wraps protein-interface specific considerations around the general multistate design / genetic algorithm framework More...

#include <ProteinInterfaceMultiStateDesignMover.hh>

Public Types
typedef multistate_design::PosType	PosType

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef utility::pointer::owning_ptr < genetic_algorithm::GeneticAlgorithm >	GeneticAlgorithmOP

Public Types inherited from protocols::simple_moves::PackRotamersMover
typedef core::pack::interaction_graph::InteractionGraphBaseOP	InteractionGraphBaseOP

typedef core::pack::interaction_graph::InteractionGraphBaseCOP	InteractionGraphBaseCOP

typedef core::pack::rotamer_set::RotamerSetsOP	RotamerSetsOP

typedef core::pack::rotamer_set::RotamerSetsCOP	RotamerSetsCOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryCOP	TaskFactoryCOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	ProteinInterfaceMultiStateDesignMover ()

virtual	~ProteinInterfaceMultiStateDesignMover ()

virtual void	apply (Pose &)
	Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More...

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

void	output_results (Pose &)

virtual void	parse_my_tag (TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &)
	parse XML (specifically in the context of the parser/scripting scheme) More...

virtual moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme More...

virtual moves::MoverOP	clone () const
	required in the context of the parser/scripting scheme More...

void	restrict_sequence_profile (core::pose::Pose const &pose, core::pack::task::PackerTaskOP const ptask) const

unsigned long	sequence_space (core::pack::task::PackerTaskCOP ptask) const

void	output_alternative_states (core::pose::Pose const &output_pose) const

Public Member Functions inherited from protocols::simple_moves::PackRotamersMover
	PackRotamersMover ()
	default constructor More...

	PackRotamersMover (std::string const &)
	constructor with typename More...

	PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1)
	Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More...

virtual	~PackRotamersMover ()

	PackRotamersMover (PackRotamersMover const &other)

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

bool	task_is_valid (Pose const &pose) const
	when the PackerTask was not generated locally, verify compatibility with pose More...

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)

virtual void	parse_score_function (TagCOP, basic::datacache::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

virtual void	parse_task_operations (TagCOP, basic::datacache::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...

void	score_function (ScoreFunctionCOP sf)
	Sets the ScoreFunction to <sf> More...

void	task_factory (TaskFactoryCOP tf)
	Sets the TaskFactory to <tf> More...

void	task (PackerTaskCOP t)
	Sets the PackerTask to <t> More...

void	nloop (core::Size nloop_in)

ScoreFunctionCOP	score_function () const
	Returns the ScoreFunction. More...

PackerTaskCOP	task () const
	Returns the PackerTask. More...

core::Size	nloop () const

TaskFactoryCOP	task_factory () const
	Returns the TaskFactory. More...

RotamerSetsCOP	rotamer_sets () const

InteractionGraphBaseCOP	ig () 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	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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	initialize (Pose &)

void	run ()

void	add_states (Pose const &)
	add target and competitor states More...

Private Attributes
GeneticAlgorithmOP	gen_alg_

multistate_design::MultiStatePackerOP	multistate_packer_

core::Size	rb_jump_

core::scoring::ScoreFunctionOP	scorefxn_

core::Size	generations_

core::Size	pop_size_

core::Size	num_packs_

core::Size	pop_from_ss_

core::Size	numresults_

core::Real	fraction_by_recombination_

core::Real	mutate_rate_

core::Real	boltz_temp_

core::Real	anchor_offset_

std::string	checkpoint_prefix_

core::Size	checkpoint_interval_

bool	checkpoint_gz_

bool	checkpoint_rename_

bool	unbound_

bool	unfolded_

bool	input_is_positive_

bool	use_unbound_for_sequence_profile_

core::Real	bump_threshold_

bool	compare_energy_to_ground_state_

utility::vector1 < core::pose::PoseOP >	state_poses_
	states More...

utility::vector1 < core::pose::PoseOP >	saved_state_poses_

utility::vector1< bool >	state_positive_
	for dumping out pdbs of negative states at the end More...

utility::vector1< bool >	state_unfolded_

utility::vector1< bool >	state_unbound_

utility::vector1 < core::pack::task::TaskFactoryCOP >	state_task_factory_

std::string	fname_prefix_

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. More...

Protected Member Functions inherited from protocols::simple_moves::PackRotamersMover
virtual void	setup (Pose &pose)
	get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More...

virtual core::PackerEnergy	run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const

virtual void	note_packertask_settings (Pose const &)
	note PackerTask's packable and designable residues as string info 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...

Detailed Description

wraps protein-interface specific considerations around the general multistate design / genetic algorithm framework

Member Typedef Documentation

typedef utility::pointer::owning_ptr< genetic_algorithm::GeneticAlgorithm > protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::GeneticAlgorithmOP

typedef core::pack::task::PackerTaskCOP protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::PackerTaskCOP

typedef multistate_design::PosType protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::PosType

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::ProteinInterfaceMultiStateDesignMover ( )

References anchor_offset, Boltz_temp, checkpoint, fraction_by_recombination, generations, gz, interval, ms, mutate_rate, num_packs, numresults, option, pop_from_ss, pop_size, prefix, rename, saved_state_poses_, state_poses_, state_positive_, state_unbound_, and state_unfolded_.

Referenced by clone(), and fresh_instance().

protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::~ProteinInterfaceMultiStateDesignMover ( )

virtual

Member Function Documentation

void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::add_states ( Pose const & pose )

private

add target and competitor states

we build one target (bound) and two competitor (unbound and unfolded) states.

References input_is_positive_, multistate_packer_, protocols::protein_interface_design::movers::part_complex(), rb_jump_, runtime_assert, saved_state_poses_, scorefxn_, state_poses_, state_positive_, state_task_factory_, state_unbound_, state_unfolded_, protocols::simple_moves::PackRotamersMover::task_factory(), unbound_, protocols::protein_interface_design::movers::unfold_complex(), unfolded, and unfolded_.

Referenced by initialize().

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

virtual

Performs side-chain packing based on the input PackerTask using the input ScoreFunction.

example(s): packmover.apply(pose) See Also: PackerTask ScoreFunction

Reimplemented from protocols::simple_moves::PackRotamersMover.

References initialize(), output_alternative_states(), output_results(), and run().

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

References ProteinInterfaceMultiStateDesignMover().

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

References ProteinInterfaceMultiStateDesignMover().

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

virtual

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

Reimplemented from protocols::simple_moves::PackRotamersMover.

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

void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize ( Pose & pose )

private

void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_alternative_states ( core::pose::Pose const & output_pose ) const

References core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), core::pose::Pose::dump_scored_pdb(), fname_prefix_, pack_rotamers(), core::pack::task::TaskFactory::push_back(), core::pose::Pose::replace_residue(), resi, core::pose::Pose::residue(), runtime_assert, saved_state_poses_, scorefxn_, state_positive_, protocols::simple_moves::PackRotamersMover::task_factory(), tf, core::pose::Pose::total_residue(), protocols::protein_interface_design::movers::TR, and core::pose::Pose::update_residue_neighbors().

Referenced by apply().

void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_results ( Pose & pose )

References protocols::dna::PDBOutput::add_info(), end, protocols::genetic_algorithm::Entity::fitness(), gen_alg_, protocols::moves::Mover::info(), multistate_packer_, numresults_, option, prefix, protocols::dna::PDBOutput::reference_pose(), protocols::dna::PDBOutput::score_function(), scorefxn_, t_info, protocols::protein_interface_design::movers::TR, protocols::genetic_algorithm::Entity::traits(), and user.

Referenced by apply().

void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap,
		protocols::filters::Filters_map const &	filters,
		moves::Movers_map const &	movers,
		Pose const &	pose
	)

virtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::simple_moves::PackRotamersMover.

