used to design a protein to hbond preferentially to a set of target residues on the partner. Hbonds involving backbone or sidechain on the target can be counted, and whether to design donors or acceptors can also be defined. More...

#include <DesignMinimizeHbonds.hh>

Inheritance diagram for protocols::protein_interface_design::movers::DesignMinimizeHbonds:

[legend]

Collaboration diagram for protocols::protein_interface_design::movers::DesignMinimizeHbonds:

[legend]

Public Types
typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::pose::Pose	Pose

Public Member Functions
	DesignMinimizeHbonds ()

	DesignMinimizeHbonds (ScoreFunctionCOP scorefxn_repack, ScoreFunctionCOP scorefxn_minimize, utility::vector1< core::Size > const target_residues, bool const donors, bool const acceptors, bool const bb_hbond, bool const sc_hbond, core::Real const hbond_energy_threshold, core::Real interface_distance_cutoff=8.0, bool const repack_partner1=true, bool const repack_partner2=false, bool const repack_non_ala=true)

	DesignMinimizeHbonds (ScoreFunctionOP scorefxn_repack, ScoreFunctionOP scorefxn_minimize, core::Size const target_residue, bool const donors, bool const acceptors, bool const bb_hbond, bool const sc_hbond, core::Real const hbond_energy_threshold, core::Real interface_distance_cutoff=8.0, bool const repack_partner1=true, bool const repack_partner2=false, bool const repack_non_ala=true)

virtual	~DesignMinimizeHbonds ()

void	apply (Pose &pose)

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

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

protocols::moves::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	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

Public Member Functions inherited from protocols::simple_moves::DesignRepackMover
	DesignRepackMover ()

	DesignRepackMover (std::string const name)

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

void	min_rb (utility::vector1< bool > const min_rb)

void	min_rb (bool const min_rb)
	in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More...

utility::vector1< bool > const &	min_rb () const

bool	min_rb_set () const

void	min_sc (utility::vector1< bool > const &min_sc)

utility::vector1< bool > const &	min_sc () const

bool	min_sc_set () const

void	min_bb (utility::vector1< bool > const &min_bb)

utility::vector1< bool > const &	min_bb () const

bool	min_bb_set () const

bool	optimize_foldtree () const

void	optimize_foldtree (bool const opt)

void	prevent_repacking (utility::vector1< core::Size > const p)

utility::vector1< core::Size > const &	prevent_repacking () const

void	restrict_to_repacking (utility::vector1< core::Size > const p)

utility::vector1< core::Size > const &	restrict_to_repacking () const

void	design (bool const des)

bool	design () const

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

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

core::scoring::ScoreFunctionOP	scorefxn_repack () const

core::scoring::ScoreFunctionOP	scorefxn_minimize () const

core::pack::task::PackerTaskCOP	task () const

core::pack::task::PackerTaskOP &	task ()

void	clear_task ()
	after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More...

void	clear_task_factory ()

void	use_preset_task (bool const bt)

bool	use_preset_task () const

void	task_factory (core::pack::task::TaskFactoryOP p)

core::pack::task::TaskFactoryOP &	task_factory ()

core::pack::task::TaskFactoryOP	task_factory () const

virtual	~DesignRepackMover ()

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)

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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Attributes
bool	donors_

bool	acceptors_

bool	bb_hbond_

bool	sc_hbond_

core::Real	hbond_energy_threshold_

core::Real	interface_distance_cutoff_

Additional Inherited Members
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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 inherited from protocols::simple_moves::DesignRepackMover
core::scoring::ScoreFunctionOP	scorefxn_repack_

core::scoring::ScoreFunctionOP	scorefxn_minimize_

bool	repack_partner1_

bool	repack_partner2_

bool	design_partner1_

bool	design_partner2_

utility::vector1< bool >	min_sc_

utility::vector1< bool >	curr_min_sc_

utility::vector1< bool >	min_rb_

utility::vector1< bool >	min_bb_

utility::vector1< bool >	curr_min_bb_

utility::vector1< bool >	curr_min_rb_

bool	min_rb_set_

bool	min_sc_set_

bool	min_bb_set_

utility::vector1< core::Size >	target_residues_

core::Real	interface_distance_cutoff_

bool	repack_non_ala_

bool	optimize_foldtree_

bool	automatic_repacking_definition_

core::pack::task::PackerTaskOP	task_

bool	use_preset_task_

utility::vector1< bool >	allowed_aas_

utility::vector1< core::Size >	prevent_repacking_

utility::vector1< core::Size >	restrict_to_repacking_

core::pack::task::TaskFactoryOP	task_factory_

bool	symmetry_

Detailed Description

used to design a protein to hbond preferentially to a set of target residues on the partner. Hbonds involving backbone or sidechain on the target can be counted, and whether to design donors or acceptors can also be defined.

Member Typedef Documentation

typedef core::pose::Pose protocols::protein_interface_design::movers::DesignMinimizeHbonds::Pose

typedef core::scoring::ScoreFunction protocols::protein_interface_design::movers::DesignMinimizeHbonds::ScoreFunction

typedef core::scoring::ScoreFunctionCOP protocols::protein_interface_design::movers::DesignMinimizeHbonds::ScoreFunctionCOP

typedef core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::DesignMinimizeHbonds::ScoreFunctionOP

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds ( )

References protocols::simple_moves::DesignRepackMover::automatic_repacking_definition_, protocols::simple_moves::DesignRepackMover::min_bb_set_, protocols::simple_moves::DesignRepackMover::min_rb_set_, protocols::simple_moves::DesignRepackMover::min_sc_set_, and protocols::simple_moves::DesignRepackMover::optimize_foldtree_.

Referenced by clone().

protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds	(	ScoreFunctionCOP	scorefxn_repack,
		ScoreFunctionCOP	scorefxn_minimize,
		utility::vector1< core::Size > const	target_residues,
		bool const	donors,
		bool const	acceptors,
		bool const	bb_hbond,
		bool const	sc_hbond,
		core::Real const	hbond_energy_threshold,
		core::Real	interface_distance_cutoff = `8.0`,
		bool const	repack_partner1 = `true`,
		bool const	repack_partner2 = `false`,
		bool const	repack_non_ala = `true`
	)

References acceptors_, bb_hbond_, donors_, hbond_energy_threshold_, interface_distance_cutoff_, protocols::simple_moves::DesignRepackMover::repack_non_ala_, protocols::simple_moves::DesignRepackMover::repack_partner1_, protocols::simple_moves::DesignRepackMover::repack_partner2_, sc_hbond_, protocols::simple_moves::DesignRepackMover::scorefxn_minimize_, protocols::simple_moves::DesignRepackMover::scorefxn_repack_, and protocols::simple_moves::DesignRepackMover::target_residues_.

protocols::protein_interface_design::movers::DesignMinimizeHbonds::DesignMinimizeHbonds	(	ScoreFunctionOP	scorefxn_repack,
		ScoreFunctionOP	scorefxn_minimize,
		core::Size const	target_residue,
		bool const	donors,
		bool const	acceptors,
		bool const	bb_hbond,
		bool const	sc_hbond,
		core::Real const	hbond_energy_threshold,
		core::Real	interface_distance_cutoff = `8.0`,
		bool const	repack_partner1 = `true`,
		bool const	repack_partner2 = `false`,
		bool const	repack_non_ala = `true`
	)

References acceptors_, bb_hbond_, donors_, hbond_energy_threshold_, interface_distance_cutoff_, protocols::simple_moves::DesignRepackMover::repack_non_ala_, protocols::simple_moves::DesignRepackMover::repack_partner1_, protocols::simple_moves::DesignRepackMover::repack_partner2_, sc_hbond_, protocols::simple_moves::DesignRepackMover::scorefxn_minimize(), protocols::simple_moves::DesignRepackMover::scorefxn_minimize_, protocols::simple_moves::DesignRepackMover::scorefxn_repack(), protocols::simple_moves::DesignRepackMover::scorefxn_repack_, and protocols::simple_moves::DesignRepackMover::target_residues_.

protocols::protein_interface_design::movers::DesignMinimizeHbonds::~DesignMinimizeHbonds ( )

virtual

Member Function Documentation

void protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply ( pose::Pose & pose)

virtual

Residues within a 10.0 Ang sphere around the set of target residues are designed with acceptors or donors (or both) and the design is minimized. All residues that were changed but are not hbonded to the target residues are reverted. If only backbone hbonding is desired all residues except PRO, CYS, and GLY are used in design.

Reimplemented from protocols::simple_moves::DesignRepackMover.

protocols::moves::MoverOP protocols::protein_interface_design::movers::DesignMinimizeHbonds::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Implements protocols::simple_moves::DesignRepackMover.

References DesignMinimizeHbonds().

protocols::moves::MoverOP protocols::protein_interface_design::movers::DesignMinimizeHbonds::fresh_instance ( ) const

inlinevirtual

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).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Implements protocols::simple_moves::DesignRepackMover.

std::string protocols::protein_interface_design::movers::DesignMinimizeHbonds::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::protein_interface_design::movers::DesignMinimizeHbondsCreator::mover_name().

void protocols::protein_interface_design::movers::DesignMinimizeHbonds::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References acceptors_, bb_hbond_, donors_, core::scoring::hbond_bb_sc, hbond_energy_threshold_, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, interface_distance_cutoff_, protocols::simple_moves::DesignRepackMover::parse_my_tag(), sc_hbond_, protocols::simple_moves::DesignRepackMover::scorefxn_minimize_, protocols::simple_moves::DesignRepackMover::scorefxn_repack_, protocols::simple_moves::DesignRepackMover::target_residues_, and protocols::protein_interface_design::movers::TR().

Member Data Documentation

bool protocols::protein_interface_design::movers::DesignMinimizeHbonds::acceptors_

private

Referenced by apply(), DesignMinimizeHbonds(), and parse_my_tag().

bool protocols::protein_interface_design::movers::DesignMinimizeHbonds::bb_hbond_

private

Referenced by apply(), DesignMinimizeHbonds(), and parse_my_tag().

bool protocols::protein_interface_design::movers::DesignMinimizeHbonds::donors_

private

Referenced by apply(), DesignMinimizeHbonds(), and parse_my_tag().

core::Real protocols::protein_interface_design::movers::DesignMinimizeHbonds::hbond_energy_threshold_

private

Referenced by apply(), DesignMinimizeHbonds(), and parse_my_tag().

core::Real protocols::protein_interface_design::movers::DesignMinimizeHbonds::interface_distance_cutoff_

private

Referenced by apply(), DesignMinimizeHbonds(), and parse_my_tag().

bool protocols::protein_interface_design::movers::DesignMinimizeHbonds::sc_hbond_

private

Referenced by apply(), DesignMinimizeHbonds(), and parse_my_tag().

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

src/protocols/protein_interface_design/movers/DesignMinimizeHbonds.hh
src/protocols/protein_interface_design/movers/DesignMinimizeHbonds.cc

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation