#include <ddG.hh>

Inheritance diagram for protocols::simple_moves::ddG:

Collaboration diagram for protocols::simple_moves::ddG:

Public Types
typedef core::Real	Real

typedef core::scoring::ScoreType	ScoreType

typedef core::pose::Pose	Pose

Public Member Functions
	ddG ()

	ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump=1, bool const symmetry=false)

	ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump, utility::vector1< core::Size > const &chain_ids, bool const symmetry)

virtual void	apply (Pose &pose)
	a dummy apply so that instantiation of this baseclass would be possible. More...

void	calculate (Pose const &pose_in)
	compute the energy of the repacked complex in the bound and unbound states More...

void	symm_ddG (core::pose::Pose &pose_in)

void	no_repack_ddG (core::pose::Pose &pose_in)

void	report_ddG (std::ostream &out) const

Real	sum_ddG () const

core::Size	rb_jump () const

void	rb_jump (core::Size j)

core::Size	repeats () const

void	repeats (core::Size repeats)

virtual	~ddG ()

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...

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

void	parse_my_tag (utility::tag::TagPtr const, 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...

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

protocols::moves::MoverOP	relax_mover () const

void	relax_mover (protocols::moves::MoverOP m)

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

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

void	use_custom_task (bool uct)

bool	use_custom_task () const

void	repack_bound (bool rpb)

bool	repack_bound () const

void	relax_bound (bool rlb)

bool	relax_bound () const

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

Static Public Attributes
static const Real	DEFAULT_TRANSLATION_DISTANCE = 100.0

Private Member Functions
void	fill_energy_vector (Pose const &pose, std::map< ScoreType, Real > &energy_map)

void	fill_per_residue_energy_vector (Pose const &pose, std::map< Size, Real > &energy_map)

Private Attributes
std::map< ScoreType, Real >	bound_energies_

std::map< ScoreType, Real >	unbound_energies_

std::map< Size, Real >	bound_per_residue_energies_

std::map< Size, Real >	unbound_per_residue_energies_

Real	bound_total_energy_

Real	unbound_total_energy_

Size	repeats_

core::scoring::ScoreFunctionOP	scorefxn_

core::Size	rb_jump_

utility::vector1< core::Size >	chain_ids_

bool	symmetry_

bool	per_residue_ddg_

bool	repack_

protocols::moves::MoverOP	relax_mover_

core::pack::task::TaskFactoryOP	task_factory_

bool	use_custom_task_

bool	repack_bound_

bool	relax_bound_

core::scoring::methods::PBLifetimeCacheOP	pb_cached_data_
	info carrier for poisson-boltzmann potential energy computation More...

bool	pb_enabled_
	true when PB potential is part of scorefxn More...

Real	translate_by_
	distance in A to separate moledules More...

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_

Member Typedef Documentation

typedef core::pose::Pose protocols::simple_moves::ddG::Pose

typedef core::Real protocols::simple_moves::ddG::Real

typedef core::scoring::ScoreType protocols::simple_moves::ddG::ScoreType

Constructor & Destructor Documentation

protocols::simple_moves::ddG::ddG ( )

References bound_energies_, bound_per_residue_energies_, unbound_energies_, and unbound_per_residue_energies_.

Referenced by clone(), and fresh_instance().

protocols::simple_moves::ddG::ddG	(	core::scoring::ScoreFunctionCOP	scorefxn_in,
		core::Size const	jump = `1`,
		bool const	symmetry = `false`
	)

References bound_energies_, bound_per_residue_energies_, core::scoring::PB_elec, pb_enabled_, scorefxn_, protocols::simple_moves::TR(), unbound_energies_, and unbound_per_residue_energies_.

protocols::simple_moves::ddG::ddG	(	core::scoring::ScoreFunctionCOP	scorefxn_in,
		core::Size const	jump,
		utility::vector1< core::Size > const &	chain_ids,
		bool const	symmetry
	)

References bound_energies_, bound_per_residue_energies_, chain_ids_, core::scoring::PB_elec, pb_enabled_, scorefxn_, protocols::simple_moves::TR(), unbound_energies_, and unbound_per_residue_energies_.

protocols::simple_moves::ddG::~ddG ( )

virtual

Member Function Documentation

void protocols::simple_moves::ddG::apply ( Pose & )

virtual

a dummy apply so that instantiation of this baseclass would be possible.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References bound_per_residue_energies_, calculate(), protocols::nonlocal::current_job(), core::pose::Pose::data(), protocols::jd2::JobDistributor::get_instance(), core::pose::Pose::n_residue(), pb_cached_data_, per_residue_ddg_, repeats_, report_ddG(), scorefxn_, sum_ddG(), protocols::simple_moves::TR(), and unbound_per_residue_energies_.

void protocols::simple_moves::ddG::calculate ( pose::Pose const & pose_original)

compute the energy of the repacked complex in the bound and unbound states

Parameters

pose_in The base pose.

Returns: Nothing, but the base pose's cache be augmented with extra cached data if the scorefunction contains non-zero PB_elec term.

References core::pack::task::operation::RestrictToInterface::add_jump(), core::pack::task::operation::RestrictToRepacking::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::RestrictToInterface::apply(), bound_energies_, bound_per_residue_energies_, chain_ids_, core::pack::task::TaskFactory::create_packer_task(), protocols::simple_moves::DesignRepackMover::design_partner1_, protocols::simple_moves::DesignRepackMover::design_partner2_, fill_energy_vector(), fill_per_residue_energy_vector(), core::pose::get_jump_id_from_chain_id(), core::pose::symmetry::is_symmetric(), no_repack_ddG(), core::pack::pack_rotamers(), pb_cached_data_, pb_enabled_, per_residue_ddg_, rb_jump_, relax_bound(), relax_mover(), repack_, repack_bound(), protocols::simple_moves::DesignRepackMover::repack_partner1_, protocols::simple_moves::DesignRepackMover::repack_partner2_, scorefxn_, symm_ddG(), protocols::simple_moves::DesignRepackMover::task_, protocols::swa::translate(), translate_by_, unbound_energies_, and unbound_per_residue_energies_.

Referenced by apply(), protocols::simple_filters::DdgFilter::compute(), and ddG_cycles().

protocols::moves::MoverOP protocols::simple_moves::ddG::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 ddG().

void protocols::simple_moves::ddG::fill_energy_vector	(	pose::Pose const &	pose,
		std::map< ScoreType, Real > &	energy_map
	)

private

a private function for storing energy values

References core::pose::Pose::energies(), core::scoring::n_score_types, core::scoring::pro_close, scorefxn_, and core::scoring::Energies::total_energies().

Referenced by calculate(), no_repack_ddG(), and symm_ddG().

void protocols::simple_moves::ddG::fill_per_residue_energy_vector	(	pose::Pose const &	pose,
		std::map< Size, Real > &	energy_map
	)

private

References core::pose::Pose::energies(), core::scoring::n_score_types, core::scoring::pro_close, core::scoring::Energies::residue_total_energies(), scorefxn_, and core::pose::Pose::total_residue().

Referenced by calculate(), no_repack_ddG(), and symm_ddG().

protocols::moves::MoverOP protocols::simple_moves::ddG::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.

References ddG().

std::string protocols::simple_moves::ddG::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

void protocols::simple_moves::ddG::no_repack_ddG ( core::pose::Pose & pose_in)

References bound_energies_, bound_per_residue_energies_, chain_ids_, fill_energy_vector(), fill_per_residue_energy_vector(), core::pose::get_jump_id_from_chain_id(), pb_cached_data_, pb_enabled_, per_residue_ddg_, rb_jump_, relax_mover(), scorefxn_, protocols::swa::translate(), translate_by_, unbound_energies_, and unbound_per_residue_energies_.

Referenced by calculate().

void protocols::simple_moves::ddG::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 chain_ids_, DEFAULT_TRANSLATION_DISTANCE, protocols::moves::DataMap::get(), core::pose::get_chain_id_from_chain(), protocols::rosetta_scripts::parse_task_operations(), core::scoring::PB_elec, pb_enabled_, per_residue_ddg_, rb_jump_, relax_bound_, repack_, repack_bound_, repeats_, scorefxn_, symmetry_, task_factory(), protocols::simple_moves::TR(), translate_by_, and use_custom_task().

core::Size protocols::simple_moves::ddG::rb_jump ( ) const

inline

References rb_jump_.

void protocols::simple_moves::ddG::rb_jump ( core::Size j)

inline

References rb_jump_.

void protocols::simple_moves::ddG::relax_bound ( bool rlb)

inline

References relax_bound_.

Referenced by protocols::simple_filters::DdgFilter::compute().

bool protocols::simple_moves::ddG::relax_bound ( ) const

inline

References relax_bound_.

Referenced by calculate(), and symm_ddG().

protocols::moves::MoverOP protocols::simple_moves::ddG::relax_mover ( ) const

inline

References relax_mover_.

Referenced by calculate(), protocols::simple_filters::DdgFilter::compute(), no_repack_ddG(), and symm_ddG().

void protocols::simple_moves::ddG::relax_mover ( protocols::moves::MoverOP m)

inline

References relax_mover_.

void protocols::simple_moves::ddG::repack_bound ( bool rpb)

inline

References repack_bound_.

Referenced by protocols::simple_filters::DdgFilter::compute().

bool protocols::simple_moves::ddG::repack_bound ( ) const

inline

References repack_bound_.

Referenced by calculate(), and symm_ddG().

core::Size protocols::simple_moves::ddG::repeats ( ) const

inline

References repeats_.

void protocols::simple_moves::ddG::repeats ( core::Size repeats)

inline

References repeats(), and repeats_.

Referenced by repeats().

void protocols::simple_moves::ddG::report_ddG ( std::ostream & out) const

output the ddG values

References bound_energies_, sum_ddG(), and unbound_energies_.

Referenced by apply(), and protocols::simple_filters::DdgFilter::compute().

Real protocols::simple_moves::ddG::sum_ddG ( ) const

returns the total ddG

References bound_energies_, and unbound_energies_.

Referenced by apply(), protocols::simple_filters::DdgFilter::compute(), ddG_cycles(), and report_ddG().

void protocols::simple_moves::ddG::symm_ddG ( core::pose::Pose & pose_in)

void protocols::simple_moves::ddG::task_factory ( core::pack::task::TaskFactoryOP task_factory)

inline

References task_factory(), and task_factory_.

Referenced by protocols::simple_filters::DdgFilter::compute(), and task_factory().

core::pack::task::TaskFactoryOP protocols::simple_moves::ddG::task_factory ( ) const

inline

References task_factory_.

Referenced by parse_my_tag().

void protocols::simple_moves::ddG::use_custom_task ( bool uct)

inline

References use_custom_task_.

Referenced by protocols::simple_filters::DdgFilter::compute().

bool protocols::simple_moves::ddG::use_custom_task ( ) const

inline

References use_custom_task_.

Referenced by parse_my_tag(), and symm_ddG().

Member Data Documentation

std::map< ScoreType, Real > protocols::simple_moves::ddG::bound_energies_

private

Referenced by calculate(), ddG(), no_repack_ddG(), report_ddG(), sum_ddG(), and symm_ddG().

std::map< Size, Real > protocols::simple_moves::ddG::bound_per_residue_energies_

private

Referenced by apply(), calculate(), ddG(), no_repack_ddG(), and symm_ddG().

Real protocols::simple_moves::ddG::bound_total_energy_

private

utility::vector1<core::Size> protocols::simple_moves::ddG::chain_ids_

private

Referenced by calculate(), ddG(), no_repack_ddG(), and parse_my_tag().

const Real protocols::simple_moves::ddG::DEFAULT_TRANSLATION_DISTANCE = 100.0

static

Distance in A to separate the molecules away from bound-state. NOTES by Sachko Honda: This value used to be hard coded to 1000 for unbound poses, whereas the default 100 was used for bounded. The choice of value 1000 was arbitrary by the original author. The value is now reduced to 100 in order to help the PDE solver (APBS) from blowing up, by default, but can be a user-defined value via RosettaScript option or command-line option.

Referenced by parse_my_tag().

core::scoring::methods::PBLifetimeCacheOP protocols::simple_moves::ddG::pb_cached_data_

private

info carrier for poisson-boltzmann potential energy computation

Referenced by apply(), calculate(), no_repack_ddG(), and symm_ddG().