Rosetta Protocols  2014.35
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>

Public Member Functions

virtual ~FragmentSampler ()
 FragmentSampler (topology_broker::TopologyBrokerOP broker)
 This constructor does not work – Fix it before using it. More...
virtual moves::MoverOP clone () const
 FragmentSampler has virtual functions... use this to obtain a new instance. More...
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
virtual void set_cycles (core::Real increase_cycles=1.0)
virtual 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)
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 ~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
void set_type (std::string const &setting)
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
void set_current_tag (std::string const &new_tag)
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP get_input_pose () const
PoseCOP get_native_pose () const
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
void type (const std::string &type_in)
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_type () const
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
virtual Stringsinfo ()
 non-const accessor More...
virtual Strings const & info () const
 const accessor 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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

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 &, Size, Size)
virtual void prepare_loop_in_stage4 (core::pose::Pose &, Size, 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

Size stage1_cycles_
Size stage2_cycles_
Size stage3_cycles_
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_
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::stringStrings

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

Constructor & Destructor Documentation

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

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

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

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

Referenced by clone().

Member Function Documentation

void protocols::abinitio::FragmentSampler::apply ( core::pose::Pose pose)
bool protocols::abinitio::FragmentSampler::bQuickTest ( ) const

References bQuickTest_.

Referenced by set_default_options().

bool protocols::abinitio::FragmentSampler::check_loops ( core::pose::Pose pose)
void protocols::abinitio::FragmentSampler::checkpointed_cycle_block ( core::pose::Pose pose,
StageID  stage_id,
void(FragmentSampler::*)(core::pose::Pose &)  cycles 
moves::MoverOP protocols::abinitio::FragmentSampler::clone ( ) const

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

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

References FragmentSampler().

scoring::ScoreFunction const & protocols::abinitio::FragmentSampler::current_scorefxn ( ) const
void protocols::abinitio::FragmentSampler::current_scorefxn ( core::scoring::ScoreFunction const &  scorefxn)
void protocols::abinitio::FragmentSampler::do_stage1_cycles ( core::pose::Pose pose)
void protocols::abinitio::FragmentSampler::do_stage2_cycles ( core::pose::Pose pose)
void protocols::abinitio::FragmentSampler::do_stage3_cycles ( core::pose::Pose pose)

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(), numeric::mod(), mover(), option, 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().

void protocols::abinitio::FragmentSampler::do_stage4_cycles ( core::pose::Pose pose)
virtual checkpoint::CheckPointer& protocols::abinitio::FragmentSampler::get_checkpoints ( )
std::string protocols::abinitio::FragmentSampler::get_name ( ) const

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

Implements protocols::moves::Mover.

Reimplemented in protocols::abinitio::ConstraintFragmentSampler.

basic::ProfTag protocols::abinitio::FragmentSampler::id2proftag ( StageID  id)
std::string const& protocols::abinitio::FragmentSampler::id2string ( StageID  id)
bool protocols::abinitio::FragmentSampler::just_smooth_cycles ( ) const

References just_smooth_cycles_.

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

References mc_.

moves::MonteCarloOP protocols::abinitio::FragmentSampler::mc_ptr ( )
moves::MoverOP protocols::abinitio::FragmentSampler::mover ( core::pose::Pose const &  pose,
StageID  stage_id,
core::scoring::ScoreFunction const &  scorefxn,
core::Real  progress = 1.0 
void protocols::abinitio::FragmentSampler::prepare_loop_in_stage3 ( core::pose::Pose pose,
Size  iteration,
Size  total 
void protocols::abinitio::FragmentSampler::prepare_loop_in_stage4 ( core::pose::Pose pose,
Size  iteration,
Size  total 
void protocols::abinitio::FragmentSampler::prepare_stage1 ( core::pose::Pose pose)
void protocols::abinitio::FragmentSampler::prepare_stage2 ( core::pose::Pose pose)
void protocols::abinitio::FragmentSampler::prepare_stage3 ( core::pose::Pose pose)

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

Referenced by apply().

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

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

Referenced by apply().

void protocols::abinitio::FragmentSampler::recover_low ( core::pose::Pose pose,
StageID  stage 
void protocols::abinitio::FragmentSampler::register_options ( )
void protocols::abinitio::FragmentSampler::replace_scorefxn ( core::pose::Pose pose,
StageID  stage,
core::Real  intra_stage_progress 
void protocols::abinitio::FragmentSampler::set_current_weight ( core::scoring::ScoreType  type,
core::Real  setting 
void protocols::abinitio::FragmentSampler::set_cycles ( core::Real  increase_cycles = 1.0)
void protocols::abinitio::FragmentSampler::set_default_mc ( core::scoring::ScoreFunction const &  scorefxn)
void protocols::abinitio::FragmentSampler::set_default_options ( )
void protocols::abinitio::FragmentSampler::set_default_scores ( )
void protocols::abinitio::FragmentSampler::set_defaults ( )
void protocols::abinitio::FragmentSampler::set_mc ( moves::MonteCarloOP  mc_in)

References mc_.

Referenced by set_default_mc().

void protocols::abinitio::FragmentSampler::set_score_weight ( core::scoring::ScoreType  type,
core::Real  setting,
StageID  stage = ALL_STAGES 
void protocols::abinitio::FragmentSampler::set_stage4_cycles ( core::Size  stage4_cycles_new)

References stage4_cycles_.

core::Size protocols::abinitio::FragmentSampler::stage1_cycles ( ) const
core::Size protocols::abinitio::FragmentSampler::stage2_cycles ( ) const

References stage2_cycles_.

Referenced by do_stage2_cycles().

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

References stage3_cycles_.

Referenced by do_stage3_cycles().

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

References stage4_cycles_.

Referenced by do_stage4_cycles().

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

References topology_broker_.

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

Member Data Documentation

bool protocols::abinitio::FragmentSampler::apply_large_frags_

Referenced by set_default_options().

bool protocols::abinitio::FragmentSampler::bQuickTest_

Referenced by bQuickTest(), and set_default_options().

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

Referenced by get_checkpoints().

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

Referenced by id2proftag().

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

Referenced by id2string().

bool protocols::abinitio::FragmentSampler::just_smooth_cycles_
moves::MonteCarloOP protocols::abinitio::FragmentSampler::mc_
utility::vector1< StageID > protocols::abinitio::FragmentSampler::recover_low_stages_

Referenced by recover_low(), and set_default_options().

core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage1_
core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage2_
core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage3a_
core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage3b_
core::scoring::ScoreFunctionOP protocols::abinitio::FragmentSampler::score_stage4_
bool protocols::abinitio::FragmentSampler::short_insert_region_
utility::vector1< StageID > protocols::abinitio::FragmentSampler::skip_stages_

Referenced by apply(), and set_default_options().

Size protocols::abinitio::FragmentSampler::stage1_cycles_

Referenced by set_cycles(), and stage1_cycles().

Size protocols::abinitio::FragmentSampler::stage2_cycles_

Referenced by set_cycles(), and stage2_cycles().

Size protocols::abinitio::FragmentSampler::stage3_cycles_

Referenced by set_cycles(), and stage3_cycles().

Size protocols::abinitio::FragmentSampler::stage4_cycles_
core::Real protocols::abinitio::FragmentSampler::temperature_
topology_broker::TopologyBrokerOP protocols::abinitio::FragmentSampler::topology_broker_

Referenced by apply(), and topology_broker().

Size protocols::abinitio::FragmentSampler::total_trials_

Referenced by apply(), and checkpointed_cycle_block().

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