#include <EnzdesFixBBProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesFixBBProtocol:

Collaboration diagram for protocols::enzdes::EnzdesFixBBProtocol:

Public Member Functions
	EnzdesFixBBProtocol ()

	~EnzdesFixBBProtocol ()

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

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

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

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

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 Attributes
bool	start_from_random_rb_conf_

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

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)