#include <CanonicalSamplingMover.hh>

Inheritance diagram for protocols::canonical_sampling::CanonicalSamplingMover:

Collaboration diagram for protocols::canonical_sampling::CanonicalSamplingMover:

Public Member Functions
	CanonicalSamplingMover ()

	CanonicalSamplingMover (core::scoring::ScoreFunctionOP sfxn, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP ptr, int ntrial)

void	add_mover (protocols::moves::MoverOP m, core::Real weight)

std::string	get_ABGEO_string (core::pose::Pose &pose, protocols::loops::Loops &loop)

void	ntrials (int ntrial)

void	set_defaults_from_cmdline ()

void	set_temp (core::Real temperature)

core::Real	get_temp ()

void	set_interval_pose_dump (int p_interval)

void	set_interval_data_dump (int d_interval)

void	set_scorefunction (core::scoring::ScoreFunctionOP sfxn)

void	detailed_balance (bool truefalse)

bool	detailed_balance () const

core::Real	transition_threshold () const

void	use_MPI_sync_pools (bool truefalse)

bool	use_MPI_sync_pools () const

void	use_MPI_bcast (bool truefalse)

bool	use_MPI_bcast () const

void	use_hierarchical_clustering (bool truefalse)

bool	use_hierarchical_clustering () const

void	output_only_cluster_transitions (bool truefalse)

void	set_poolrmsd (protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP ptr)

virtual 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::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::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...

Private Member Functions
core::Real	periodic_range (core::Real a, core::Real x)

void	dump_xtc_format_decoy (std::ostream &os, core::pose::Pose const &pose, loops::Loops const &loop_to_dump)

void	dump_decoy_or_score (std::ostream &os, core::pose::Pose const &pose, core::Size i_trial, std::string const &jobname, loops::Loops const &loop_to_dump, bool score_only=false)

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

Static Private Attributes
static bool	options_registered_

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::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

Definition at line 44 of file CanonicalSamplingMover.hh.

Constructor & Destructor Documentation

protocols::canonical_sampling::CanonicalSamplingMover::CanonicalSamplingMover ( )

Definition at line 162 of file CanonicalSamplingMover.cc.

References set_defaults_from_cmdline().

protocols::canonical_sampling::CanonicalSamplingMover::CanonicalSamplingMover	(	core::scoring::ScoreFunctionOP	sfxn,
		protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP	ptr,
		int	ntrial
	)

Definition at line 182 of file CanonicalSamplingMover.cc.

References set_defaults_from_cmdline().

Member Function Documentation

void protocols::canonical_sampling::CanonicalSamplingMover::add_mover	(	protocols::moves::MoverOP	m,
		core::Real	weight
	)

Definition at line 233 of file CanonicalSamplingMover.cc.

References randmove_.

void protocols::canonical_sampling::CanonicalSamplingMover::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 440 of file CanonicalSamplingMover.cc.

References protocols::viewer::add_conformation_viewer(), core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::atom_pair_constraint, boinc_mode_, core::scoring::CA_rmsd(), core::pose::Pose::conformation(), protocols::jd2::JobDistributor::current_job(), protocols::jd2::current_output_name(), detailed_balance_, dump_decoy_or_score(), protocols::swa::rna::file_exists(), get_ABGEO_string(), core::io::silent::SilentStructFactory::get_instance(), protocols::jd2::JobDistributor::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct_in(), core::io::silent::gzip(), core::init(), interval_posedump_, interval_transitiondump_, protocols::jd2::JobDistributor::job_outputter(), protocols::canonical_sampling::jobname_dirhash(), mc_, MPI_bcast_, MPI_synchronize_pools_, protocols::moves::Mover::name(), ntrials_, output_only_cluster_transition_, pool_rms_, core::io::raw_data::precision(), ramp_temperature_, randmove_, core::io::silent::SilentFileData::read_file(), core::io::silent::SilentFileData::read_tags_fast(), core::pose::Pose::remove_constraints(), save_loops_only_, core::io::silent::SilentFileData::set_filename(), setup_constraints(), sfxn_, core::pose::Pose::total_residue(), protocols::canonical_sampling::tr(), transition_threshold_, and use_hierarchical_clustering_.

void protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance ( bool truefalse)

Definition at line 301 of file CanonicalSamplingMover.cc.

References detailed_balance_.

bool protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance ( ) const

inline

Definition at line 74 of file CanonicalSamplingMover.hh.

Referenced by set_defaults_from_cmdline().

void protocols::canonical_sampling::CanonicalSamplingMover::dump_decoy_or_score	(	std::ostream &	os,
		core::pose::Pose const &	pose,
		core::Size	i_trial,
		std::string const &	jobname,
		loops::Loops const &	loop_to_dump,
		bool	score_only = `false`
	)

private

void CanonicalSamplingMover::dump_xtc_format_decoy( std::ostream& os, core::pose::Pose const& pose, loops::Loops const& loop_to_dump ) {

}

Definition at line 373 of file CanonicalSamplingMover.cc.

References protocols::loops::Loops::begin(), boinc_mode_, dump_loops_only_, protocols::loops::Loops::end(), core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), interval_posedump_, interval_transitiondump_, protocols::loops::Loops::num_loop(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by apply().

void protocols::canonical_sampling::CanonicalSamplingMover::dump_xtc_format_decoy	(	std::ostream &	os,
		core::pose::Pose const &	pose,
		loops::Loops const &	loop_to_dump
	)

private

std::string protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string	(	core::pose::Pose &	pose,
		protocols::loops::Loops &	loop
	)

Definition at line 254 of file CanonicalSamplingMover.cc.

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), core::scoring::omega, core::pose::Pose::omega(), periodic_range(), protocols::swa::phi(), core::pose::Pose::phi(), protocols::swa::psi(), and core::pose::Pose::psi().

Referenced by apply().

std::string protocols::canonical_sampling::CanonicalSamplingMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 834 of file CanonicalSamplingMover.cc.

core::Real protocols::canonical_sampling::CanonicalSamplingMover::get_temp ( )

inline

Definition at line 65 of file CanonicalSamplingMover.hh.

void protocols::canonical_sampling::CanonicalSamplingMover::ntrials ( int ntrial)

Definition at line 288 of file CanonicalSamplingMover.cc.

References ntrials_.

Referenced by set_defaults_from_cmdline().

void protocols::canonical_sampling::CanonicalSamplingMover::output_only_cluster_transitions ( bool truefalse)

Definition at line 315 of file CanonicalSamplingMover.cc.

References output_only_cluster_transition_.

Referenced by set_defaults_from_cmdline().

core::Real protocols::canonical_sampling::CanonicalSamplingMover::periodic_range	(	core::Real	a,
		core::Real	x
	)

private

Definition at line 242 of file CanonicalSamplingMover.cc.

Referenced by get_ABGEO_string().

void protocols::canonical_sampling::CanonicalSamplingMover::register_options ( )

static

Definition at line 112 of file CanonicalSamplingMover.cc.

References options_registered_.

void protocols::canonical_sampling::CanonicalSamplingMover::set_defaults_from_cmdline ( )

Definition at line 208 of file CanonicalSamplingMover.cc.

References boinc_mode_, detailed_balance(), dump_loops_only_, ntrials(), options_registered_, output_only_cluster_transitions(), ramp_temperature_, save_loops_only_, set_interval_data_dump(), set_interval_pose_dump(), and transition_threshold_.

Referenced by CanonicalSamplingMover().

void protocols::canonical_sampling::CanonicalSamplingMover::set_interval_data_dump ( int d_interval)

Definition at line 297 of file CanonicalSamplingMover.cc.

References interval_transitiondump_.

Referenced by set_defaults_from_cmdline().

void protocols::canonical_sampling::CanonicalSamplingMover::set_interval_pose_dump ( int p_interval)

Definition at line 295 of file CanonicalSamplingMover.cc.

References interval_posedump_.

Referenced by set_defaults_from_cmdline().

void protocols::canonical_sampling::CanonicalSamplingMover::set_poolrmsd ( protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP ptr)

Definition at line 311 of file CanonicalSamplingMover.cc.

References pool_rms_.

void protocols::canonical_sampling::CanonicalSamplingMover::set_scorefunction ( core::scoring::ScoreFunctionOP sfxn)

Definition at line 299 of file CanonicalSamplingMover.cc.

References sfxn_.

void protocols::canonical_sampling::CanonicalSamplingMover::set_temp ( core::Real temperature)

Definition at line 290 of file CanonicalSamplingMover.cc.

References mc_, sfxn_, and temperature_.

void protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints ( core::pose::Pose & pose)

private

Definition at line 319 of file CanonicalSamplingMover.cc.

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by apply().

core::Real protocols::canonical_sampling::CanonicalSamplingMover::transition_threshold ( ) const

inline

Definition at line 76 of file CanonicalSamplingMover.hh.

void protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering ( bool truefalse)

Definition at line 308 of file CanonicalSamplingMover.cc.

References use_hierarchical_clustering_.

bool protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering ( ) const

inline

Definition at line 85 of file CanonicalSamplingMover.hh.

void protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_bcast ( bool truefalse)

Definition at line 306 of file CanonicalSamplingMover.cc.

References MPI_bcast_.

bool protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_bcast ( ) const

inline

Definition at line 82 of file CanonicalSamplingMover.hh.

void protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_sync_pools ( bool truefalse)

Definition at line 304 of file CanonicalSamplingMover.cc.

References MPI_synchronize_pools_.

bool protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_sync_pools ( ) const

inline

Definition at line 79 of file CanonicalSamplingMover.hh.

Member Data Documentation

bool protocols::canonical_sampling::CanonicalSamplingMover::boinc_mode_

private

Definition at line 136 of file CanonicalSamplingMover.hh.

Referenced by apply(), dump_decoy_or_score(), and set_defaults_from_cmdline().

bool protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance_

private

Definition at line 124 of file CanonicalSamplingMover.hh.

Referenced by apply(), and detailed_balance().

bool protocols::canonical_sampling::CanonicalSamplingMover::dump_loops_only_

private

Definition at line 129 of file CanonicalSamplingMover.hh.

Referenced by dump_decoy_or_score(), and set_defaults_from_cmdline().

core::Size protocols::canonical_sampling::CanonicalSamplingMover::interval_posedump_

private

Definition at line 121 of file CanonicalSamplingMover.hh.

Referenced by apply(), dump_decoy_or_score(), and set_interval_pose_dump().

core::Size protocols::canonical_sampling::CanonicalSamplingMover::interval_transitiondump_

private

Definition at line 122 of file CanonicalSamplingMover.hh.

Referenced by apply(), dump_decoy_or_score(), and set_interval_data_dump().

protocols::moves::MonteCarloOP protocols::canonical_sampling::CanonicalSamplingMover::mc_

private

Definition at line 116 of file CanonicalSamplingMover.hh.

Referenced by apply(), and set_temp().

bool protocols::canonical_sampling::CanonicalSamplingMover::MPI_bcast_

private

Definition at line 126 of file CanonicalSamplingMover.hh.

Referenced by apply(), and use_MPI_bcast().

bool protocols::canonical_sampling::CanonicalSamplingMover::MPI_synchronize_pools_

private

Definition at line 125 of file CanonicalSamplingMover.hh.

Referenced by apply(), and use_MPI_sync_pools().

core::Size protocols::canonical_sampling::CanonicalSamplingMover::ntrials_

private

Definition at line 123 of file CanonicalSamplingMover.hh.

Referenced by apply(), and ntrials().

bool protocols::canonical_sampling::CanonicalSamplingMover::options_registered_

staticprivate

Definition at line 134 of file CanonicalSamplingMover.hh.

Referenced by register_options(), and set_defaults_from_cmdline().

bool protocols::canonical_sampling::CanonicalSamplingMover::output_only_cluster_transition_

private

Definition at line 130 of file CanonicalSamplingMover.hh.

Referenced by apply(), and output_only_cluster_transitions().

protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP protocols::canonical_sampling::CanonicalSamplingMover::pool_rms_

private

Definition at line 119 of file CanonicalSamplingMover.hh.

Referenced by apply(), and set_poolrmsd().

bool protocols::canonical_sampling::CanonicalSamplingMover::ramp_temperature_

private

Definition at line 135 of file CanonicalSamplingMover.hh.

Referenced by apply(), and set_defaults_from_cmdline().

moves::RandomMoverOP protocols::canonical_sampling::CanonicalSamplingMover::randmove_

private

Definition at line 118 of file CanonicalSamplingMover.hh.

Referenced by add_mover(), and apply().

bool protocols::canonical_sampling::CanonicalSamplingMover::save_loops_only_

private

Definition at line 128 of file CanonicalSamplingMover.hh.

Referenced by apply(), and set_defaults_from_cmdline().

core::scoring::ScoreFunctionOP protocols::canonical_sampling::CanonicalSamplingMover::sfxn_

private

Definition at line 117 of file CanonicalSamplingMover.hh.

Referenced by apply(), set_scorefunction(), and set_temp().

core::Real protocols::canonical_sampling::CanonicalSamplingMover::temperature_

private

Definition at line 132 of file CanonicalSamplingMover.hh.

Referenced by set_temp().

core::Real protocols::canonical_sampling::CanonicalSamplingMover::transition_threshold_

private

Definition at line 131 of file CanonicalSamplingMover.hh.

Referenced by apply(), and set_defaults_from_cmdline().

bool protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering_

private

Definition at line 127 of file CanonicalSamplingMover.hh.

Referenced by apply(), and use_hierarchical_clustering().

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

src/protocols/canonical_sampling/CanonicalSamplingMover.hh
src/protocols/canonical_sampling/CanonicalSamplingMover.cc

Private Attributes
protocols::moves::MonteCarloOP	mc_

core::scoring::ScoreFunctionOP	sfxn_

moves::RandomMoverOP	randmove_

protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP	pool_rms_

core::Size	interval_posedump_

core::Size	interval_transitiondump_

core::Size	ntrials_

bool	detailed_balance_

bool	MPI_synchronize_pools_

bool	MPI_bcast_

bool	use_hierarchical_clustering_

bool	save_loops_only_

bool	dump_loops_only_

bool	output_only_cluster_transition_

core::Real	transition_threshold_

core::Real	temperature_

bool	ramp_temperature_

bool	boinc_mode_

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation