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protocols::simple_moves::GenericMonteCarloMover Class Reference

#include <GenericMonteCarloMover.hh>

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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)
 
Moveroperator= (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 Stringsinfo ()
 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< FilterOPfilters_
 Pose is evaluated by FilterOP which can do report_sm() during MC trials. More...
 
utility::vector1< booladaptive_
 
utility::vector1< Realtemperatures_
 acceptance criterion temperature More...
 
utility::vector1< Stringsample_types_
 
utility::vector1< Reallast_accepted_scores_
 
utility::vector1< core::Sizenum_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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::GenericMonteCarloMover::GenericMonteCarloMover ( )

default constructor

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

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

References initialize().

protocols::simple_moves::GenericMonteCarloMover::~GenericMonteCarloMover ( )

destructor

Member Function Documentation

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

Referenced by apply(), and parse_my_tag().

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

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.

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.

References next_trigger_id_, and triggers_.

void protocols::simple_moves::GenericMonteCarloMover::apply ( Pose pose)
virtual
bool protocols::simple_moves::GenericMonteCarloMover::boltzmann ( Pose pose)
GenericMonteCarloMover::MoverOP protocols::simple_moves::GenericMonteCarloMover::clone ( ) const
virtual

create copy constructor

clone this object

Reimplemented from protocols::moves::Mover.

References GenericMonteCarloMover().

Referenced by parse_my_tag().

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

return the lowest score

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.

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.

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.

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

void protocols::simple_moves::GenericMonteCarloMover::initialize ( )
GenericMonteCarloMover::PoseOP protocols::simple_moves::GenericMonteCarloMover::last_accepted_pose ( ) const

return the last accepted pose

References last_accepted_pose_.

Referenced by apply().

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

return the last accepted score

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

return the lowest score

References lowest_score_.

Referenced by boltzmann(), and show_scores().

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

return the lowest score pose

References lowest_score_pose_.

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

return mc_accepted

References mc_accepted_.

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

Returns the number of triggers.

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
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

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

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.

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

void protocols::simple_moves::GenericMonteCarloMover::reset ( Pose pose)
void protocols::simple_moves::GenericMonteCarloMover::reset_baselines ( bool const  r)
inline
bool protocols::simple_moves::GenericMonteCarloMover::reset_baselines ( ) const
inline
void protocols::simple_moves::GenericMonteCarloMover::save_trial_number_to_checkpoint ( core::Size const  i) const

References saved_trial_number_file_.

Referenced by apply().

std::string protocols::simple_moves::GenericMonteCarloMover::saved_accept_file_name ( ) const
void protocols::simple_moves::GenericMonteCarloMover::saved_accept_file_name ( std::string const  s)
std::string protocols::simple_moves::GenericMonteCarloMover::saved_trial_number_file ( ) const
void protocols::simple_moves::GenericMonteCarloMover::saved_trial_number_file ( std::string const  s)
ScoreFunctionOP protocols::simple_moves::GenericMonteCarloMover::score_function ( ) const
inline

Return the score function in use.

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

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.

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.

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

References maxtrials_.

void protocols::simple_moves::GenericMonteCarloMover::set_mover ( MoverOP const &  mover)

set mover

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.

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.

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

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.

References filters_, and scorefxn_.

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

set task multiplier to calculate trials from task

References task_scaling_.

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

set temperature

set temperatrue

References temperature_.

void protocols::simple_moves::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_, 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

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)

References stopping_condition_.

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

References stopping_condition_.

Referenced by apply(), and parse_my_tag().

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

setter

References factory_.

Referenced by parse_task_operations().

Member Data Documentation

int protocols::simple_moves::GenericMonteCarloMover::accept_counter_
private
core::Size protocols::simple_moves::GenericMonteCarloMover::adaptation_period_
private
utility::vector1< bool > protocols::simple_moves::GenericMonteCarloMover::adaptive_
private

Referenced by add_filter(), and boltzmann().

bool protocols::simple_moves::GenericMonteCarloMover::adaptive_movers_
private
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.

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

Real protocols::simple_moves::GenericMonteCarloMover::current_score_
private

current score

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.

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

Real protocols::simple_moves::GenericMonteCarloMover::energy_gap_counter_
private
TaskFactoryOP protocols::simple_moves::GenericMonteCarloMover::factory_
private

task factory

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.

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"

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

PoseOP protocols::simple_moves::GenericMonteCarloMover::last_accepted_pose_
private

accepted structure

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

Real protocols::simple_moves::GenericMonteCarloMover::last_accepted_score_
private

accepted structure

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

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

lowest energy structure we've seen

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

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

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

MCA protocols::simple_moves::GenericMonteCarloMover::mc_accepted_
private

result of the last call to boltzmann

Referenced by boltzmann(), and mc_accpeted().

MoverOP protocols::simple_moves::GenericMonteCarloMover::mover_
private

mover

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

Referenced by apply(), and parse_my_tag().

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

Next trigger identifier to be assigned.

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.

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

Size protocols::simple_moves::GenericMonteCarloMover::number_designable_
private

number of designable positions

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.)

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())

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)

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

bool protocols::simple_moves::GenericMonteCarloMover::reset_baselines_
private
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

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

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

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?

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

std::string protocols::simple_moves::GenericMonteCarloMover::saved_trial_number_file_
private
ScoreFunctionOP protocols::simple_moves::GenericMonteCarloMover::scorefxn_
private

Pose is evaluated by ScoreFunctionOP during MC trials.

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

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

Referenced by stopping_condition().

PackerTaskOP protocols::simple_moves::GenericMonteCarloMover::task_
private

task

Size protocols::simple_moves::GenericMonteCarloMover::task_scaling_
private

multiply the number_designable_ by task_scaling to get the number of trials

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

Real protocols::simple_moves::GenericMonteCarloMover::temperature_
private

acceptance criterion temperature

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

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

acceptance criterion temperature

Referenced by add_filter(), and boltzmann().

int protocols::simple_moves::GenericMonteCarloMover::trial_counter_
private

diagnostics

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.

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.

Referenced by boltzmann(), and parse_my_tag().


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