#include <GenericMonteCarloMover.hh>

Inheritance diagram for protocols::monte_carlo::GenericMonteCarloMover:

Public Types
typedef std::string	String

typedef core::Size	Size

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef protocols::filters::FilterOP	FilterOP

typedef protocols::moves::MoverOP	MoverOP

typedef core::pack::task::PackerTask	PackerTask

typedef core::pack::task::PackerTaskOP	PackerTaskOP

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

typedef core::pack::task::TaskFactoryOP	TaskFactoryOP

typedef protocols::rosetta_scripts::ParsedProtocolOP	ParsedProtocolOP

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef protocols::filters::Filters_map	Filters_map

typedef protocols::moves::Movers_map	Movers_map

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
	GenericMonteCarloMover ()
	default constructor More...

	GenericMonteCarloMover (Size const maxtrials, Size const max_accepted_trials, Size const task_scaling, MoverOP const &mover, Real const temperature=0.0, String const &sample_type="low", bool const drift=true)
	value constructor without score function More...

	GenericMonteCarloMover (Size const maxtrials, Size const max_accepted_trials, Size const task_scaling, MoverOP const &mover, TaskFactoryOP factory_in, Real const temperature=0.0, String const &sample_type="low", bool const drift=true)
	value constructor with score function More...

	~GenericMonteCarloMover () override
	destructor More...

MoverOP	clone () const override
	create copy constructor More...

MoverOP	fresh_instance () const override
	create this type of objectt More...

void	initialize ()
	initialize object used in constructor More...

void	apply (Pose &pose) override
	apply GenericMonteCarloMover (Mover) More...

void	reset (Pose &pose)
	reset MC iterations, with pose used for the last & best structures More...

void	recover_low (Pose &pose)
	return the simulation state to the lowest energy structure we've seen More...

bool	boltzmann (Pose &pose)
	core of MC More...

virtual bool	boltzmann (Pose &pose, utility::vector1< core::Real > const &random_nums)
	core of MC – evaulates a pose based on the scores/filters + temperatures. random_num is a vector of random numbers between 0 and 1 with size equal to the number of MC criteria More...

void	accept (Pose &pose, utility::vector1< core::Real > const &provisional_scores, protocols::moves::MCA const mca_status)
	Does what the mover needs to do when a pose is accepted, given a pose and scores. More...

Size	num_designable (Pose &pose, PackerTaskOP &task)

PoseOP	last_accepted_pose () const
	return the last accepted pose More...

Real	last_accepted_score () const
	return the last accepted score More...

PoseOP	lowest_score_pose () const
	return the lowest score pose More...

Real	lowest_score () const
	return the lowest score More...

Real	current_score () const
	return the lowest score More...

protocols::moves::MCA	mc_accpeted () const
	return mc_accepted More...

ScoreFunctionOP	score_function () const
	Return the score function in use. More...

Size	add_trigger (const GenericMonteCarloMoverTrigger &trigger)
	Adds a new trigger, returning its id. More...

Size	num_triggers () const
	Returns the number of triggers. More...

Size	maxtrials () const
	Returns maximum number of trials. More...

Size	max_accepted_trials () const
	Returns maximum number of accepted trials. More...

Size	task_scaling () const
	Returns the task scaling value. More...

void	remove_trigger (Size trigger_id)
	Removes the trigger with the specified id. More...

void	set_maxtrials (Size const ntrial)
	set max trials of MC trials More...

void	set_max_accepted_trials (Size const n_max_accepted_trial)
	set max accepted trials of MC trials More...

void	set_task_scaling (Size const scaling)
	set task multiplier to calculate trials from task More...

void	set_mover (MoverOP mover) override
	set mover More...

void	set_scorefxn (ScoreFunctionOP const &sfxn)
	Pose is evaluated by ScoreFunctionOP during MC trials. More...

void	set_temperature (Real const temp)
	set temperature More...

void	set_sampletype (String const &type)
	set sample type, max or min when sample_type == max, sample pose which have higher score when sample_type == min, sample pose which have lower score More...

void	set_drift (bool const drift)
	if drift=false, the pose is set back to the initial pose at each MC trial Of course, this is not MC sampling. More...

void	set_stop_sampling (bool const stop_sampling)
	if set to true, the MC mover will stop sampling More...

void	set_preapply (bool const preapply=false)
	if preapply=true, auto-accept the first application of the submover, ignoring boltzman criteria. More...

void	set_recover_low (bool const recover_low)
	if recover_low=true, after apply() the structure is the lowest energy structure, rather than the last accepted structure. More...

void	set_boltz_rank (bool const boltz_rank)
	if boltz_rank=true, rank structures by the temperature-weighted sum of scores, rather than a single filter More...

void	show_scores (std::ostream &out) const
	show scores of last_accepted_score and "best_score" ( = flip_sign_ * lowest_score ) More...

void	show_counters (std::ostream &out) const
	show counters of ntrial and acceptance ratio More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &) override
	parse xml file More...

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

void	add_filter (FilterOP filter, bool const adaptive, Real const temp, String const &sample_type, bool rank_by=false)
	set filter Pose is evaluated by FilterOP which can do report_sm() or ScoreFunctionOP during MC trials You can choose either way FilterOP or ScoreFunction. More...

void	stopping_condition (protocols::filters::FilterOP filter)

protocols::filters::FilterOP	stopping_condition () const

void	adaptive_movers (bool const a)

bool	adaptive_movers () const

void	adaptation_period (core::Size const a)

core::Size	adaptation_period () const

std::string	saved_accept_file_name () const

void	saved_accept_file_name (std::string const )

std::string	saved_trial_number_file () const

void	saved_trial_number_file (std::string const )

core::Size	load_trial_number_from_checkpoint (core::pose::Pose &)

void	save_trial_number_to_checkpoint (core::Size const i) const

void	reset_baselines (bool const r)

bool	reset_baselines () const

void	set_keep_filters (bool const k)

bool	keep_filters () const

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

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

Size	trial_counter () const

void	trial_counter (core::Size const i)

Size	accept_counter () const

utility::vector1< Real >	temperatures () const

void	temperatures (utility::vector1< Real > const &temps)

bool	recover_low () const

MoverOP	mover () const override

utility::vector1< FilterOP > const &	filters () const

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

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

ScoreFunctionOP	scorefxn () const

utility::pointer::shared_ptr < basic::datacache::DataMapObj < bool > >	mover_stopping_condition () const

bool	preapply () const

bool	drift () const

bool	stop_sampling () const

bool	boltz_rank () const

utility::vector1< String > const &	sample_types () const

utility::vector1< core::Real > const &	last_accepted_scores () const

void	last_accepted_scores (utility::vector1< core::Real > const &scores)

utility::vector1< core::Real > const &	last_tested_scores () const

utility::vector1< core::Real > const &	lowest_scores () const

void	lowest_scores (utility::vector1< core::Real > const &scores)

void	lowest_score (core::Real const score)

void	last_accepted_score (core::Real const score)

void	lowest_score_pose (core::pose::PoseOP pose)
	Set the lowest scoring pose. More...

void	last_accepted_pose (core::pose::PoseOP pose)
	Set the last pose that was accepted. More...

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

bool	mover_provides_citation_info () const override
	This mover provides citation info (returns true). More...

utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const override
	Provide the citation (Fleishman 2011). More...

utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const override
	Provides unpublished citation info for any unpublished movers and filters that this mover invokes. More...

Public Member Functions inherited from protocols::moves::MoverApplyingMover
	MoverApplyingMover (std::string const &name)

	MoverApplyingMover (MoverApplyingMover const &)=default

	~MoverApplyingMover () override=default

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

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

virtual core::Real	last_proposal_density_ratio ()

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	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static utility::tag::XMLSchemaComplexTypeGeneratorOP	define_composition_schema (utility::tag::XMLSchemaDefinition &)

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
Real	scoring (Pose &pose)
	evalute pose by ScoreFunctionOP or FilterOP More...

void	fire_all_triggers (Size cycle, Size num_cycles, const Pose &pose, ScoreFunctionOP scoring)
	Executes all triggers. The order of trigger execution is undefined. Do not assume, depend, or in any way rely on a particular ordering. More...

utility::vector1< core::Real >	generate_random () const
	generate a set of random numbers to accompany the filters or scorefxn More...

std::string	progress_file () const

void	progress_file (std::string const &s)

void	set_mc_accepted (moves::MCA const m)
	Sets mc_accpeted. 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
int	trial_counter_ = 0

utility::vector1< core::Size >	num_rejections_
	Count the number of rejections each filter resulted in. More...

Private Types
typedef protocols::moves::MoverApplyingMover	Super

Private Attributes
Size	maxtrials_ = 10
	max number of MC trials More...

Size	max_accepted_trials_ = 0
	max number of accepted MC trials More...

Size	number_designable_ = 0
	number of designable positions More...

Size	task_scaling_ = 5
	multiply the number_designable_ by task_scaling to get the number of trials More...

MoverOP	mover_
	mover More...

PackerTaskOP	task_
	task More...

TaskFactoryOP	factory_
	task factory More...

utility::vector1< FilterOP >	filters_
	Pose is evaluated by FilterOP which can do report_sm() during MC trials. More...

utility::vector1< bool >	adaptive_

utility::vector1< Real >	temperatures_
	acceptance criterion temperature, per temperature More...

utility::vector1< String >	sample_types_
	low/high, dflt low More...

utility::vector1< Real >	last_accepted_scores_

utility::vector1< Real >	lowest_scores_
	best filter scores More...

utility::vector1< Real >	last_tested_scores_

ScoreFunctionOP	scorefxn_
	Pose is evaluated by ScoreFunctionOP during MC trials. More...

Real	temperature_ = 0.0
	acceptance criterion temperature More...

String	sample_type_ = "low"
	set sample type, max or min when sample_type == "high", sample pose which have higher score when sample_type == "low", sample pose which have lower score More...

bool	drift_ = true
	if drift=false, the pose is set back to the initial pose at each MC trial Of course, this is not MC sampling. More...

bool	stop_sampling_ = false
	if set to true, the MC mover will stop sampling More...

bool	preapply_ = true
	Should we apply (and accept) the first application of the mover regardless of boltzman criteria? (Defaults true for historical reasons.) More...

bool	recover_low_ = true
	At the end of application, is the structure the last accepted structure (recover_low_==false) or is it the lowest energy structure (recover_low_=true) More...

Size	rank_by_filter_ = 1
	By which filter (by index) are poses ranked by for non-Boltzman purposes (e.g. recover_low()) More...

bool	boltz_rank_ = false
	If boltz_rank_=true, instead of ranking by a single filter, rank by the temperature-weighted sum of all scores. More...

Real	current_score_ = 0.0
	current More...

Real	last_accepted_score_ = 0.0
	accepted structure More...

Real	lowest_score_ = 0.0
	lowest energy structure we've seen More...

PoseOP	last_accepted_pose_
	accepted structure More...

PoseOP	lowest_score_pose_
	lowest energy structure we've seen More...

moves::MCA	mc_accepted_ = moves::MCA_accepted_score_beat_last
	result of the last call to boltzmann More...

Real	flip_sign_ = 1
	to change the sing of calculated "score" More...

int	accept_counter_ = 0
	diagnostics More...

Real	energy_gap_counter_ = 0.0

Size	next_trigger_id_ = 1
	Next trigger identifier to be assigned. More...

boost::unordered_map< Size, GenericMonteCarloMoverTrigger >	triggers_
	Collection of function callbacks. More...

protocols::filters::FilterOP	stopping_condition_
	dflt false_filter; use this to stop an MC trajectory before maxtrials_ (if filter evaluates to true) More...

utility::pointer::shared_ptr < basic::datacache::DataMapObj < bool > >	mover_stopping_condition_
	dflt NULL; if the mover defined a stopping condition on the datamap then this assumes the mover's value. In this way, the Mover can tell GenericMC to stop execution, e.g., if it has iterated over all internal possibilities More...

bool	adaptive_movers_ = false
	change the mover probabilities according to the accept rates?; only works if the mover is a ParsedProtocol type with mode=single_random More...

core::Size	adaptation_period_ = 0
	dflt max( 10, trials/10 ); only works with adaptive; how often should the run probabilities be adapted? More...

std::string	saved_accept_file_name_
	dflt ""; if a file name is specified, after each accept a pdb file is dumped to disk. This is useful for checkpointing More...

std::string	saved_trial_number_file_
	dflt ""; if specified checkpoints the current trial number and recovers from it More...

utility::pointer::shared_ptr < basic::datacache::DataMapObj < std::string > >	mover_tag_
	dflt NULL; this is used by the called movers to set a certain tag. If saved_accept_file_name_ is set, then at exit the tag coming from the chosen mover is written to disk as, <saved_accept_file_name>.mover_tag. To work, mover_tag_ must be exposed to the movers being called. More...

std::string	user_defined_mover_name_
	dflt ""; the mover being called by GenericMC. Used to add values to the poses DataCache. More...

bool	reset_baselines_ = true
	reset the filters' baseline at trial=1? More...

bool	keep_filters_ = false
	avoid clearing filters if a score function is given. Used in the EvolutionDynamicsMover which inherits from genericMCmover. More...

std::string	progress_file_
	a file name where data on each step is saved. More...

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::monte_carlo::GenericMonteCarloMover::DataMap

typedef protocols::filters::FilterOP protocols::monte_carlo::GenericMonteCarloMover::FilterOP

typedef protocols::filters::Filters_map protocols::monte_carlo::GenericMonteCarloMover::Filters_map

typedef protocols::moves::MoverOP protocols::monte_carlo::GenericMonteCarloMover::MoverOP

typedef protocols::moves::Movers_map protocols::monte_carlo::GenericMonteCarloMover::Movers_map

typedef core::pack::task::PackerTask protocols::monte_carlo::GenericMonteCarloMover::PackerTask

typedef core::pack::task::PackerTaskCOP protocols::monte_carlo::GenericMonteCarloMover::PackerTaskCOP

typedef core::pack::task::PackerTaskOP protocols::monte_carlo::GenericMonteCarloMover::PackerTaskOP

typedef protocols::rosetta_scripts::ParsedProtocolOP protocols::monte_carlo::GenericMonteCarloMover::ParsedProtocolOP

typedef core::pose::Pose protocols::monte_carlo::GenericMonteCarloMover::Pose

typedef core::pose::PoseOP protocols::monte_carlo::GenericMonteCarloMover::PoseOP

typedef core::Real protocols::monte_carlo::GenericMonteCarloMover::Real

typedef core::scoring::ScoreFunction protocols::monte_carlo::GenericMonteCarloMover::ScoreFunction

typedef core::scoring::ScoreFunctionOP protocols::monte_carlo::GenericMonteCarloMover::ScoreFunctionOP

typedef core::Size protocols::monte_carlo::GenericMonteCarloMover::Size

typedef std::string protocols::monte_carlo::GenericMonteCarloMover::String

typedef protocols::moves::MoverApplyingMover protocols::monte_carlo::GenericMonteCarloMover::Super

private

typedef utility::tag::TagCOP protocols::monte_carlo::GenericMonteCarloMover::TagCOP

typedef core::pack::task::TaskFactoryOP protocols::monte_carlo::GenericMonteCarloMover::TaskFactoryOP

Constructor & Destructor Documentation

protocols::monte_carlo::GenericMonteCarloMover::GenericMonteCarloMover ( )

default constructor

References initialize().

protocols::monte_carlo::GenericMonteCarloMover::GenericMonteCarloMover	(	Size const	maxtrials,
		Size const	max_accepted_trials,
		Size const	task_scaling,
		MoverOP const &	mover,
		Real const	temperature = `0.0`,
		String const &	sample_type = `"low"`,
		bool const	drift = `true`
	)

value constructor without score function

value constructor without a score function

References initialize().

protocols::monte_carlo::GenericMonteCarloMover::GenericMonteCarloMover	(	Size const	maxtrials,
		Size const	max_accepted_trials,
		Size const	task_scaling,
		MoverOP const &	mover,
		TaskFactoryOP	factory_in,
		Real const	temperature = `0.0`,
		String const &	sample_type = `"low"`,
		bool const	drift = `true`
	)

value constructor with score function

value constructor with a TaskFactory

value constructor with task operation via TaskFactory

References initialize().

protocols::monte_carlo::GenericMonteCarloMover::~GenericMonteCarloMover ( )

overridedefault

destructor

Member Function Documentation

void protocols::monte_carlo::GenericMonteCarloMover::accept	(	Pose &	pose,
		utility::vector1< core::Real > const &	provisional_scores,
		protocols::moves::MCA const	mca_status
	)

Does what the mover needs to do when a pose is accepted, given a pose and scores.

References accept_counter_, core::pose::add_comment(), boltz_rank_, core::pose::Pose::dump_pdb(), energy_gap_counter_, filters_, last_accepted_pose_, last_accepted_score(), last_accepted_score_, last_accepted_scores_, lowest_score(), lowest_score_, lowest_score_pose_, lowest_scores_, mc_accepted_, protocols::moves::MCA_accepted_score_beat_low, mover_tag_, core::io::mmtf::pdb_comments, rank_by_filter_, saved_accept_file_name_, temperatures_, protocols::TR(), and user_defined_mover_name_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), apply(), protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), and boltzmann().

Size protocols::monte_carlo::GenericMonteCarloMover::accept_counter ( ) const

inline

References accept_counter_.

void protocols::monte_carlo::GenericMonteCarloMover::adaptation_period ( core::Size const a )

inline

References core::pose::motif::a(), and adaptation_period_.

core::Size protocols::monte_carlo::GenericMonteCarloMover::adaptation_period ( ) const

inline

References adaptation_period_.

Referenced by apply(), and parse_my_tag().

utility::vector1< bool > const& protocols::monte_carlo::GenericMonteCarloMover::adaptive ( ) const

inline

References adaptive_.

Referenced by boltzmann(), and parse_my_tag().

void protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers ( bool const a )

inline

References core::pose::motif::a(), and adaptive_movers_.

bool protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers ( ) const

inline

References adaptive_movers_.

Referenced by apply(), and parse_my_tag().

void protocols::monte_carlo::GenericMonteCarloMover::add_filter	(	FilterOP	filter,
		bool const	adaptive,
		Real const	temp,
		String const &	sample_type,
		bool	rank_by = `false`
	)

set filter Pose is evaluated by FilterOP which can do report_sm() or ScoreFunctionOP during MC trials You can choose either way FilterOP or ScoreFunction.

References adaptive_, filters_, last_accepted_scores_, num_rejections_, rank_by_filter_, sample_types_, scorefxn_, and temperatures_.

Referenced by parse_my_tag().

Size protocols::monte_carlo::GenericMonteCarloMover::add_trigger ( const GenericMonteCarloMoverTrigger & trigger )

Adds a new trigger, returning its id.

Example: #include <functional>

bool no_op(core::Size stage, core::Size num_stages, core::Size cycle, core::Size num_cycles, const core::pose::Pose&, core::scoring::ScoreFunctionOP) {}

Trigger callback = std::bind(&no_op, STAGE, NUM_STAGES, _1, _2, _3, _4); Size trigger_id = add_trigger(callback);

The current stage and number of stages must be bound at creation time. This information provides the triggers with context about the current progress of the simulation as a whole.

If the trigger returns true, rescoring occurs.

References next_trigger_id_, and triggers_.

void protocols::monte_carlo::GenericMonteCarloMover::apply ( Pose & pose )

overridevirtual

apply GenericMonteCarloMover (Mover)

comment

Implements protocols::moves::Mover.

Reimplemented in protocols::monte_carlo::GenericSimulatedAnnealer.

References core::pose::motif::a(), accept(), adaptation_period(), adaptive_movers(), boltzmann(), core::scoring::Energies::clear(), drift_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), factory_, protocols::moves::FAIL_BAD_INPUT, protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, filters_, fire_all_triggers(), last_accepted_pose(), load_trial_number_from_checkpoint(), max_accepted_trials(), maxtrials_, mover_, mover_stopping_condition_, num_designable(), number_designable_, core::io::mmtf::pdb_comments, preapply_, recover_low(), recover_low_, protocols::hotspot_hashing::reject, reset(), save_trial_number_to_checkpoint(), saved_accept_file_name_, score_function(), scorefxn_, protocols::moves::Mover::set_last_move_status(), show_counters(), show_scores(), protocols::loops::stop, stop_sampling(), stopping_condition(), task_scaling_, and protocols::TR().

Referenced by protocols::evolution::EvolutionaryDynamicsMover::apply().

bool protocols::monte_carlo::GenericMonteCarloMover::boltz_rank ( ) const

inline

References boltz_rank_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures(), and set_boltz_rank().

bool protocols::monte_carlo::GenericMonteCarloMover::boltzmann ( Pose & pose )

core of MC

References generate_random().

Referenced by apply(), and protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result().

bool protocols::monte_carlo::GenericMonteCarloMover::boltzmann	(	Pose &	pose,
		utility::vector1< core::Real > const &	random_nums
	)

virtual

core of MC – evaulates a pose based on the scores/filters + temperatures. random_num is a vector of random numbers between 0 and 1 with size equal to the number of MC criteria

Uses filters or scorefunction to evaluate a pose and either accept or reject it.

Uses the filters or scorefunction to evaluates a pose and compare it to the last accepted and best poses.

Parameters

pose	= the pose to be evaluated
random_nums	= a vector of random numbers between 0 and 1, to be used for accepting poses that are not necessarily improved on filter/scorefxn value over the last accepted pose. Values of 0 indicate that only values that are improvements will be accepted, and values of 1 indicate that everything will be accepted regardless of scorefxn/filter value. Must have the same size as filters_

Reimplemented in protocols::evolution::EvolutionaryDynamicsMover.

References accept(), adaptive(), adaptive_, core::pose::Pose::chain_sequence(), core::pose::Pose::conformation(), current_score_, filters_, core::pose::get_all_comments(), last_accepted_score(), last_accepted_scores_, last_tested_scores_, lowest_scores_, protocols::mean_field::max(), mc_accepted_, protocols::moves::MCA_accepted_score_beat_last, protocols::moves::MCA_accepted_thermally, protocols::moves::MCA_rejected, protocols::mean_field::min(), core::conformation::Conformation::num_chains(), num_rejections_, protocols::simple_moves::bb_sampler::probability, progress_file(), progress_file_, sample_types_, scoring(), show_scores(), temperature_, temperatures_, protocols::TR(), TR_energies(), and trial_counter_.

GenericMonteCarloMover::MoverOP protocols::monte_carlo::GenericMonteCarloMover::clone ( ) const

overridevirtual

create copy constructor

clone this object

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::monte_carlo::GenericSimulatedAnnealer.

Referenced by parse_my_tag().

GenericMonteCarloMover::Real protocols::monte_carlo::GenericMonteCarloMover::current_score ( ) const

return the lowest score

References current_score_.

Referenced by show_scores().

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::monte_carlo::GenericMonteCarloMover::define_composition_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), protocols::moves::complex_type_name_for_mover(), protocols::monte_carlo::gen_mc_ct_namer(), and mover_name().

Referenced by protocols::evolution::EvolutionaryDynamicsMover::provide_xml_schema(), protocols::monte_carlo::GenericSimulatedAnnealer::provide_xml_schema(), and provide_xml_schema().

bool protocols::monte_carlo::GenericMonteCarloMover::drift ( ) const

inline

References drift_.

Referenced by set_drift().

utility::vector1< FilterOP > const& protocols::monte_carlo::GenericMonteCarloMover::filters ( ) const

inline

References filters_.

void protocols::monte_carlo::GenericMonteCarloMover::fire_all_triggers	(	Size	cycle,
		Size	num_cycles,
		const Pose &	pose,
		ScoreFunctionOP	scoring
	)

protected

Executes all triggers. The order of trigger execution is undefined. Do not assume, depend, or in any way rely on a particular ordering.

References last_accepted_pose_, last_accepted_score_, lowest_score_, lowest_score_pose_, protocols::hybridization::t, and triggers_.

Referenced by apply().

GenericMonteCarloMover::MoverOP protocols::monte_carlo::GenericMonteCarloMover::fresh_instance ( ) const

overridevirtual

create this type of objectt

create this type of object

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::monte_carlo::GenericSimulatedAnnealer.

utility::vector1< core::Real > protocols::monte_carlo::GenericMonteCarloMover::generate_random ( ) const

protected

generate a set of random numbers to accompany the filters or scorefxn

References filters_, and core::scoring::rg.

Referenced by boltzmann().

std::string protocols::monte_carlo::GenericMonteCarloMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::monte_carlo::GenericSimulatedAnnealer.

References mover_name().

Referenced by provide_citation_info().

void protocols::monte_carlo::GenericMonteCarloMover::initialize ( )

initialize object used in constructor

initialize

References accept_counter_, energy_gap_counter_, flip_sign_, last_accepted_scores_, lowest_scores_, next_trigger_id_, sample_type_, and trial_counter_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::EvolutionaryDynamicsMover(), GenericMonteCarloMover(), and parse_my_tag().

bool protocols::monte_carlo::GenericMonteCarloMover::keep_filters ( ) const

inline

References keep_filters_.

GenericMonteCarloMover::PoseOP protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose ( ) const

return the last accepted pose

References last_accepted_pose_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), apply(), protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result(), protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), and protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file().

void protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose ( core::pose::PoseOP pose )

Set the last pose that was accepted.

References last_accepted_pose_.

GenericMonteCarloMover::Real protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score ( ) const

return the last accepted score

References last_accepted_score_.

Referenced by accept(), boltzmann(), protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures(), and show_scores().

void protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score ( core::Real const score )

inline

References last_accepted_score_, and protocols::hybridization::score.

utility::vector1< core::Real > const& protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores ( ) const

inline

References last_accepted_scores_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result(), protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), protocols::monte_carlo::GenericSimulatedAnnealer::reset(), protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file(), protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures(), and protocols::monte_carlo::GenericSimulatedAnnealer::score_pose().

void protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores ( utility::vector1< core::Real > const & scores )

inline

References last_accepted_scores_.

utility::vector1< core::Real > const& protocols::monte_carlo::GenericMonteCarloMover::last_tested_scores ( ) const

inline

References last_tested_scores_.

core::Size protocols::monte_carlo::GenericMonteCarloMover::load_trial_number_from_checkpoint ( core::pose::Pose & pose )

References core::sequence::end, filters_, core::conformation::membrane::in, mover_tag_, reset(), reset_baselines(), saved_trial_number_file_, and protocols::TR().

Referenced by apply().

GenericMonteCarloMover::Real protocols::monte_carlo::GenericMonteCarloMover::lowest_score ( ) const

return the lowest score

References lowest_score_.

Referenced by accept(), protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures(), and show_scores().

void protocols::monte_carlo::GenericMonteCarloMover::lowest_score ( core::Real const score )

inline

References lowest_score_, and protocols::hybridization::score.

GenericMonteCarloMover::PoseOP protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose ( ) const

return the lowest score pose

References lowest_score_pose_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), and protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file().

void protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose ( core::pose::PoseOP pose )

Set the lowest scoring pose.

References lowest_score_pose_.

utility::vector1< core::Real > const& protocols::monte_carlo::GenericMonteCarloMover::lowest_scores ( ) const

inline

References lowest_scores_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file(), protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures(), and protocols::monte_carlo::GenericSimulatedAnnealer::score_pose().

void protocols::monte_carlo::GenericMonteCarloMover::lowest_scores ( utility::vector1< core::Real > const & scores )

inline

References lowest_scores_.

Size protocols::monte_carlo::GenericMonteCarloMover::max_accepted_trials ( ) const

inline

Returns maximum number of accepted trials.

References max_accepted_trials_.

Referenced by apply().

Size protocols::monte_carlo::GenericMonteCarloMover::maxtrials ( ) const

inline

Returns maximum number of trials.

References maxtrials_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply().

MCA protocols::monte_carlo::GenericMonteCarloMover::mc_accpeted ( ) const

return mc_accepted

References mc_accepted_.

MoverOP protocols::monte_carlo::GenericMonteCarloMover::mover ( ) const

inlineoverridevirtual

Implements protocols::moves::MoverApplyingMover.

References mover_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), protocols::monte_carlo::GenericSimulatedAnnealer::apply_mover(), set_mover(), and show_counters().

std::string protocols::monte_carlo::GenericMonteCarloMover::mover_name ( )

static

Referenced by define_composition_schema(), get_name(), protocols::monte_carlo::GenericMonteCarloMoverCreator::keyname(), and provide_xml_schema().

bool protocols::monte_carlo::GenericMonteCarloMover::mover_provides_citation_info ( ) const

overridevirtual

This mover provides citation info (returns true).

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > > protocols::monte_carlo::GenericMonteCarloMover::mover_stopping_condition ( ) const

inline

References mover_stopping_condition_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), and protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result().

GenericMonteCarloMover::Size protocols::monte_carlo::GenericMonteCarloMover::num_designable	(	Pose &	pose,
		PackerTaskOP &	task
	)

References core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), and apply().

utility::vector1< core::Size > const& protocols::monte_carlo::GenericMonteCarloMover::num_rejections ( ) const

inline

References num_rejections_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann().

Size protocols::monte_carlo::GenericMonteCarloMover::num_triggers ( ) const

Returns the number of triggers.

References triggers_.

void protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	filters,
		Movers_map const &	movers,
		Pose const &
	)

overridevirtual

parse xml file

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::monte_carlo::GenericSimulatedAnnealer.

References adaptation_period(), adaptive(), adaptive_movers(), add_filter(), boltz_rank_, clone(), drift_, filters_, protocols::environment::find_mover(), initialize(), keep_filters_, protocols::mean_field::max(), max_accepted_trials_, maxtrials_, mover_, mover_stopping_condition_, mover_tag_, protocols::rosetta_scripts::parse_filter(), parse_task_operations(), preapply_, progress_file(), rank_by_filter_, recover_low_, reset_baselines(), sample_type_, saved_accept_file_name_, saved_trial_number_file_, scorefxn_, stopping_condition(), task_scaling_, temperature_, and protocols::TR().

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::parse_my_tag(), and protocols::evolution::EvolutionaryDynamicsMover::parse_my_tag().

void protocols::monte_carlo::GenericMonteCarloMover::parse_task_operations	(	TagCOP	tag,
		basic::datacache::DataMap const &	datamap,
		Filters_map const &	,
		Movers_map const &
	)

virtual

parse "task_operations" XML option (can be employed virtually by derived Packing movers)

parse "task_operations" XML option

References core::pack::task::parse_task_operations(), task_factory(), and protocols::TR().

Referenced by parse_my_tag().

bool protocols::monte_carlo::GenericMonteCarloMover::preapply ( ) const

inline

References preapply_.

Referenced by set_preapply().

std::string protocols::monte_carlo::GenericMonteCarloMover::progress_file ( ) const

inlineprotected

References progress_file_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), boltzmann(), and parse_my_tag().

void protocols::monte_carlo::GenericMonteCarloMover::progress_file ( std::string const & s )

inlineprotected

References progress_file_.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::monte_carlo::GenericMonteCarloMover::provide_authorship_info_for_unpublished ( ) const

overridevirtual

Provides unpublished citation info for any unpublished movers and filters that this mover invokes.

Returns: A list of pairs of (author, e-mail address). Empty list if none are unpublished.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References filters_, mover_, scorefxn_, and stopping_condition_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::monte_carlo::GenericMonteCarloMover::provide_citation_info ( ) const

overridevirtual

Provide the citation (Fleishman 2011).

Returns: A vector of citation collections for this mover and any published movers and filters that it invokes.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References filters_, get_name(), mover_, scorefxn_, and stopping_condition_.

void protocols::monte_carlo::GenericMonteCarloMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References define_composition_schema(), and mover_name().

Referenced by protocols::monte_carlo::GenericMonteCarloMoverCreator::provide_xml_schema().

void protocols::monte_carlo::GenericMonteCarloMover::recover_low ( Pose & pose )

return the simulation state to the lowest energy structure we've seen

References last_accepted_pose_, lowest_score_pose_, and protocols::TR().

bool protocols::monte_carlo::GenericMonteCarloMover::recover_low ( ) const

inline

References recover_low_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), apply(), and set_recover_low().

void protocols::monte_carlo::GenericMonteCarloMover::remove_trigger ( Size trigger_id )

Removes the trigger with the specified id.

References protocols::TR(), and triggers_.

void protocols::monte_carlo::GenericMonteCarloMover::reset ( Pose & pose )

reset MC iterations, with pose used for the last & best structures

reset this GenericMonteCarloMover

References accept_counter_, boltz_rank_, energy_gap_counter_, filters_, last_accepted_pose_, last_accepted_score_, last_accepted_scores_, lowest_score_, lowest_score_pose_, lowest_scores_, num_rejections_, rank_by_filter_, sample_types_, protocols::hybridization::score, scoring(), core::pose::Pose::size(), temperatures_, protocols::TR(), and trial_counter_.

Referenced by apply(), load_trial_number_from_checkpoint(), and protocols::monte_carlo::GenericSimulatedAnnealer::reset().

void protocols::monte_carlo::GenericMonteCarloMover::reset_baselines ( bool const r )

inline

References reset_baselines_.

bool protocols::monte_carlo::GenericMonteCarloMover::reset_baselines ( ) const

inline

References reset_baselines_.

Referenced by load_trial_number_from_checkpoint(), and parse_my_tag().

utility::vector1< String > const& protocols::monte_carlo::GenericMonteCarloMover::sample_types ( ) const

inline

References sample_types_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), and protocols::monte_carlo::GenericSimulatedAnnealer::score_pose().

void protocols::monte_carlo::GenericMonteCarloMover::save_trial_number_to_checkpoint ( core::Size const i ) const

References core::conformation::membrane::out, and saved_trial_number_file_.

Referenced by apply().

std::string protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name ( ) const

References saved_accept_file_name_.

void protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name ( std::string const s )

References saved_accept_file_name_.

std::string protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file ( ) const

References saved_trial_number_file_.

void protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file ( std::string const s )

References saved_trial_number_file_.

ScoreFunctionOP protocols::monte_carlo::GenericMonteCarloMover::score_function ( ) const

inline

Return the score function in use.

References scorefxn_.

Referenced by apply().

ScoreFunctionOP protocols::monte_carlo::GenericMonteCarloMover::scorefxn ( ) const

inline

References scorefxn_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply().

GenericMonteCarloMover::Real protocols::monte_carlo::GenericMonteCarloMover::scoring ( Pose & pose )

protected

evalute pose by ScoreFunctionOP or FilterOP

score pose based on filter or scorefxn

References flip_sign_, protocols::hybridization::score, and scorefxn_.

Referenced by boltzmann(), and reset().

void protocols::monte_carlo::GenericMonteCarloMover::set_boltz_rank ( bool const boltz_rank )

if boltz_rank=true, rank structures by the temperature-weighted sum of scores, rather than a single filter

The score used here is the effective combined energy function that the Monte Carlo sampler is sampling over.

References boltz_rank(), and boltz_rank_.

void protocols::monte_carlo::GenericMonteCarloMover::set_drift ( bool const drift )

if drift=false, the pose is set back to the initial pose at each MC trial Of course, this is not MC sampling.

if drift=false, the pose is set back to the initial pose Of course, this is not MC sampling.

References drift(), and drift_.

void protocols::monte_carlo::GenericMonteCarloMover::set_keep_filters ( bool const k )

inline

References keep_filters_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::parse_my_tag().

void protocols::monte_carlo::GenericMonteCarloMover::set_max_accepted_trials ( Size const n_max_accepted_trial )

set max accepted trials of MC trials

set the maximum number of trials that should be accepted

References max_accepted_trials_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::parse_my_tag().

void protocols::monte_carlo::GenericMonteCarloMover::set_maxtrials ( Size const ntrial )

set max trials of MC trials

set max trials of monte carlo iterations

References maxtrials_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::parse_my_tag().

void protocols::monte_carlo::GenericMonteCarloMover::set_mc_accepted ( moves::MCA const m )

inlineprotected

Sets mc_accpeted.

References mc_accepted_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann().

void protocols::monte_carlo::GenericMonteCarloMover::set_mover ( MoverOP mover )

overridevirtual

set mover

Implements protocols::moves::MoverApplyingMover.

References mover(), and mover_.

void protocols::monte_carlo::GenericMonteCarloMover::set_preapply ( bool const preapply = false )

if preapply=true, auto-accept the first application of the submover, ignoring boltzman criteria.

References preapply(), and preapply_.

void protocols::monte_carlo::GenericMonteCarloMover::set_recover_low ( bool const recover_low )

if recover_low=true, after apply() the structure is the lowest energy structure, rather than the last accepted structure.

if recover_low=true, after apply() the returned is the lowest energy structure, rather than the last accepted structure.

References recover_low(), and recover_low_.

void protocols::monte_carlo::GenericMonteCarloMover::set_sampletype ( String const & type )

set sample type, max or min when sample_type == max, sample pose which have higher score when sample_type == min, sample pose which have lower score

set sample type, high or low when sample_type == high, sample pose which have higher value of scorey when sample_type == low, sample pose which have lower value of score

References sample_type_, and protocols::moves::Mover::type().

void protocols::monte_carlo::GenericMonteCarloMover::set_scorefxn ( ScoreFunctionOP const & sfxn )

Pose is evaluated by ScoreFunctionOP during MC trials.

set scorefxn Pose is evaluated by FilterOP which can do report_sm() or ScoreFunctionOP during MC trials You can choose either way FilterOP or ScoreFunction.

References filters_, and scorefxn_.

void protocols::monte_carlo::GenericMonteCarloMover::set_stop_sampling ( bool const stop_sampling )

if set to true, the MC mover will stop sampling

References stop_sampling(), and stop_sampling_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann().

void protocols::monte_carlo::GenericMonteCarloMover::set_task_scaling ( Size const scaling )

set task multiplier to calculate trials from task

References task_scaling_.

void protocols::monte_carlo::GenericMonteCarloMover::set_temperature ( Real const temp )

set temperature

set temperatrue

References temperature_.

void protocols::monte_carlo::GenericMonteCarloMover::show_counters ( std::ostream & out ) const

show counters of ntrial and acceptance ratio

show counters

References protocols::comparative_modeling::features::A, accept_counter_, energy_gap_counter_, core::chemical::element::F, flip_sign_, core::chemical::element::I, core::scoring::sasa::LJ, mover(), mover_, num_rejections_, scorefxn_, and trial_counter_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), and apply().

void protocols::monte_carlo::GenericMonteCarloMover::show_scores ( std::ostream & out ) const

show scores of last_accepted_score and "best_score" ( = flip_sign_ * lowest_score )

show scores of last_accepted_score and lowest_score

References current_score(), core::chemical::element::F, flip_sign_, core::chemical::element::I, last_accepted_score(), lowest_score(), sample_type_, and trial_counter_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), apply(), and boltzmann().

bool protocols::monte_carlo::GenericMonteCarloMover::stop_sampling ( ) const

inline

References stop_sampling_.

Referenced by apply(), and set_stop_sampling().

void protocols::monte_carlo::GenericMonteCarloMover::stopping_condition ( protocols::filters::FilterOP filter )

References stopping_condition_.

protocols::filters::FilterOP protocols::monte_carlo::GenericMonteCarloMover::stopping_condition ( ) const

References stopping_condition_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), apply(), protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result(), and parse_my_tag().

void protocols::monte_carlo::GenericMonteCarloMover::task_factory ( core::pack::task::TaskFactoryOP tf )

References factory_.

core::pack::task::TaskFactoryOP protocols::monte_carlo::GenericMonteCarloMover::task_factory ( ) const

inline

References factory_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), and parse_task_operations().

Size protocols::monte_carlo::GenericMonteCarloMover::task_scaling ( ) const

inline

Returns the task scaling value.

References task_scaling_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply().

utility::vector1< Real > protocols::monte_carlo::GenericMonteCarloMover::temperatures ( ) const

inline

References temperatures_.

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::apply(), protocols::monte_carlo::GenericSimulatedAnnealer::calc_boltz_score(), protocols::monte_carlo::GenericSimulatedAnnealer::reset(), and protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures().

void protocols::monte_carlo::GenericMonteCarloMover::temperatures ( utility::vector1< Real > const & temps )

inline

References temperatures_.

Size protocols::monte_carlo::GenericMonteCarloMover::trial_counter ( ) const

inline

References trial_counter_.

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann().

void protocols::monte_carlo::GenericMonteCarloMover::trial_counter ( core::Size const i )

inline

References trial_counter_.

Member Data Documentation

int protocols::monte_carlo::GenericMonteCarloMover::accept_counter_ = 0

private

diagnostics

Referenced by accept(), accept_counter(), initialize(), reset(), and show_counters().

core::Size protocols::monte_carlo::GenericMonteCarloMover::adaptation_period_ = 0

private

dflt max( 10, trials/10 ); only works with adaptive; how often should the run probabilities be adapted?

Referenced by adaptation_period().

utility::vector1< bool > protocols::monte_carlo::GenericMonteCarloMover::adaptive_

private

Referenced by adaptive(), add_filter(), and boltzmann().

bool protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers_ = false

private

change the mover probabilities according to the accept rates?; only works if the mover is a ParsedProtocol type with mode=single_random

Referenced by adaptive_movers().

bool protocols::monte_carlo::GenericMonteCarloMover::boltz_rank_ = false

private

If boltz_rank_=true, instead of ranking by a single filter, rank by the temperature-weighted sum of all scores.

Referenced by accept(), boltz_rank(), parse_my_tag(), reset(), and set_boltz_rank().

Real protocols::monte_carlo::GenericMonteCarloMover::current_score_ = 0.0

private

current

Referenced by boltzmann(), and current_score().

bool protocols::monte_carlo::GenericMonteCarloMover::drift_ = true

private

if drift=false, the pose is set back to the initial pose at each MC trial Of course, this is not MC sampling.

Referenced by apply(), drift(), parse_my_tag(), and set_drift().

Real protocols::monte_carlo::GenericMonteCarloMover::energy_gap_counter_ = 0.0

private

Referenced by accept(), initialize(), reset(), and show_counters().

TaskFactoryOP protocols::monte_carlo::GenericMonteCarloMover::factory_

private

task factory

Referenced by apply(), and task_factory().

utility::vector1< FilterOP > protocols::monte_carlo::GenericMonteCarloMover::filters_

private

Pose is evaluated by FilterOP which can do report_sm() during MC trials.

Referenced by accept(), add_filter(), apply(), boltzmann(), filters(), generate_random(), load_trial_number_from_checkpoint(), parse_my_tag(), provide_authorship_info_for_unpublished(), provide_citation_info(), reset(), and set_scorefxn().

Real protocols::monte_carlo::GenericMonteCarloMover::flip_sign_ = 1

private

to change the sing of calculated "score"

Referenced by initialize(), scoring(), show_counters(), and show_scores().

bool protocols::monte_carlo::GenericMonteCarloMover::keep_filters_ = false

private

avoid clearing filters if a score function is given. Used in the EvolutionDynamicsMover which inherits from genericMCmover.

Referenced by keep_filters(), parse_my_tag(), and set_keep_filters().

PoseOP protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose_

private

accepted structure

Referenced by accept(), fire_all_triggers(), last_accepted_pose(), recover_low(), and reset().

Real protocols::monte_carlo::GenericMonteCarloMover::last_accepted_score_ = 0.0

private

accepted structure

Referenced by accept(), fire_all_triggers(), last_accepted_score(), and reset().

utility::vector1< Real > protocols::monte_carlo::GenericMonteCarloMover::last_accepted_scores_

private

Referenced by accept(), add_filter(), boltzmann(), initialize(), last_accepted_scores(), and reset().

utility::vector1< Real > protocols::monte_carlo::GenericMonteCarloMover::last_tested_scores_

private

Referenced by boltzmann(), and last_tested_scores().

Real protocols::monte_carlo::GenericMonteCarloMover::lowest_score_ = 0.0

private

lowest energy structure we've seen

Referenced by accept(), fire_all_triggers(), lowest_score(), and reset().

PoseOP protocols::monte_carlo::GenericMonteCarloMover::lowest_score_pose_

private

lowest energy structure we've seen

Referenced by accept(), fire_all_triggers(), lowest_score_pose(), recover_low(), and reset().

utility::vector1< Real > protocols::monte_carlo::GenericMonteCarloMover::lowest_scores_

private

best filter scores

Referenced by accept(), boltzmann(), initialize(), lowest_scores(), and reset().

Size protocols::monte_carlo::GenericMonteCarloMover::max_accepted_trials_ = 0

private

max number of accepted MC trials

Referenced by max_accepted_trials(), parse_my_tag(), and set_max_accepted_trials().

Size protocols::monte_carlo::GenericMonteCarloMover::maxtrials_ = 10

private

max number of MC trials

Referenced by apply(), maxtrials(), parse_my_tag(), and set_maxtrials().

moves::MCA protocols::monte_carlo::GenericMonteCarloMover::mc_accepted_ = moves::MCA_accepted_score_beat_last

private

result of the last call to boltzmann

Referenced by accept(), boltzmann(), mc_accpeted(), and set_mc_accepted().

MoverOP protocols::monte_carlo::GenericMonteCarloMover::mover_

private

mover

Referenced by apply(), mover(), parse_my_tag(), provide_authorship_info_for_unpublished(), provide_citation_info(), set_mover(), and show_counters().

utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > > protocols::monte_carlo::GenericMonteCarloMover::mover_stopping_condition_

private

dflt NULL; if the mover defined a stopping condition on the datamap then this assumes the mover's value. In this way, the Mover can tell GenericMC to stop execution, e.g., if it has iterated over all internal possibilities

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

utility::pointer::shared_ptr< basic::datacache::DataMapObj< std::string > > protocols::monte_carlo::GenericMonteCarloMover::mover_tag_

private

dflt NULL; this is used by the called movers to set a certain tag. If saved_accept_file_name_ is set, then at exit the tag coming from the chosen mover is written to disk as, <saved_accept_file_name>.mover_tag. To work, mover_tag_ must be exposed to the movers being called.

Referenced by accept(), load_trial_number_from_checkpoint(), and parse_my_tag().

Size protocols::monte_carlo::GenericMonteCarloMover::next_trigger_id_ = 1

private

Next trigger identifier to be assigned.

Referenced by add_trigger(), and initialize().

utility::vector1< core::Size > protocols::monte_carlo::GenericMonteCarloMover::num_rejections_

protected

Count the number of rejections each filter resulted in.

Referenced by add_filter(), protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), boltzmann(), num_rejections(), reset(), and show_counters().

Size protocols::monte_carlo::GenericMonteCarloMover::number_designable_ = 0

private

number of designable positions

Referenced by apply().

bool protocols::monte_carlo::GenericMonteCarloMover::preapply_ = true

private

Should we apply (and accept) the first application of the mover regardless of boltzman criteria? (Defaults true for historical reasons.)

Referenced by apply(), parse_my_tag(), preapply(), and set_preapply().

std::string protocols::monte_carlo::GenericMonteCarloMover::progress_file_

private

a file name where data on each step is saved.

Referenced by boltzmann(), and progress_file().

Size protocols::monte_carlo::GenericMonteCarloMover::rank_by_filter_ = 1

private

By which filter (by index) are poses ranked by for non-Boltzman purposes (e.g. recover_low())

Referenced by accept(), add_filter(), parse_my_tag(), and reset().

bool protocols::monte_carlo::GenericMonteCarloMover::recover_low_ = true

private

At the end of application, is the structure the last accepted structure (recover_low_==false) or is it the lowest energy structure (recover_low_=true)

Referenced by apply(), parse_my_tag(), recover_low(), and set_recover_low().

bool protocols::monte_carlo::GenericMonteCarloMover::reset_baselines_ = true

private

reset the filters' baseline at trial=1?

Referenced by reset_baselines().

String protocols::monte_carlo::GenericMonteCarloMover::sample_type_ = "low"

private

set sample type, max or min when sample_type == "high", sample pose which have higher score when sample_type == "low", sample pose which have lower score

Referenced by initialize(), parse_my_tag(), set_sampletype(), and show_scores().

utility::vector1< String > protocols::monte_carlo::GenericMonteCarloMover::sample_types_

private

low/high, dflt low

Referenced by add_filter(), boltzmann(), reset(), and sample_types().

std::string protocols::monte_carlo::GenericMonteCarloMover::saved_accept_file_name_

private

dflt ""; if a file name is specified, after each accept a pdb file is dumped to disk. This is useful for checkpointing

Referenced by accept(), apply(), parse_my_tag(), and saved_accept_file_name().

std::string protocols::monte_carlo::GenericMonteCarloMover::saved_trial_number_file_

private

dflt ""; if specified checkpoints the current trial number and recovers from it

Referenced by load_trial_number_from_checkpoint(), parse_my_tag(), save_trial_number_to_checkpoint(), and saved_trial_number_file().

ScoreFunctionOP protocols::monte_carlo::GenericMonteCarloMover::scorefxn_

private

Pose is evaluated by ScoreFunctionOP during MC trials.

Referenced by add_filter(), apply(), parse_my_tag(), provide_authorship_info_for_unpublished(), provide_citation_info(), score_function(), scorefxn(), scoring(), set_scorefxn(), and show_counters().

bool protocols::monte_carlo::GenericMonteCarloMover::stop_sampling_ = false

private

if set to true, the MC mover will stop sampling

Referenced by set_stop_sampling(), and stop_sampling().

protocols::filters::FilterOP protocols::monte_carlo::GenericMonteCarloMover::stopping_condition_

private

dflt false_filter; use this to stop an MC trajectory before maxtrials_ (if filter evaluates to true)

Referenced by provide_authorship_info_for_unpublished(), provide_citation_info(), and stopping_condition().

PackerTaskOP protocols::monte_carlo::GenericMonteCarloMover::task_

private

task

Size protocols::monte_carlo::GenericMonteCarloMover::task_scaling_ = 5

private

multiply the number_designable_ by task_scaling to get the number of trials

Referenced by apply(), parse_my_tag(), set_task_scaling(), and task_scaling().

Real protocols::monte_carlo::GenericMonteCarloMover::temperature_ = 0.0

private

acceptance criterion temperature

Referenced by boltzmann(), parse_my_tag(), and set_temperature().

utility::vector1< Real > protocols::monte_carlo::GenericMonteCarloMover::temperatures_

private

acceptance criterion temperature, per temperature

Referenced by accept(), add_filter(), boltzmann(), reset(), and temperatures().

int protocols::monte_carlo::GenericMonteCarloMover::trial_counter_ = 0

protected

Referenced by protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), boltzmann(), initialize(), reset(), show_counters(), show_scores(), and trial_counter().

boost::unordered_map<Size, GenericMonteCarloMoverTrigger> protocols::monte_carlo::GenericMonteCarloMover::triggers_

private

Collection of function callbacks.

Referenced by add_trigger(), fire_all_triggers(), num_triggers(), and remove_trigger().

std::string protocols::monte_carlo::GenericMonteCarloMover::user_defined_mover_name_

private

dflt ""; the mover being called by GenericMC. Used to add values to the poses DataCache.

Referenced by accept().

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

src/protocols/monte_carlo/GenericMonteCarloMover.hh
src/protocols/monte_carlo/GenericMonteCarloMover.cc

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