Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Private Types | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
protocols::abinitio::FragmentSampler Class Reference

#include <FragmentSampler.hh>

Inheritance diagram for protocols::abinitio::FragmentSampler:
Inheritance graph

Public Member Functions

 ~FragmentSampler () override
 FragmentSampler (topology_broker::TopologyBrokerOP broker)
 This constructor does not work – Fix it before using it. More...
moves::MoverOP clone () const override
 FragmentSampler has virtual functions... use this to obtain a new instance. More...
void apply (core::pose::Pose &pose) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void set_cycles (core::Real increase_cycles=1.0)
void set_score_weight (core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES)
 sets a score weight for all stages of abinitio More...
virtual checkpoint::CheckPointerget_checkpoints ()
void topology_broker (topology_broker::TopologyBrokerOP set)
core::scoring::ScoreFunction const & current_scorefxn () const
bool just_smooth_cycles () const
core::Size stage1_cycles () const
core::Size stage2_cycles () const
core::Size stage3_cycles () const
void set_stage4_cycles (core::Size stage4_cycles_new)
core::Size stage4_cycles () const
bool bQuickTest () const
bool check_loops (core::pose::Pose &pose)
- 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...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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 Stringsinfo ()
 non-const accessor More...
virtual Strings const & info () const
 const accessor More...
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions

static void register_options ()
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
static void register_options ()
 Overload this static method if you access options within the mover. More...

Protected Member Functions

topology_broker::TopologyBroker const & topology_broker ()
void set_mc (moves::MonteCarloOP)
moves::MonteCarlomc ()
moves::MonteCarlo const & mc () const
void set_defaults ()
void current_scorefxn (core::scoring::ScoreFunction const &scorefxn)
void recover_low (core::pose::Pose &pose, StageID stage)
virtual void replace_scorefxn (core::pose::Pose &pose, StageID stage, core::Real intra_stage_progress)
void set_current_weight (core::scoring::ScoreType type, core::Real setting)
virtual void do_stage1_cycles (core::pose::Pose &pose)
virtual void do_stage2_cycles (core::pose::Pose &pose)
virtual void do_stage3_cycles (core::pose::Pose &pose)
virtual void do_stage4_cycles (core::pose::Pose &pose)
virtual moves::MoverOP mover (core::pose::Pose const &pose, StageID stage_id, core::scoring::ScoreFunction const &scorefxn, core::Real progress=1.0)
virtual void prepare_stage1 (core::pose::Pose &pose)
virtual void prepare_stage2 (core::pose::Pose &pose)
virtual void prepare_stage3 (core::pose::Pose &pose)
virtual void prepare_stage4 (core::pose::Pose &pose)
virtual void prepare_loop_in_stage3 (core::pose::Pose &, core::Size, core::Size)
virtual void prepare_loop_in_stage4 (core::pose::Pose &, core::Size, core::Size)
moves::MonteCarloOP mc_ptr ()
- 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

core::Size stage1_cycles_
core::Size stage2_cycles_
core::Size stage3_cycles_
core::Size stage4_cycles_

Private Types

typedef moves::Mover Parent
typedef moves::Mover BaseClass

Private Member Functions

void set_default_options ()
void set_default_scores ()
void set_default_mc (core::scoring::ScoreFunction const &scorefxn)
void checkpointed_cycle_block (core::pose::Pose &, StageID, void(FragmentSampler::*cycles)(core::pose::Pose &))
std::string const & id2string (StageID id)
basic::ProfTag id2proftag (StageID id)

Private Attributes

core::scoring::ScoreFunctionOP score_stage1_
core::scoring::ScoreFunctionOP score_stage2_
core::scoring::ScoreFunctionOP score_stage3a_
core::scoring::ScoreFunctionOP score_stage3b_
core::scoring::ScoreFunctionOP score_stage4_
bool apply_large_frags_
bool short_insert_region_
bool just_smooth_cycles_
bool bQuickTest_
core::Real temperature_
moves::MonteCarloOP mc_
core::Size total_trials_
topology_broker::TopologyBrokerOP topology_broker_
checkpoint::CheckPointer checkpoints_
utility::vector1< StageIDrecover_low_stages_
utility::vector1< StageIDskip_stages_

Static Private Attributes

static std::string const id2string_ [] = { "all_stages", "stage1", "stage2", "stage3", "stage3", "stage3", "stage4"}
static basic::ProfTag const id2proftag_ [] = { basic::STAGE1, basic::STAGE1, basic::STAGE2, basic::STAGE3, basic::STAGE3, basic::STAGE3, basic::STAGE4 }

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings

Detailed Description

@ detail general usage: FragmentSampler abinitio; abinitio.init( pose ); ... while(nstruct) { abinitio.apply( pose ); }

call FragmentSampler::register_options() before core::init::init to add relevant options to the applications help

, with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:

The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() ...

Behaviour can be changed in the following ways:

use non-classic FragmentMover --> eg. not uniformly sampled fragments, but using some weighting --> large and small moves doesn't have to be 3mers and 9mers... use other movers... —> or other fragets for the "convenience constructor" use custom trial classes --> overload update_moves()

change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves ...

change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()

Member Typedef Documentation

◆ BaseClass

◆ Parent

Constructor & Destructor Documentation

◆ ~FragmentSampler()

protocols::abinitio::FragmentSampler::~FragmentSampler ( )

◆ FragmentSampler()

protocols::abinitio::FragmentSampler::FragmentSampler ( topology_broker::TopologyBrokerOP  broker)

This constructor does not work – Fix it before using it.

@detail large (stage1/stage2) small(stage2/stage3/stage4) smooth_small ( stage3/stage4)

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

Member Function Documentation

◆ apply()

void protocols::abinitio::FragmentSampler::apply ( core::pose::Pose )

◆ bQuickTest()

bool protocols::abinitio::FragmentSampler::bQuickTest ( ) const

References bQuickTest_.

Referenced by set_default_options().

◆ check_loops()

bool protocols::abinitio::FragmentSampler::check_loops ( core::pose::Pose pose)

◆ checkpointed_cycle_block()

void protocols::abinitio::FragmentSampler::checkpointed_cycle_block ( core::pose::Pose pose,
StageID  stage_id,
void(FragmentSampler::*)(core::pose::Pose &)  cycles 

◆ clone()

moves::MoverOP protocols::abinitio::FragmentSampler::clone ( ) const

FragmentSampler has virtual functions... use this to obtain a new instance.

Reimplemented from protocols::moves::Mover.

◆ current_scorefxn() [1/2]

scoring::ScoreFunction const & protocols::abinitio::FragmentSampler::current_scorefxn ( ) const

◆ current_scorefxn() [2/2]

void protocols::abinitio::FragmentSampler::current_scorefxn ( core::scoring::ScoreFunction const &  scorefxn)

◆ do_stage1_cycles()

void protocols::abinitio::FragmentSampler::do_stage1_cycles ( core::pose::Pose pose)

◆ do_stage2_cycles()

void protocols::abinitio::FragmentSampler::do_stage2_cycles ( core::pose::Pose pose)

◆ do_stage3_cycles()

void protocols::abinitio::FragmentSampler::do_stage3_cycles ( core::pose::Pose pose)

@detail stage3 cycles: nloop1 : outer iterations nloop2 : inner iterations stage3_cycle : trials per inner iteration every inner iteration we switch between score_stage3a ( default: score2 ) and score_stage3b ( default: score 5 )

prepare_loop_in_stage3() is called before the stage3_cycles() of trials are started.

first outer loop-iteration is done with TrialMover trial_large() all following iterations with trial_small()

start each iteration with the lowest_score_pose. ( mc->recover_low() – called in prepare_loop_in_stage3() )

References protocols::moves::RepeatMover::apply(), protocols::checkpoint::CheckPointer::checkpoint(), current_scorefxn(), protocols::checkpoint::CheckPointer::debug(), get_checkpoints(), protocols::moves::Mover::get_current_tag(), mc_ptr(), mover(), protocols::jd2::output_intermediate_pose(), prepare_loop_in_stage3(), recover_low(), short_insert_region_, stage3_cycles(), protocols::abinitio::STAGE_3a, protocols::abinitio::STAGE_3b, and tr().

Referenced by apply().

◆ do_stage4_cycles()

void protocols::abinitio::FragmentSampler::do_stage4_cycles ( core::pose::Pose pose)

◆ get_checkpoints()

virtual checkpoint::CheckPointer& protocols::abinitio::FragmentSampler::get_checkpoints ( )

◆ get_name()

std::string protocols::abinitio::FragmentSampler::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ id2proftag()

basic::ProfTag protocols::abinitio::FragmentSampler::id2proftag ( StageID  id)

◆ id2string()

std::string const& protocols::abinitio::FragmentSampler::id2string ( StageID  id)

◆ just_smooth_cycles()

bool protocols::abinitio::FragmentSampler::just_smooth_cycles ( ) const

References just_smooth_cycles_.

◆ mc() [1/2]

moves::MonteCarlo& protocols::abinitio::FragmentSampler::mc ( )

◆ mc() [2/2]

moves::MonteCarlo const& protocols::abinitio::FragmentSampler::mc ( ) const

References mc_.

◆ mc_ptr()

moves::MonteCarloOP protocols::abinitio::FragmentSampler::mc_ptr ( )

◆ mover()

moves::MoverOP protocols::abinitio::FragmentSampler::mover ( core::pose::Pose const &  pose,
StageID  stage_id,
core::scoring::ScoreFunction const &  scorefxn,
core::Real  progress = 1.0 

◆ prepare_loop_in_stage3()

void protocols::abinitio::FragmentSampler::prepare_loop_in_stage3 ( core::pose::Pose pose,
core::Size  iteration,
core::Size  total 

◆ prepare_loop_in_stage4()

void protocols::abinitio::FragmentSampler::prepare_loop_in_stage4 ( core::pose::Pose pose,
core::Size  iteration,
core::Size  total 

◆ prepare_stage1()

void protocols::abinitio::FragmentSampler::prepare_stage1 ( core::pose::Pose pose)

◆ prepare_stage2()

void protocols::abinitio::FragmentSampler::prepare_stage2 ( core::pose::Pose pose)

◆ prepare_stage3()

void protocols::abinitio::FragmentSampler::prepare_stage3 ( core::pose::Pose pose)

References replace_scorefxn(), and protocols::abinitio::STAGE_3a.

Referenced by apply().

◆ prepare_stage4()

void protocols::abinitio::FragmentSampler::prepare_stage4 ( core::pose::Pose pose)

References replace_scorefxn(), and protocols::abinitio::STAGE_4.

Referenced by apply().

◆ recover_low()

void protocols::abinitio::FragmentSampler::recover_low ( core::pose::Pose pose,
StageID  stage 

◆ register_options()

void protocols::abinitio::FragmentSampler::register_options ( )

@detail call this: FragmentSampler::register_options() before devel::init(). Derived classes that overload this function should also call Parent::register_options()

References core::pack::interaction_graph::debug, and protocols::moves::Mover::register_options().

◆ replace_scorefxn()

void protocols::abinitio::FragmentSampler::replace_scorefxn ( core::pose::Pose pose,
StageID  stage,
core::Real  intra_stage_progress 

◆ set_current_weight()

void protocols::abinitio::FragmentSampler::set_current_weight ( core::scoring::ScoreType  type,
core::Real  setting 

◆ set_cycles()

void protocols::abinitio::FragmentSampler::set_cycles ( core::Real  increase_cycles = 1.0)

◆ set_default_mc()

void protocols::abinitio::FragmentSampler::set_default_mc ( core::scoring::ScoreFunction const &  scorefxn)

◆ set_default_options()

void protocols::abinitio::FragmentSampler::set_default_options ( )

◆ set_default_scores()

void protocols::abinitio::FragmentSampler::set_default_scores ( )

◆ set_defaults()

void protocols::abinitio::FragmentSampler::set_defaults ( )

◆ set_mc()

void protocols::abinitio::FragmentSampler::set_mc ( moves::MonteCarloOP  mc_in)

References mc_.

Referenced by set_default_mc().

◆ set_score_weight()

void protocols::abinitio::FragmentSampler::set_score_weight ( core::scoring::ScoreType  type,
core::Real  setting,
StageID  stage = ALL_STAGES 

◆ set_stage4_cycles()

void protocols::abinitio::FragmentSampler::set_stage4_cycles ( core::Size  stage4_cycles_new)

References stage4_cycles_.

◆ stage1_cycles()

core::Size protocols::abinitio::FragmentSampler::stage1_cycles ( ) const

◆ stage2_cycles()

core::Size protocols::abinitio::FragmentSampler::stage2_cycles ( ) const

References stage2_cycles_.

Referenced by do_stage2_cycles().

◆ stage3_cycles()

core::Size protocols::abinitio::FragmentSampler::stage3_cycles ( ) const

References stage3_cycles_.

Referenced by do_stage3_cycles().

◆ stage4_cycles()

core::Size protocols::abinitio::FragmentSampler::stage4_cycles ( ) const

References stage4_cycles_.

Referenced by do_stage4_cycles().

◆ topology_broker() [1/2]

topology_broker::TopologyBroker const & protocols::abinitio::FragmentSampler::topology_broker ( )

◆ topology_broker() [2/2]

void protocols::abinitio::FragmentSampler::topology_broker ( topology_broker::TopologyBrokerOP  set)

References topology_broker_.

Member Data Documentation

◆ apply_large_frags_

bool protocols::abinitio::FragmentSampler::apply_large_frags_

Referenced by set_default_options().

◆ bQuickTest_

bool protocols::abinitio::FragmentSampler::bQuickTest_

Referenced by bQuickTest(), and set_default_options().

◆ checkpoints_

checkpoint::CheckPointer protocols::abinitio::FragmentSampler::checkpoints_

Referenced by get_checkpoints().

◆ id2proftag_

basic::ProfTag const protocols::abinitio::FragmentSampler::id2proftag_ = { basic::STAGE1, basic::STAGE1, basic::STAGE2, basic::STAGE3, basic::STAGE3, basic::STAGE3, basic::STAGE4 }

Referenced by id2proftag().

◆ id2string_

std::string const protocols::abinitio::FragmentSampler::id2string_ = { "all_stages", "stage1", "stage2", "stage3", "stage3", "stage3", "stage4"}

Referenced by id2string().

◆ just_smooth_cycles_

bool protocols::abinitio::FragmentSampler::just_smooth_cycles_

◆ mc_

moves::MonteCarloOP protocols::abinitio::FragmentSampler::mc_

◆ recover_low_stages_

utility::vector1< StageID > protocols::abinitio::FragmentSampler::recover_low_stages_

Referenced by recover_low(), and set_default_options().

◆ score_stage1_

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage1_

◆ score_stage2_

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage2_

◆ score_stage3a_

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage3a_

◆ score_stage3b_

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage3b_

◆ score_stage4_

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage4_

◆ short_insert_region_

bool protocols::abinitio::FragmentSampler::short_insert_region_

◆ skip_stages_

utility::vector1< StageID > protocols::abinitio::FragmentSampler::skip_stages_

Referenced by apply(), and set_default_options().

◆ stage1_cycles_

core::Size protocols::abinitio::FragmentSampler::stage1_cycles_

Referenced by set_cycles(), and stage1_cycles().

◆ stage2_cycles_

core::Size protocols::abinitio::FragmentSampler::stage2_cycles_

Referenced by set_cycles(), and stage2_cycles().

◆ stage3_cycles_

core::Size protocols::abinitio::FragmentSampler::stage3_cycles_

Referenced by set_cycles(), and stage3_cycles().

◆ stage4_cycles_

core::Size protocols::abinitio::FragmentSampler::stage4_cycles_

◆ temperature_

core::Real protocols::abinitio::FragmentSampler::temperature_

◆ topology_broker_

topology_broker::TopologyBrokerOP protocols::abinitio::FragmentSampler::topology_broker_

Referenced by apply(), and topology_broker().

◆ total_trials_

core::Size protocols::abinitio::FragmentSampler::total_trials_

Referenced by apply(), and checkpointed_cycle_block().

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