protocols::simple_moves::GenericMonteCarloMover Class Reference

#include <GenericMonteCarloMover.hh>

Inheritance diagram for protocols::simple_moves::GenericMonteCarloMover:

Collaboration diagram for protocols::simple_moves::GenericMonteCarloMover:

Public Types
typedef protocols::moves::Mover	Super
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 utility::tag::TagPtr	TagPtr
typedef protocols::moves::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::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

Public Member Functions
	GenericMonteCarloMover ()
	default constructor More...
	GenericMonteCarloMover (Size const maxtrials, 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 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 ()
	destructor More...
virtual MoverOP	clone () const
	create copy constructor More...
virtual MoverOP	fresh_instance () const
	create this type of objectt More...
void	initialize ()
	initialize object used in constructor More...
virtual void	apply (Pose &pose)
	apply GenericMonteCarloMover (Mover) More...
virtual String	get_name () const
	Each derived class must specify its name. The class name. 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...
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...
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...
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_task_scaling (Size const scaling)
	set task multiplier to calculate trials from task More...
void	set_mover (MoverOP const &mover)
	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_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...
virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &)
	parse xml file More...
virtual void	parse_task_operations (TagPtr const, 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
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

Private 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...
void	task_factory (core::pack::task::TaskFactoryOP tf)
	setter More...

Private Attributes
Size	maxtrials_
	max number of MC trials More...
Size	number_designable_
	number of designable positions More...
Size	task_scaling_
	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 More...
utility::vector1< String >	sample_types_
utility::vector1< Real >	last_accepted_scores_
utility::vector1< core::Size >	num_rejections_
	Count the number of rejections each filter resulted in. More...
ScoreFunctionOP	scorefxn_
	Pose is evaluated by ScoreFunctionOP during MC trials. More...
Real	temperature_
	acceptance criterion temperature More...
String	sample_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...
bool	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...
bool	preapply_
	Should we apply (and accept) the first application of the mover regardless of boltzman criteria? (Defaults true for historical reasons.) More...
bool	recover_low_
	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_
	By which filter (by index) are poses ranked by for non-Boltzman purposes (e.g. recover_low()) More...
bool	boltz_rank_
	If boltz_rank_=true, instead of ranking by a single filter, rank by the temperature-weighted sum of all scores. More...
Real	current_score_
	current score More...
Real	last_accepted_score_
	accepted structure More...
Real	lowest_score_
	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...
MCA	mc_accepted_
	result of the last call to boltzmann More...
Real	flip_sign_
	to change the sing of calculated "score" More...
int	trial_counter_
	diagnostics More...
int	accept_counter_
Real	energy_gap_counter_
Size	next_trigger_id_
	Next trigger identifier to be assigned. More...
boost::unordered_map< Size, GenericMonteCarloMoverTrigger >	triggers_
	Collection of function callbacks. More...
protocols::filters::FilterOP	stopping_condition_
utility::pointer::owning_ptr < protocols::moves::DataMapObj < bool > >	mover_stopping_condition_
bool	adaptive_movers_
core::Size	adaptation_period_
std::string	saved_accept_file_name_
	dflt max( 10, trials/10 ); only works with adaptive; how often should the run probabilities be adapted? More...
std::string	saved_trial_number_file_
utility::pointer::owning_ptr < protocols::moves::DataMapObj < std::string > >	mover_tag_
std::string	user_defined_mover_name_
	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...
bool	reset_baselines_

Additional Inherited Members
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()
static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Definition at line 61 of file GenericMonteCarloMover.hh.

Member Typedef Documentation

typedef protocols::moves::DataMap protocols::simple_moves::GenericMonteCarloMover::DataMap

Definition at line 79 of file GenericMonteCarloMover.hh.

typedef protocols::filters::FilterOP protocols::simple_moves::GenericMonteCarloMover::FilterOP

Definition at line 71 of file GenericMonteCarloMover.hh.

typedef protocols::filters::Filters_map protocols::simple_moves::GenericMonteCarloMover::Filters_map

Definition at line 80 of file GenericMonteCarloMover.hh.

typedef protocols::moves::MoverOP protocols::simple_moves::GenericMonteCarloMover::MoverOP

Definition at line 72 of file GenericMonteCarloMover.hh.

typedef protocols::moves::Movers_map protocols::simple_moves::GenericMonteCarloMover::Movers_map

Definition at line 81 of file GenericMonteCarloMover.hh.

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

Definition at line 73 of file GenericMonteCarloMover.hh.

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

Definition at line 75 of file GenericMonteCarloMover.hh.

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

Definition at line 74 of file GenericMonteCarloMover.hh.

typedef core::pose::Pose protocols::simple_moves::GenericMonteCarloMover::Pose

Definition at line 67 of file GenericMonteCarloMover.hh.

typedef core::pose::PoseOP protocols::simple_moves::GenericMonteCarloMover::PoseOP

Definition at line 68 of file GenericMonteCarloMover.hh.

typedef core::Real protocols::simple_moves::GenericMonteCarloMover::Real

Definition at line 66 of file GenericMonteCarloMover.hh.

typedef core::scoring::ScoreFunction protocols::simple_moves::GenericMonteCarloMover::ScoreFunction

Definition at line 69 of file GenericMonteCarloMover.hh.

typedef core::scoring::ScoreFunctionOP protocols::simple_moves::GenericMonteCarloMover::ScoreFunctionOP

Definition at line 70 of file GenericMonteCarloMover.hh.

typedef core::Size protocols::simple_moves::GenericMonteCarloMover::Size

Definition at line 65 of file GenericMonteCarloMover.hh.

typedef std::string protocols::simple_moves::GenericMonteCarloMover::String

Definition at line 64 of file GenericMonteCarloMover.hh.

typedef protocols::moves::Mover protocols::simple_moves::GenericMonteCarloMover::Super

Definition at line 63 of file GenericMonteCarloMover.hh.

typedef utility::tag::TagPtr protocols::simple_moves::GenericMonteCarloMover::TagPtr

Definition at line 78 of file GenericMonteCarloMover.hh.

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

Definition at line 76 of file GenericMonteCarloMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::GenericMonteCarloMover::GenericMonteCarloMover

(

)

default constructor

Definition at line 92 of file GenericMonteCarloMover.cc.

References initialize().

Referenced by clone(), and fresh_instance().

protocols::simple_moves::GenericMonteCarloMover::GenericMonteCarloMover	(	Size const	maxtrials,
		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

Definition at line 122 of file GenericMonteCarloMover.cc.

References initialize().

protocols::simple_moves::GenericMonteCarloMover::GenericMonteCarloMover	(	Size const	maxtrials,
		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

Definition at line 151 of file GenericMonteCarloMover.cc.

References initialize().

protocols::simple_moves::GenericMonteCarloMover::~GenericMonteCarloMover

(

)

destructor

Definition at line 181 of file GenericMonteCarloMover.cc.

Member Function Documentation

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

inline

Definition at line 270 of file GenericMonteCarloMover.hh.

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

inline

Definition at line 271 of file GenericMonteCarloMover.hh.

Referenced by apply(), and parse_my_tag().

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

inline

Definition at line 268 of file GenericMonteCarloMover.hh.

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

inline

Definition at line 269 of file GenericMonteCarloMover.hh.

Referenced by apply(), and parse_my_tag().

void protocols::simple_moves::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.

Definition at line 287 of file GenericMonteCarloMover.cc.

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

Referenced by parse_my_tag().

Size protocols::simple_moves::GenericMonteCarloMover::add_trigger

(

const GenericMonteCarloMoverTrigger &

trigger)

Adds a new trigger, returning its id.

Example: #include <boost/bind.hpp> #include <boost/function.hpp>

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 = boost::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.

Definition at line 981 of file GenericMonteCarloMover.cc.

References next_trigger_id_, and triggers_.

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

virtual

apply GenericMonteCarloMover (Mover)

comment

Implements protocols::moves::Mover.

Definition at line 676 of file GenericMonteCarloMover.cc.

References protocols::hotspot_hashing::accept, adaptation_period(), adaptive_movers(), boltzmann(), drift_, core::pose::Pose::dump_pdb(), 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(), maxtrials_, mover_, mover_stopping_condition_, num_designable(), number_designable_, 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, stopping_condition(), task_scaling_, and protocols::simple_moves::TR().

bool protocols::simple_moves::GenericMonteCarloMover::boltzmann

(

Pose &

pose)

core of MC

Definition at line 473 of file GenericMonteCarloMover.cc.

References protocols::hotspot_hashing::accept, accept_counter_, adaptive_, core::pose::add_comment(), boltz_rank_, current_score_, 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_, mc_accepted_, mc_RG(), protocols::moves::MCA_accepted_score_beat_last, protocols::moves::MCA_accepted_score_beat_low, protocols::moves::MCA_accepted_thermally, protocols::moves::MCA_rejected, mover_tag_, num_rejections_, rank_by_filter_, sample_types_, saved_accept_file_name_, scoring(), show_scores(), temperature_, temperatures_, protocols::simple_moves::TR(), TR_energies(), trial_counter_, and user_defined_mover_name_.

Referenced by apply().

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

virtual

create copy constructor

clone this object

Reimplemented from protocols::moves::Mover.

Definition at line 185 of file GenericMonteCarloMover.cc.

References GenericMonteCarloMover().

Referenced by parse_my_tag().

GenericMonteCarloMover::Real protocols::simple_moves::GenericMonteCarloMover::current_score

(

)

const

return the lowest score

Definition at line 250 of file GenericMonteCarloMover.cc.

References current_score_.

Referenced by show_scores().

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

private

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

Definition at line 963 of file GenericMonteCarloMover.cc.

References last_accepted_pose_, last_accepted_score_, lowest_score_, lowest_score_pose_, core::scoring::hbonds::t(), and triggers_.

Referenced by apply().

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

virtual

create this type of objectt

create this type of object

Reimplemented from protocols::moves::Mover.

Definition at line 194 of file GenericMonteCarloMover.cc.

References GenericMonteCarloMover().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 824 of file GenericMonteCarloMover.cc.

References protocols::simple_moves::GenericMonteCarloMoverCreator::mover_name().

void protocols::simple_moves::GenericMonteCarloMover::initialize

(

)

initialize object used in constructor

initialize

Definition at line 201 of file GenericMonteCarloMover.cc.

References accept_counter_, energy_gap_counter_, flip_sign_, last_accepted_scores_, next_trigger_id_, sample_type_, protocols::simple_moves::TR(), and trial_counter_.

Referenced by GenericMonteCarloMover(), and parse_my_tag().

GenericMonteCarloMover::PoseOP protocols::simple_moves::GenericMonteCarloMover::last_accepted_pose

(

)

const

return the last accepted pose

Definition at line 222 of file GenericMonteCarloMover.cc.

References last_accepted_pose_.

Referenced by apply().

GenericMonteCarloMover::Real protocols::simple_moves::GenericMonteCarloMover::last_accepted_score

(

)

const

return the last accepted score

Definition at line 229 of file GenericMonteCarloMover.cc.

References last_accepted_score_.

Referenced by boltzmann(), and show_scores().

core::Size protocols::simple_moves::GenericMonteCarloMover::load_trial_number_from_checkpoint

(

core::pose::Pose &

pose)

Definition at line 594 of file GenericMonteCarloMover.cc.

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

Referenced by apply().

GenericMonteCarloMover::Real protocols::simple_moves::GenericMonteCarloMover::lowest_score

(

)

const

return the lowest score

Definition at line 243 of file GenericMonteCarloMover.cc.

References lowest_score_.

Referenced by boltzmann(), and show_scores().

GenericMonteCarloMover::PoseOP protocols::simple_moves::GenericMonteCarloMover::lowest_score_pose

(

)

const

return the lowest score pose

Definition at line 236 of file GenericMonteCarloMover.cc.

References lowest_score_pose_.

MCA protocols::simple_moves::GenericMonteCarloMover::mc_accpeted

(

)

const

return mc_accepted

Definition at line 257 of file GenericMonteCarloMover.cc.

References mc_accepted_.

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

Definition at line 456 of file GenericMonteCarloMover.cc.

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

Referenced by apply().

Size protocols::simple_moves::GenericMonteCarloMover::num_triggers

(

)

const

Returns the number of triggers.

Definition at line 996 of file GenericMonteCarloMover.cc.

References triggers_.

void protocols::simple_moves::GenericMonteCarloMover::parse_my_tag ( TagPtr const  tag, DataMap &  data, Filters_map const &  filters, Movers_map const &  movers, Pose const &    )

virtual

parse xml file

Reimplemented from protocols::moves::Mover.

Definition at line 830 of file GenericMonteCarloMover.cc.

References adaptation_period(), adaptive_movers(), add_filter(), boltz_rank_, clone(), drift_, filters_, protocols::moves::DataMap::get(), protocols::moves::get_set_from_datamap(), protocols::moves::DataMap::has(), initialize(), maxtrials_, mover_, mover_stopping_condition_, mover_tag_, protocols::rosetta_scripts::parse_filter(), parse_task_operations(), preapply_, rank_by_filter_, recover_low_, reset_baselines(), sample_type_, saved_accept_file_name_, saved_trial_number_file_, scorefxn_, stopping_condition(), task_scaling_, temperature_, protocols::simple_moves::TR(), and user_defined_mover_name_.

void protocols::simple_moves::GenericMonteCarloMover::parse_task_operations ( TagPtr const  tag, 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

Definition at line 947 of file GenericMonteCarloMover.cc.

References protocols::rosetta_scripts::parse_task_operations(), task_factory(), and protocols::simple_moves::TR().

Referenced by parse_my_tag().

void protocols::simple_moves::GenericMonteCarloMover::recover_low

(

Pose &

pose)

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

Definition at line 405 of file GenericMonteCarloMover.cc.

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

Referenced by apply(), and set_recover_low().

void protocols::simple_moves::GenericMonteCarloMover::remove_trigger

(

Size

trigger_id)

Removes the trigger with the specified id.

Definition at line 987 of file GenericMonteCarloMover.cc.

References protocols::simple_moves::TR(), and triggers_.

void protocols::simple_moves::GenericMonteCarloMover::reset

(

Pose &

pose)

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

reset this GenericMonteCarloMover

Definition at line 419 of file GenericMonteCarloMover.cc.

References accept_counter_, energy_gap_counter_, filters_, last_accepted_pose_, last_accepted_score_, last_accepted_scores_, lowest_score_, lowest_score_pose_, num_rejections_, sample_types_, scoring(), protocols::simple_moves::TR(), and trial_counter_.

Referenced by apply(), and load_trial_number_from_checkpoint().

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

inline

Definition at line 278 of file GenericMonteCarloMover.hh.

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

inline

Definition at line 279 of file GenericMonteCarloMover.hh.

Referenced by load_trial_number_from_checkpoint(), and parse_my_tag().

void protocols::simple_moves::GenericMonteCarloMover::save_trial_number_to_checkpoint

(

core::Size const

i)

const

Definition at line 661 of file GenericMonteCarloMover.cc.

References saved_trial_number_file_.

Referenced by apply().

std::string protocols::simple_moves::GenericMonteCarloMover::saved_accept_file_name

(

)

const

Definition at line 1011 of file GenericMonteCarloMover.cc.

References saved_accept_file_name_.

void protocols::simple_moves::GenericMonteCarloMover::saved_accept_file_name

(

std::string const

s)

Definition at line 1016 of file GenericMonteCarloMover.cc.

References saved_accept_file_name_.

std::string protocols::simple_moves::GenericMonteCarloMover::saved_trial_number_file

(

)

const

Definition at line 1021 of file GenericMonteCarloMover.cc.

References saved_trial_number_file_.

void protocols::simple_moves::GenericMonteCarloMover::saved_trial_number_file

(

std::string const

s)

Definition at line 1026 of file GenericMonteCarloMover.cc.

References saved_trial_number_file_.

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

inline

Return the score function in use.

Definition at line 169 of file GenericMonteCarloMover.hh.

Referenced by apply().

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

private

evalute pose by ScoreFunctionOP or FilterOP

score pose based on filter or scorefxn

Definition at line 447 of file GenericMonteCarloMover.cc.

References flip_sign_, and scorefxn_.

Referenced by boltzmann(), and reset().

void protocols::simple_moves::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

Detailed: The score used here is the effective combined energy function

that the Monte Carlo sampler is sampling over.

Definition at line 355 of file GenericMonteCarloMover.cc.

References boltz_rank_.

void protocols::simple_moves::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.

Definition at line 334 of file GenericMonteCarloMover.cc.

References drift_.

void protocols::simple_moves::GenericMonteCarloMover::set_maxtrials

(

Size const

ntrial)

set max trials of MC trials

set max trials of monte carlo iterations

Definition at line 264 of file GenericMonteCarloMover.cc.

References maxtrials_.

void protocols::simple_moves::GenericMonteCarloMover::set_mover

(

MoverOP const &

mover)

set mover

Definition at line 278 of file GenericMonteCarloMover.cc.

References mover_.

void protocols::simple_moves::GenericMonteCarloMover::set_preapply

(

bool const

preapply = false)

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

Definition at line 341 of file GenericMonteCarloMover.cc.

References preapply_.

void protocols::simple_moves::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.

Definition at line 348 of file GenericMonteCarloMover.cc.

References recover_low(), and recover_low_.

void protocols::simple_moves::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

Definition at line 322 of file GenericMonteCarloMover.cc.

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

void protocols::simple_moves::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.

Definition at line 305 of file GenericMonteCarloMover.cc.

References filters_, and scorefxn_.

void protocols::simple_moves::GenericMonteCarloMover::set_task_scaling

(

Size const

scaling)

set task multiplier to calculate trials from task

Definition at line 271 of file GenericMonteCarloMover.cc.

References task_scaling_.

void protocols::simple_moves::GenericMonteCarloMover::set_temperature

(

Real const

temp)

set temperature

set temperatrue

Definition at line 313 of file GenericMonteCarloMover.cc.

References temperature_.

void protocols::simple_moves::GenericMonteCarloMover::show_counters

(

std::ostream &

out)

const

show counters of ntrial and acceptance ratio

show counters

Definition at line 375 of file GenericMonteCarloMover.cc.

References protocols::comparative_modeling::features::A, accept_counter_, energy_gap_counter_, flip_sign_, mover_, num_rejections_, scorefxn_, and trial_counter_.

Referenced by apply().

void protocols::simple_moves::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

Definition at line 361 of file GenericMonteCarloMover.cc.

References current_score(), flip_sign_, last_accepted_score(), lowest_score(), sample_type_, and trial_counter_.

Referenced by apply(), and boltzmann().

void protocols::simple_moves::GenericMonteCarloMover::stopping_condition

(

protocols::filters::FilterOP

filter)

Definition at line 1001 of file GenericMonteCarloMover.cc.

References stopping_condition_.

protocols::filters::FilterOP protocols::simple_moves::GenericMonteCarloMover::stopping_condition

(

)

const

Definition at line 1006 of file GenericMonteCarloMover.cc.

References stopping_condition_.

Referenced by apply(), and parse_my_tag().

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

private

setter

Definition at line 190 of file GenericMonteCarloMover.cc.

References factory_.

Referenced by parse_task_operations().

Member Data Documentation

int protocols::simple_moves::GenericMonteCarloMover::accept_counter_

private

Definition at line 380 of file GenericMonteCarloMover.hh.

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

core::Size protocols::simple_moves::GenericMonteCarloMover::adaptation_period_

private

Definition at line 391 of file GenericMonteCarloMover.hh.

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

private

Definition at line 312 of file GenericMonteCarloMover.hh.

Referenced by add_filter(), and boltzmann().

bool protocols::simple_moves::GenericMonteCarloMover::adaptive_movers_

private

Definition at line 390 of file GenericMonteCarloMover.hh.

bool protocols::simple_moves::GenericMonteCarloMover::boltz_rank_

private

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

Definition at line 355 of file GenericMonteCarloMover.hh.

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

Real protocols::simple_moves::GenericMonteCarloMover::current_score_

private

current score

Definition at line 358 of file GenericMonteCarloMover.hh.

Referenced by boltzmann(), and current_score().

bool protocols::simple_moves::GenericMonteCarloMover::drift_

private

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

Definition at line 338 of file GenericMonteCarloMover.hh.

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

Real protocols::simple_moves::GenericMonteCarloMover::energy_gap_counter_

private

Definition at line 381 of file GenericMonteCarloMover.hh.

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

TaskFactoryOP protocols::simple_moves::GenericMonteCarloMover::factory_

private

task factory

Definition at line 308 of file GenericMonteCarloMover.hh.

Referenced by apply(), and task_factory().

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

private

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

Definition at line 311 of file GenericMonteCarloMover.hh.

Referenced by add_filter(), apply(), boltzmann(), load_trial_number_from_checkpoint(), parse_my_tag(), reset(), and set_scorefxn().

Real protocols::simple_moves::GenericMonteCarloMover::flip_sign_

private

to change the sing of calculated "score"

Definition at line 376 of file GenericMonteCarloMover.hh.

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

PoseOP protocols::simple_moves::GenericMonteCarloMover::last_accepted_pose_

private

accepted structure

Definition at line 367 of file GenericMonteCarloMover.hh.

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

Real protocols::simple_moves::GenericMonteCarloMover::last_accepted_score_

private

accepted structure

Definition at line 361 of file GenericMonteCarloMover.hh.

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

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

private

Definition at line 317 of file GenericMonteCarloMover.hh.

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

Real protocols::simple_moves::GenericMonteCarloMover::lowest_score_

private

lowest energy structure we've seen

Definition at line 364 of file GenericMonteCarloMover.hh.

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

PoseOP protocols::simple_moves::GenericMonteCarloMover::lowest_score_pose_

private

lowest energy structure we've seen

Definition at line 370 of file GenericMonteCarloMover.hh.

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

Size protocols::simple_moves::GenericMonteCarloMover::maxtrials_

private

max number of MC trials

Definition at line 293 of file GenericMonteCarloMover.hh.

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

MCA protocols::simple_moves::GenericMonteCarloMover::mc_accepted_

private

result of the last call to boltzmann

Definition at line 373 of file GenericMonteCarloMover.hh.

Referenced by boltzmann(), and mc_accpeted().

MoverOP protocols::simple_moves::GenericMonteCarloMover::mover_

private

mover

Definition at line 302 of file GenericMonteCarloMover.hh.

Referenced by apply(), parse_my_tag(), set_mover(), and show_counters().

utility::pointer::owning_ptr< protocols::moves::DataMapObj< bool > > protocols::simple_moves::GenericMonteCarloMover::mover_stopping_condition_

private

Definition at line 389 of file GenericMonteCarloMover.hh.

Referenced by apply(), and parse_my_tag().

utility::pointer::owning_ptr< protocols::moves::DataMapObj< std::string > > protocols::simple_moves::GenericMonteCarloMover::mover_tag_

private

Definition at line 394 of file GenericMonteCarloMover.hh.

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

Size protocols::simple_moves::GenericMonteCarloMover::next_trigger_id_

private

Next trigger identifier to be assigned.

Definition at line 384 of file GenericMonteCarloMover.hh.

Referenced by add_trigger(), and initialize().

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

private

Count the number of rejections each filter resulted in.

Definition at line 320 of file GenericMonteCarloMover.hh.

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

Size protocols::simple_moves::GenericMonteCarloMover::number_designable_

private

number of designable positions

Definition at line 296 of file GenericMonteCarloMover.hh.

Referenced by apply().

bool protocols::simple_moves::GenericMonteCarloMover::preapply_

private

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

Definition at line 342 of file GenericMonteCarloMover.hh.

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

Size protocols::simple_moves::GenericMonteCarloMover::rank_by_filter_

private

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

Definition at line 351 of file GenericMonteCarloMover.hh.

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

bool protocols::simple_moves::GenericMonteCarloMover::recover_low_

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)

Definition at line 347 of file GenericMonteCarloMover.hh.

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

bool protocols::simple_moves::GenericMonteCarloMover::reset_baselines_

private

Definition at line 396 of file GenericMonteCarloMover.hh.

String protocols::simple_moves::GenericMonteCarloMover::sample_type_

private

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

Definition at line 334 of file GenericMonteCarloMover.hh.

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

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

private

Definition at line 316 of file GenericMonteCarloMover.hh.

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

std::string protocols::simple_moves::GenericMonteCarloMover::saved_accept_file_name_

private

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

Definition at line 392 of file GenericMonteCarloMover.hh.

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

std::string protocols::simple_moves::GenericMonteCarloMover::saved_trial_number_file_

private

Definition at line 393 of file GenericMonteCarloMover.hh.

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

ScoreFunctionOP protocols::simple_moves::GenericMonteCarloMover::scorefxn_

private

Pose is evaluated by ScoreFunctionOP during MC trials.

Definition at line 323 of file GenericMonteCarloMover.hh.

Referenced by add_filter(), apply(), parse_my_tag(), scoring(), set_scorefxn(), and show_counters().

protocols::filters::FilterOP protocols::simple_moves::GenericMonteCarloMover::stopping_condition_

private

Definition at line 388 of file GenericMonteCarloMover.hh.

Referenced by stopping_condition().

PackerTaskOP protocols::simple_moves::GenericMonteCarloMover::task_

private

task

Definition at line 305 of file GenericMonteCarloMover.hh.

Size protocols::simple_moves::GenericMonteCarloMover::task_scaling_

private

multiply the number_designable_ by task_scaling to get the number of trials

Definition at line 299 of file GenericMonteCarloMover.hh.

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

Real protocols::simple_moves::GenericMonteCarloMover::temperature_

private

acceptance criterion temperature

Definition at line 329 of file GenericMonteCarloMover.hh.

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

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

private

acceptance criterion temperature

Definition at line 315 of file GenericMonteCarloMover.hh.

Referenced by add_filter(), and boltzmann().

int protocols::simple_moves::GenericMonteCarloMover::trial_counter_

private

diagnostics

Definition at line 379 of file GenericMonteCarloMover.hh.

Referenced by boltzmann(), initialize(), reset(), show_counters(), and show_scores().

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

private

Collection of function callbacks.

Definition at line 387 of file GenericMonteCarloMover.hh.

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

std::string protocols::simple_moves::GenericMonteCarloMover::user_defined_mover_name_

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.

Definition at line 395 of file GenericMonteCarloMover.hh.

Referenced by boltzmann(), and parse_my_tag().

---

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

• src/protocols/simple_moves/GenericMonteCarloMover.hh
• src/protocols/simple_moves/GenericMonteCarloMover.cc