References anchor_offset_, boltz_temp_, bump_threshold_, checkpoint_gz_, checkpoint_interval_, checkpoint_prefix_, checkpoint_rename_, compare_energy_to_ground_state_, fname_prefix_, fraction_by_recombination_, generations_, input_is_positive_, mutate_rate_, num_packs_, numresults_, protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), pop_from_ss_, pop_size_, core::import_pose::pose_from_pdb(), rb_jump_, runtime_assert, saved_state_poses_, scorefxn_, state_poses_, state_positive_, state_task_factory_, state_unbound_, state_unfolded_, protocols::simple_moves::PackRotamersMover::task_factory(), tf, protocols::protein_interface_design::movers::TR, unbound_, unfolded, unfolded_, and use_unbound_for_sequence_profile_.

void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTaskOP const	ptask
	)		const

void protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::run ( )

private

References gen_alg_, t_info, and protocols::protein_interface_design::movers::TR.

Referenced by apply().

unsigned long protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::sequence_space ( core::pack::task::PackerTaskCOP ptask ) const

References size().

Referenced by restrict_sequence_profile().

Member Data Documentation

core::Real protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::anchor_offset_

private

Referenced by initialize(), and parse_my_tag().

core::Real protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::boltz_temp_

private

Referenced by initialize(), and parse_my_tag().

core::Real protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::bump_threshold_

private

Referenced by parse_my_tag(), and restrict_sequence_profile().

bool protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::checkpoint_gz_

private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::checkpoint_interval_

private

Referenced by initialize(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::checkpoint_prefix_

private

Referenced by initialize(), and parse_my_tag().

bool protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::checkpoint_rename_

private

Referenced by initialize(), and parse_my_tag().

bool protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::compare_energy_to_ground_state_

private

Referenced by initialize(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::fname_prefix_

private

Referenced by output_alternative_states(), and parse_my_tag().

core::Real protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::fraction_by_recombination_

private

Referenced by initialize(), and parse_my_tag().

GeneticAlgorithmOP protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::gen_alg_

private

Referenced by initialize(), output_results(), and run().

core::Size protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::generations_

private

Referenced by initialize(), and parse_my_tag().

bool protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::input_is_positive_

private

Referenced by add_states(), and parse_my_tag().

multistate_design::MultiStatePackerOP protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::multistate_packer_

private

Referenced by add_states(), initialize(), and output_results().

core::Real protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::mutate_rate_

private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::num_packs_

private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::numresults_

private

Referenced by output_results(), and parse_my_tag().

core::Size protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::pop_from_ss_

private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::pop_size_

private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::rb_jump_

private

Referenced by add_states(), parse_my_tag(), and restrict_sequence_profile().

utility::vector1< core::pose::PoseOP > protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::saved_state_poses_

private

Referenced by add_states(), output_alternative_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::scorefxn_

private

Referenced by add_states(), initialize(), output_alternative_states(), output_results(), parse_my_tag(), and restrict_sequence_profile().

utility::vector1< core::pose::PoseOP > protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::state_poses_

private

states

Referenced by add_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().

utility::vector1< bool > protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::state_positive_

private

for dumping out pdbs of negative states at the end

Referenced by add_states(), output_alternative_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().

utility::vector1< core::pack::task::TaskFactoryCOP > protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::state_task_factory_

private

Referenced by add_states(), and parse_my_tag().

utility::vector1< bool > protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::state_unbound_

private

Referenced by add_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().

utility::vector1< bool > protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::state_unfolded_

private

Referenced by add_states(), parse_my_tag(), and ProteinInterfaceMultiStateDesignMover().

bool protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::unbound_

private

Referenced by add_states(), and parse_my_tag().

bool protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::unfolded_

private

Referenced by add_states(), and parse_my_tag().

bool protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::use_unbound_for_sequence_profile_

private

Referenced by parse_my_tag(), and restrict_sequence_profile().

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

symlinks/rosetta/src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMover.hh
symlinks/rosetta/src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMover.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation