#include <EnzdesBaseProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesBaseProtocol:

Collaboration diagram for protocols::enzdes::EnzdesBaseProtocol:

Public Member Functions
	EnzdesBaseProtocol ()

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

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

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) 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

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

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 ()

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: : 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...

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	exclude_protein_protein_hack_elec_

bool	fix_catalytic_aa_

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 41 of file EnzdesBaseProtocol.hh.

Constructor & Destructor Documentation

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

Definition at line 89 of file EnzdesBaseProtocol.cc.

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::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec(), exclude_protein_protein_hack_elec_, core::chemical::FA_STANDARD, fix_catalytic_aa_, core::chemical::ChemicalManager::get_instance(), core::scoring::getScoreFunction(), 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_, core::import_pose::pose_from_pdb(), reduced_sfxn_, core::scoring::res_type_constraint, core::chemical::ChemicalManager::residue_type_set(), restype_set_, protocols::ligand_docking::LigandBaseProtocol::scorefxn_, protocols::moves::Mover::set_native_pose(), and protocols::moves::Mover::type().

Member Function Documentation

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

Definition at line 572 of file EnzdesBaseProtocol.cc.

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().

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

Definition at line 228 of file EnzdesBaseProtocol.cc.

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

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

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!

Definition at line 373 of file EnzdesBaseProtocol.cc.

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_, core::pose::Pose::residue(), setup_bbmin_ft_and_csts(), core::pose::Pose::total_residue(), protocols::enzdes::tr(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by cst_minimize().

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

Definition at line 302 of file EnzdesBaseProtocol.cc.

References 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().

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

Definition at line 583 of file EnzdesBaseProtocol.cc.

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::ResidueType::has_variant_type(), is_catalytic_position(), min_all_jumps_, minimize_ligand_torsions_, core::scoring::omega, 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::total_residue(), core::chemical::ResidueType::variant_types(), and core::chemical::ResidueType::variants_match().

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

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

Definition at line 247 of file EnzdesBaseProtocol.cc.

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

Referenced by create_enzdes_pack_task(), and remap_resid().

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

Definition at line 826 of file EnzdesBaseProtocol.cc.

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

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

protected

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

Definition at line 709 of file EnzdesBaseProtocol.cc.

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, and protocols::ligand_docking::LigandBaseProtocol::scorefxn_.

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

protected

Definition at line 698 of file EnzdesBaseProtocol.cc.

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, and protocols::ligand_docking::LigandBaseProtocol::scorefxn_.

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

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
	)		const

Definition at line 484 of file EnzdesBaseProtocol.cc.

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(), and protocols::ligand_docking::LigandBaseProtocol::soft_scorefxn_.

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

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

protected

Definition at line 728 of file EnzdesBaseProtocol.cc.

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_, protocols::toolbox::match_enzdes_util::split_up_remark_line(), core::pose::Pose::total_residue(), protocols::enzdes::tr(), and core::pose::Pose::update_residue_neighbors().

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

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
	)

Definition at line 856 of file EnzdesBaseProtocol.cc.

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

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

virtual

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

Reimplemented from protocols::ligand_docking::LigandBaseProtocol.

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

Definition at line 223 of file EnzdesBaseProtocol.cc.

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

Definition at line 692 of file EnzdesBaseProtocol.cc.

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().

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

private

Definition at line 889 of file EnzdesBaseProtocol.cc.

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

Referenced by exchange_ligands_in_pose().

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

Definition at line 816 of file EnzdesBaseProtocol.cc.

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().

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

Definition at line 821 of file EnzdesBaseProtocol.cc.

References reduced_sfxn_.

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

static

Definition at line 265 of file EnzdesBaseProtocol.cc.

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

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

virtual

Reimplemented in protocols::enzdes::EnzdesFlexBBProtocol.

Definition at line 844 of file EnzdesBaseProtocol.cc.

References design_targets().

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

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

Definition at line 560 of file EnzdesBaseProtocol.cc.

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().

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

inline

Definition at line 64 of file EnzdesBaseProtocol.hh.

References restype_set_.

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

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

inline

Definition at line 124 of file EnzdesBaseProtocol.hh.

References min_all_jumps_.

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

inline

Definition at line 137 of file EnzdesBaseProtocol.hh.

References fix_catalytic_aa_.

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

Definition at line 127 of file EnzdesBaseProtocol.hh.

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

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

Definition at line 944 of file EnzdesBaseProtocol.cc.

References protocols::ligand_docking::LigandBaseProtocol::scorefxn_.

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

Definition at line 446 of file EnzdesBaseProtocol.cc.

References bb_min_allowed_dev_, core::pose::Pose::constraint_set(), core::scoring::dssp::Dssp::get_dssp_secstruct(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), core::conformation::Residue::is_protein(), loop_bb_min_allowed_dev_, protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), core::pose::Pose::residue(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), and core::pose::Pose::total_residue().

Referenced by create_enzdes_movemap().

void protocols::enzdes::EnzdesBaseProtocol::setup_enzdes_constraints	(	core::pose::Pose &	pose,
		bool	allow_missing_remark_blocks
	)		const

protected

Definition at line 540 of file EnzdesBaseProtocol.cc.

References protocols::enzdes::ADD_NEW, protocols::enzdes::AddOrRemoveMatchCsts::apply(), is_catalytic_position(), protocols::enzdes::AddOrRemoveMatchCsts::set_accept_blocks_missing_header(), protocols::enzdes::AddOrRemoveMatchCsts::set_cst_action(), core::pose::Pose::total_residue(), and protocols::enzdes::tr().

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

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

Definition at line 346 of file EnzdesBaseProtocol.cc.

References core::pack::task::PackerTask::being_designed(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by create_enzdes_pack_task().

Member Data Documentation

utility::vector1< std::pair< std::string, std::string > > protocols::enzdes::EnzdesBaseProtocol::atoms_to_superimpose_on_

private

Definition at line 210 of file EnzdesBaseProtocol.hh.

Referenced by EnzdesBaseProtocol(), exchange_ligands_in_pose(), and read_ligand_superposition_file().

bool protocols::enzdes::EnzdesBaseProtocol::bb_backrub_

private

Definition at line 211 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_movemap(), EnzdesBaseProtocol(), and set_minimize_options().

bool protocols::enzdes::EnzdesBaseProtocol::bb_min_

private

Definition at line 211 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_movemap(), cst_minimize(), EnzdesBaseProtocol(), and set_minimize_options().

core::Real protocols::enzdes::EnzdesBaseProtocol::bb_min_allowed_dev_

private

Definition at line 204 of file EnzdesBaseProtocol.hh.

Referenced by EnzdesBaseProtocol(), and setup_bbmin_ft_and_csts().

bool protocols::enzdes::EnzdesBaseProtocol::chi_min_

private

Definition at line 211 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_movemap(), EnzdesBaseProtocol(), and set_minimize_options().

core::scoring::EnergyMap protocols::enzdes::EnzdesBaseProtocol::constraint_weights_

private

Definition at line 202 of file EnzdesBaseProtocol.hh.

Referenced by disable_constraint_scoreterms(), enable_constraint_scoreterms(), and EnzdesBaseProtocol().

std::set< core::Size > protocols::enzdes::EnzdesBaseProtocol::design_targets_

mutableprotected

Definition at line 188 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_pack_task(), design_targets(), and design_targets_score().

bool protocols::enzdes::EnzdesBaseProtocol::exclude_protein_protein_hack_elec_

private

Definition at line 216 of file EnzdesBaseProtocol.hh.

Referenced by EnzdesBaseProtocol().

bool protocols::enzdes::EnzdesBaseProtocol::fix_catalytic_aa_

private

Definition at line 216 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_pack_task(), EnzdesBaseProtocol(), and set_fix_cataa().

bool protocols::enzdes::EnzdesBaseProtocol::include_all_design_targets_in_design_interface_

protected

Definition at line 190 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_pack_task(), and EnzdesBaseProtocol().

core::Real protocols::enzdes::EnzdesBaseProtocol::lig_min_stddev_

private

Definition at line 214 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_movemap(), and EnzdesBaseProtocol().

bool protocols::enzdes::EnzdesBaseProtocol::lig_superposition_file_read_

private

Definition at line 208 of file EnzdesBaseProtocol.hh.

Referenced by exchange_ligands_in_pose(), and read_ligand_superposition_file().

core::Real protocols::enzdes::EnzdesBaseProtocol::loop_bb_min_allowed_dev_

private

Definition at line 205 of file EnzdesBaseProtocol.hh.

Referenced by EnzdesBaseProtocol(), and setup_bbmin_ft_and_csts().

bool protocols::enzdes::EnzdesBaseProtocol::min_all_jumps_

private

Definition at line 212 of file EnzdesBaseProtocol.hh.

Referenced by cst_minimize(), EnzdesBaseProtocol(), and set_all_jumps_minimizable().

bool protocols::enzdes::EnzdesBaseProtocol::minimize_all_ligand_torsions_

private

Definition at line 213 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_movemap(), and EnzdesBaseProtocol().

bool protocols::enzdes::EnzdesBaseProtocol::minimize_ligand_torsions_

private

Definition at line 211 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_movemap(), cst_minimize(), EnzdesBaseProtocol(), and set_minimize_options().

bool protocols::enzdes::EnzdesBaseProtocol::rb_min_

private

Definition at line 211 of file EnzdesBaseProtocol.hh.

Referenced by create_enzdes_movemap(), and set_minimize_options().

core::scoring::ScoreFunctionOP protocols::enzdes::EnzdesBaseProtocol::reduced_sfxn_

protected

Definition at line 186 of file EnzdesBaseProtocol.hh.

Referenced by cst_minimize(), EnzdesBaseProtocol(), protocols::enzdes::EnzdesFlexBBProtocol::EnzdesFlexBBProtocol(), and reduced_scorefxn().

std::pair< std::string, std::string > protocols::enzdes::EnzdesBaseProtocol::res_to_superimpose_

private

Definition at line 209 of file EnzdesBaseProtocol.hh.

Referenced by exchange_ligands_in_pose(), and read_ligand_superposition_file().

core::chemical::ResidueTypeSetCAP protocols::enzdes::EnzdesBaseProtocol::restype_set_

private

Definition at line 201 of file EnzdesBaseProtocol.hh.

Referenced by EnzdesBaseProtocol(), exchange_ligands_in_pose(), and restype_set().

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

src/protocols/enzdes/EnzdesBaseProtocol.hh
src/protocols/enzdes/EnzdesBaseProtocol.cc

Protected Attributes
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_

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation