#include <SecondaryMatchProtocol.hh>

Inheritance diagram for protocols::enzdes::SecondaryMatchProtocol:

[legend]

Public Member Functions
	SecondaryMatchProtocol ()

	~SecondaryMatchProtocol () override

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

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

core::Size	residues_compatible (core::conformation::ResidueCOP res1, core::conformation::ResidueCOP res2) const
	lookup function to determine whether to residues are compatible More...

bool	do_matching (core::pose::Pose &start_pose)

void	set_trial_positions (utility::vector1< core::Size > const &trial_pos)

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

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...

Protected Member Functions
void	add_enz_cst_interaction_to_pose (core::pose::Pose &pose, toolbox::match_enzdes_util::EnzConstraintParametersCOP params, toolbox::match_enzdes_util::EnzCstTemplateResCOP missing_template, toolbox::match_enzdes_util::EnzCstTemplateResCOP present_template, toolbox::match_enzdes_util::EnzConstraintIOCOP cstio)

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

bool	generate_and_dump_pose_found_residues_combinations (core::pose::PoseCOP ref_poseCOP)

bool	restype_possible_at_position (core::pose::Pose const &pose, core::chemical::ResidueTypeCOP restype, core::conformation::ResidueCOP target_residue, core::Size const trial_pos)
	rough check whether the two residues in question are close to each other More...

void	determine_found_residues_compatibility (core::pose::PoseCOP ref_poseCOP)
	this function does clash checks between all residues that were found, and saves the information in a map More...

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: @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...

Private Attributes
utility::vector1< utility::vector1< core::conformation::ResidueOP > >	found_resis_

std::map< core::conformation::ResidueCOP, std::map< core::conformation::ResidueCOP, core::Size > >	found_res_compatibility_

bool	found_res_compatibility_determined_

utility::vector1< core::Size >	trial_positions_

core::scoring::ScoreFunctionOP	reduced_scofx_

core::Size	cut1_

core::Size	cut2_

core::Size	cut3_

core::Size	cut4_

utility::vector1< toolbox::match_enzdes_util::EnzConstraintParametersCOP >	match_params_

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

Static Public Member Functions inherited from protocols::enzdes::EnzdesBaseProtocol
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 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_

Constructor & Destructor Documentation

◆ SecondaryMatchProtocol()

protocols::enzdes::SecondaryMatchProtocol::SecondaryMatchProtocol ( )

References core::scoring::ScoreFunctionFactory::create_score_function(), found_res_compatibility_, match_params_, and reduced_scofx_.

◆ ~SecondaryMatchProtocol()

protocols::enzdes::SecondaryMatchProtocol::~SecondaryMatchProtocol ( )

overridedefault

Member Function Documentation

◆ add_enz_cst_interaction_to_pose()

void protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose	(	core::pose::Pose &	pose,
		toolbox::match_enzdes_util::EnzConstraintParametersCOP	params,
		toolbox::match_enzdes_util::EnzCstTemplateResCOP	missing_template,
		toolbox::match_enzdes_util::EnzCstTemplateResCOP	present_template,
		toolbox::match_enzdes_util::EnzConstraintIOCOP	cstio
	)

protected

References core::pose::add_variant_type_to_pose_residue(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), core::pack::task::TaskFactory::create_packer_task(), core::scoring::EnergyEdge::dot(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::fa_rep, core::scoring::EnergyGraph::find_energy_edge(), found_resis_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::chemical::ResidueProperties::get_list_of_variants(), core::conformation::Residue::get_self_ptr(), core::chemical::ResidueProperties::get_variant_from_string(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::properties(), reduced_scofx_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::pose::Pose::residue_type(), restype_possible_at_position(), protocols::enzdes::EnzdesBaseProtocol::restype_set(), core::pose::Pose::size(), protocols::enzdes::enzutil::sum_constraint_scoreterms(), protocols::enzdes::tr(), trial_positions_, core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::chemical::variants_match().

Referenced by do_matching().

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::data(), do_matching(), core::pose::Pose::dump_pdb(), protocols::enzdes::EnzdesBaseProtocol::enable_constraint_scoreterms(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), find_all_allowed_positions(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, protocols::enzdes::EnzdesBaseProtocol::native_needs_load(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), reduced_scofx_, protocols::ligand_docking::LigandBaseProtocol::scorefxn(), protocols::enzdes::EnzdesBaseProtocol::set_native_needs_load(), protocols::moves::Mover::set_native_pose(), protocols::enzdes::EnzdesBaseProtocol::setup_enzdes_constraints(), protocols::kinmatch::str(), and protocols::enzdes::tr().

◆ determine_found_residues_compatibility()

void protocols::enzdes::SecondaryMatchProtocol::determine_found_residues_compatibility ( core::pose::PoseCOP ref_poseCOP )

protected

this function does clash checks between all residues that were found, and saves the information in a map

References found_res_compatibility_, found_res_compatibility_determined_, found_resis_, core::scoring::pair, and reduced_scofx_.

Referenced by generate_and_dump_pose_found_residues_combinations().

◆ do_matching()

bool protocols::enzdes::SecondaryMatchProtocol::do_matching ( core::pose::Pose & start_pose )

References add_enz_cst_interaction_to_pose(), found_resis_, generate_and_dump_pose_found_residues_combinations(), protocols::enzdes::enzutil::get_enzcst_io(), core::pose::Pose::get_self_ptr(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, match_params_, protocols::kinmatch::str(), and protocols::enzdes::tr().

Referenced by apply().

◆ find_all_allowed_positions()

void protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions ( core::pose::Pose const & pose )

protected

References cut1_, cut2_, cut3_, cut4_, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::num_jump(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::enzdes::tr(), and trial_positions_.

Referenced by apply().

◆ generate_and_dump_pose_found_residues_combinations()

bool protocols::enzdes::SecondaryMatchProtocol::generate_and_dump_pose_found_residues_combinations ( core::pose::PoseCOP ref_poseCOP )

protected

References determine_found_residues_compatibility(), found_resis_, protocols::moves::Mover::get_self_ptr(), and match_params_.

Referenced by do_matching().

◆ get_name()

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

overridevirtual

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

Reimplemented from protocols::enzdes::EnzdesBaseProtocol.

◆ residues_compatible()

core::Size protocols::enzdes::SecondaryMatchProtocol::residues_compatible	(	core::conformation::ResidueCOP	res1,
		core::conformation::ResidueCOP	res2
	)		const

lookup function to determine whether to residues are compatible

References found_res_compatibility_, found_res_compatibility_determined_, and core::id::to_string().

◆ restype_possible_at_position()

bool protocols::enzdes::SecondaryMatchProtocol::restype_possible_at_position	(	core::pose::Pose const &	pose,
		core::chemical::ResidueTypeCOP	restype,
		core::conformation::ResidueCOP	target_residue,
		core::Size const	trial_pos
	)