enzdes::SecondaryMatchProtocol::apply().

◆ generate_explicit_ligand_rotamer_poses()

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

References protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), core::conformation::Residue::name3(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::enzdes::SecondaryMatchProtocol, protocols::enzdes::EnzdesFlexBBProtocol, and protocols::enzdes::EnzdesFixBBProtocol.

◆ is_catalytic_position()

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

References protocols::enzdes::enzutil::is_catalytic_seqpos().

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::apply(), cst_minimize(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::enzdes::EnzdesFlexBBProtocol::setup_catalytic_residue_minimization_for_region(), and setup_enzdes_constraints().

◆ native_needs_load()

bool protocols::enzdes::EnzdesBaseProtocol::native_needs_load ( ) const

protected

Do we need to (lazily) load the native pose?

References native_needs_load_.

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), and protocols::enzdes::SecondaryMatchProtocol::apply().

◆ rb_min_jumps() [1/2]

utility::vector1< core::Size > protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps ( ) const

References rb_min_jumps_.

Referenced by create_enzdes_movemap().

◆ rb_min_jumps() [2/2]

void protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps ( utility::vector1< core::Size > const v )

References rb_min_jumps_.

◆ read_ligand_superposition_file()

void protocols::enzdes::EnzdesBaseProtocol::read_ligand_superposition_file ( std::string filename )

private

References atoms_to_superimpose_on_, protocols::abinitio::filename(), lig_superposition_file_read_, res_to_superimpose_, and protocols::enzdes::tr().

Referenced by exchange_ligands_in_pose().

◆ reduced_scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn ( )

References reduced_sfxn_.

◆ reduced_scorefxn() [2/2]

core::scoring::ScoreFunctionCOP protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn ( ) const

References reduced_sfxn_.

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), and protocols::enzdes::EnzdesFlexBBProtocol::setup_catalytic_residue_minimization_for_region().

◆ register_options()

void protocols::enzdes::EnzdesBaseProtocol::register_options ( )

static

References protocols::enzdes::DetectProteinLigandInterface::register_options(), protocols::enzdes::ProteinLigandInterfaceUpweighter::register_options(), and protocols::moves::Mover::register_options().

◆ remap_resid()

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

virtual

Reimplemented in protocols::enzdes::EnzdesFlexBBProtocol.

References design_targets().

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::remap_resid().

◆ remove_enzdes_constraints()

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

References protocols::enzdes::AddOrRemoveMatchCsts::apply(), protocols::enzdes::REMOVE, protocols::enzdes::AddOrRemoveMatchCsts::set_cst_action(), and protocols::enzdes::AddOrRemoveMatchCsts::set_keep_covalent().

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply(), and enzdes_pack().

◆ restype_set()

core::chemical::ResidueTypeSetCAP protocols::enzdes::EnzdesBaseProtocol::restype_set ( ) const

inline

References restype_set_.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), exchange_ligands_in_pose(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), and protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region().

◆ set_all_jumps_minimizable()

void protocols::enzdes::EnzdesBaseProtocol::set_all_jumps_minimizable ( bool const & setting )

inline

References min_all_jumps_.

◆ set_fix_cataa()

void protocols::enzdes::EnzdesBaseProtocol::set_fix_cataa ( bool const & setting )

inline

References fix_catalytic_aa_.

◆ set_minimize_options()

void protocols::enzdes::EnzdesBaseProtocol::set_minimize_options	(	bool const &	min_sc,
		bool const &	min_bb,
		bool const &	min_rb,
		bool const &	min_lig,
		bool	backrub = `false`
	)

inline

References bb_backrub_, bb_min_, chi_min_, minimize_ligand_torsions_, and rb_min_.

◆ set_native_needs_load()

void protocols::enzdes::EnzdesBaseProtocol::set_native_needs_load ( bool const setting )

protected

Set whether the native needs loading.

References native_needs_load_.

Referenced by protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), and protocols::enzdes::SecondaryMatchProtocol::apply().

◆ set_scorefxn()

void protocols::enzdes::EnzdesBaseProtocol::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

References protocols::ligand_docking::LigandBaseProtocol::scorefxn().

Referenced by EnzdesBaseProtocol().

◆ setup_bbmin_ft_and_csts()

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