protocols::protein_interface_design::movers::BackrubDDMover Class Reference

#include <BackrubDDMover.hh>

Inheritance diagram for protocols::protein_interface_design::movers::BackrubDDMover:

Collaboration diagram for protocols::protein_interface_design::movers::BackrubDDMover:

Public Types
typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP
typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP
typedef core::pose::Pose	Pose

Public Member Functions
	BackrubDDMover ()
	BackrubDDMover (ScoreFunctionCOP scorefxn, bool const backrub_partner1, bool const backrub_partner2, core::Real const interface_distance_cutoff, core::Size const backrub_moves, core::Real const mc_kt, core::Real const sidechain_move_prob, std::vector< core::Size > const &residues)
void	apply (Pose &pose)
	a dummy apply so that instantiation of this baseclass would be possible. More...
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...
virtual	~BackrubDDMover ()
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

Protected Member Functions
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...

Private Attributes
bool	backrub_partner1_
bool	backrub_partner2_
core::Real	interface_distance_cutoff_
core::Size	backrub_moves_
core::Real	mc_kt_
core::Real	sidechain_move_prob_
core::Real	small_move_prob_
core::Real	bbg_move_prob_
std::vector< core::Size >	residues_

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 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

Definition at line 34 of file BackrubDDMover.hh.

Member Typedef Documentation

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

Definition at line 39 of file BackrubDDMover.hh.

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

Definition at line 37 of file BackrubDDMover.hh.

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

Definition at line 38 of file BackrubDDMover.hh.

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::BackrubDDMover::BackrubDDMover

(

)

Definition at line 115 of file BackrubDDMover.cc.

References residues_.

protocols::protein_interface_design::movers::BackrubDDMover::BackrubDDMover	(	ScoreFunctionCOP	scorefxn,
		bool const	backrub_partner1,
		bool const	backrub_partner2,
		core::Real const	interface_distance_cutoff,
		core::Size const	backrub_moves,
		core::Real const	mc_kt,
		core::Real const	sidechain_move_prob,
		std::vector< core::Size > const &	residues
	)

Definition at line 138 of file BackrubDDMover.cc.

References core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score(), and core::scoring::mm_bend.

protocols::protein_interface_design::movers::BackrubDDMover::~BackrubDDMover ( )

virtual

Definition at line 173 of file BackrubDDMover.cc.

Member Function Documentation

void protocols::protein_interface_design::movers::BackrubDDMover::apply ( Pose &  )

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

Definition at line 181 of file BackrubDDMover.cc.

References protocols::backrub::BackrubMover::add_mainchain_segments(), protocols::simple_moves::BackboneMover::apply(), protocols::backrub::BackrubMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::BBG8T3AMover::apply(), protocols::moves::MonteCarlo::boltzmann(), protocols::backrub::BackrubMover::branchopt(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::backrub::BackrubMover::clear_segments(), core::pose::Pose::conformation(), protocols::simple_moves::BBG8T3AMover::factorA(), protocols::simple_moves::BBG8T3AMover::factorB(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_protein(), protocols::moves::MonteCarlo::lowest_score_pose(), protocols::simple_moves::BBGaussianMover::movemap(), protocols::simple_moves::BackboneMover::movemap(), protocols::simple_moves::BackboneMover::nmoves(), core::conformation::Conformation::num_chains(), protocols::backrub::BackrubMover::num_segments(), protocols::backrub::BackrubMover::optimize_branch_angles(), core::kinematics::FoldTree::partition_by_jump(), protocols::branch_angle::BranchAngleOptimizer::read_database(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::residue(), protocols::moves::Mover::set_input_pose(), protocols::moves::Mover::set_native_pose(), protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_uniform(), protocols::simple_moves::sidechain_moves::SidechainMover::set_task_factory(), protocols::moves::MonteCarlo::show_counters(), core::io::serialization::size(), protocols::protein_interface_design::star_fold_tree(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), core::pose::Pose::total_residue(), protocols::moves::Mover::type(), and protocols::branch_angle::BranchAngleOptimizer::write_database().

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

protocols::moves::MoverOP protocols::protein_interface_design::movers::BackrubDDMover::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.

Definition at line 176 of file BackrubDDMover.cc.

protocols::moves::MoverOP protocols::protein_interface_design::movers::BackrubDDMover::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.

Definition at line 54 of file BackrubDDMover.hh.

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

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

Definition at line 403 of file BackrubDDMover.cc.

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

void protocols::protein_interface_design::movers::BackrubDDMover::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  )

protectedvirtual

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.

Definition at line 407 of file BackrubDDMover.cc.

References core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score(), core::sequence::end, protocols::moves::DataMap::get(), core::pose::get_resnum(), core::scoring::mm_bend, core::pose::parse_resnum(), protocols::rosetta_scripts::parse_task_operations(), and core::pose::Pose::total_residue().

Member Data Documentation

core::Size protocols::protein_interface_design::movers::BackrubDDMover::backrub_moves_

private

Definition at line 62 of file BackrubDDMover.hh.

bool protocols::protein_interface_design::movers::BackrubDDMover::backrub_partner1_

private

Definition at line 59 of file BackrubDDMover.hh.

bool protocols::protein_interface_design::movers::BackrubDDMover::backrub_partner2_

private

Definition at line 60 of file BackrubDDMover.hh.

core::Real protocols::protein_interface_design::movers::BackrubDDMover::bbg_move_prob_

private

Definition at line 66 of file BackrubDDMover.hh.

core::Real protocols::protein_interface_design::movers::BackrubDDMover::interface_distance_cutoff_

private

Definition at line 61 of file BackrubDDMover.hh.

core::Real protocols::protein_interface_design::movers::BackrubDDMover::mc_kt_

private

Definition at line 63 of file BackrubDDMover.hh.

std::vector< core::Size > protocols::protein_interface_design::movers::BackrubDDMover::residues_

private

Definition at line 67 of file BackrubDDMover.hh.

Referenced by BackrubDDMover().

core::Real protocols::protein_interface_design::movers::BackrubDDMover::sidechain_move_prob_

private

Definition at line 64 of file BackrubDDMover.hh.

core::Real protocols::protein_interface_design::movers::BackrubDDMover::small_move_prob_

private

Definition at line 65 of file BackrubDDMover.hh.

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

• src/protocols/protein_interface_design/movers/BackrubDDMover.hh
• src/protocols/protein_interface_design/movers/BackrubDDMover.cc