Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::abinitio::ClassicAbinitio Class Reference

#include <ClassicAbinitio.hh>

Inheritance diagram for protocols::abinitio::ClassicAbinitio:
Inheritance graph
[legend]
Collaboration diagram for protocols::abinitio::ClassicAbinitio:
Collaboration graph
[legend]

Public Types

enum  StageID {
  ALL_STAGES = 0, STAGE_1, STAGE_2, STAGE_3a,
  STAGE_3b, STAGE_4, STAGE_5
}
 
- Public Types inherited from protocols::abinitio::Protocol
typedef Mover BaseClass
 
- 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

 ClassicAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int)
 This constructor does not work – Fix it before using it. More...
 
 ClassicAbinitio (core::fragment::FragSetCOP fragset_small, core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap)
 constructor: supply fragsets for large and small fragment moves More...
 
 ClassicAbinitio (ClassicAbinitio const &src)
 Explicit copy constructor since this class contains OPs of other classes. More...
 
 ~ClassicAbinitio ()
 Explicit destructor since this class contains OPs of other classes. More...
 
virtual void init (core::pose::Pose const &pose)
 setup moves, mc-object, scores More...
 
virtual moves::MoverOP clone () const
 ClassicAbinitio 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...
 
simple_moves::FragmentMoverOP smooth_move_small ()
 
simple_moves::FragmentMoverOP brute_move_small ()
 
simple_moves::FragmentMoverOP brute_move_large ()
 
virtual void set_movemap (core::kinematics::MoveMapCOP mm)
 
core::kinematics::MoveMapCOP movemap ()
 
void set_moves (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small)
 
void set_mc (moves::MonteCarloOP)
 
moves::MonteCarlomc ()
 
moves::MonteCarlo const & mc () const
 
virtual void set_cycles (core::Real increase_cycles=1.0)
 
Size total_trials () const
 
virtual void set_score_weight (core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES)
 for debugging, one wants to have access to the native pose. More...
 
bool just_smooth_cycles () const
 
Size stage1_cycles () const
 
Size stage2_cycles () const
 
Size stage3_cycles () const
 
void set_stage4_cycles (Size stage4_cycles_new)
 
Size stage4_cycles () const
 
Size stage5_cycles () const
 
bool bQuickTest () const
 
void set_skip_stage1 (bool setting)
 
void set_skip_stage2 (bool setting)
 
- Public Member Functions inherited from protocols::abinitio::Protocol
 Protocol ()
 
 ~Protocol ()
 
void set_evaluation (evaluation::MetaPoseEvaluatorOP ev)
 
void add_evaluation (evaluation::PoseEvaluatorOP ev)
 
void evaluate_pose (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const
 
evaluation::MetaPoseEvaluatorOP evaluator ()
 
void set_kinematics (abinitio::KinematicControlOP kc)
 
abinitio::KinematicControl const & kinematics ()
 
virtual bool start_from_centroid () const
 
virtual bool return_centroid () const
 
virtual void return_centroid (bool setting)
 
void set_fullatom_scorefxn (core::scoring::ScoreFunctionOP sfxn)
 
void set_centroid_scorefxn (core::scoring::ScoreFunctionOP sfxn)
 
void set_silentout_file_name (std::string str)
 
core::scoring::ScoreFunctionOP fullatom_scorefxn ()
 
core::scoring::ScoreFunctionOP centroid_scorefxn ()
 
virtual checkpoint::CheckPointerget_checkpoints ()
 
- 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)
 
virtual void parse_my_tag (TagPtr const tag, 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
 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...
 
virtual MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Static Public Member Functions

static void register_options ()
 
- Static Public Member Functions inherited from protocols::abinitio::Protocol
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. 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...
 

Public Attributes

bool bSkipStage1_
 
bool bSkipStage2_
 
bool bSkipStage3_
 
bool bSkipStage4_
 
bool bSkipStage5_
 
utility::vector1< StageIDrecover_low_stages_
 

Protected Member Functions

virtual void update_moves ()
 
virtual void set_defaults (core::pose::Pose const &pose)
 
virtual void set_default_options ()
 
virtual void set_default_mc (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn)
 
virtual void set_default_scores ()
 
core::scoring::ScoreFunction
const & 
current_scorefxn () const
 
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 bool do_stage1_cycles (core::pose::Pose &pose)
 
virtual bool do_stage2_cycles (core::pose::Pose &pose)
 
virtual bool do_stage3_cycles (core::pose::Pose &pose)
 
virtual bool do_stage4_cycles (core::pose::Pose &pose)
 
virtual bool do_stage5_cycles (core::pose::Pose &pose)
 
virtual moves::TrialMoverOP stage1_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
 
virtual moves::TrialMoverOP stage2_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
 
virtual moves::TrialMoverOP stage3_mover (core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in)
 
virtual moves::TrialMoverOP stage4_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in)
 
virtual moves::TrialMoverOP stage5_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
 
virtual void set_trials ()
 
moves::TrialMoverOP trial_large ()
 
moves::TrialMoverOP trial_small ()
 
moves::TrialMoverOP trial_smooth ()
 
virtual bool prepare_stage1 (core::pose::Pose &pose)
 
virtual bool prepare_stage2 (core::pose::Pose &pose)
 
virtual bool prepare_stage3 (core::pose::Pose &pose)
 
virtual bool prepare_stage4 (core::pose::Pose &pose)
 
virtual bool prepare_stage5 (core::pose::Pose &pose)
 
virtual bool prepare_loop_in_stage3 (core::pose::Pose &, Size, Size)
 
virtual bool prepare_loop_in_stage4 (core::pose::Pose &, Size, Size)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
moves::MonteCarloOP mc_ptr ()
 

Protected Attributes

Size stage1_cycles_
 
Size stage2_cycles_
 
Size stage3_cycles_
 
Size stage4_cycles_
 
Size stage5_cycles_
 

Private Types

typedef Protocol Parent
 

Private Member Functions

ClassicAbinitio const & operator= (ClassicAbinitio const &src)
 Private, unimplemented assignment operator to prevent assignment of this class. Copy-constructor copying only. More...
 

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_
 
core::scoring::ScoreFunctionOP score_stage5_
 
bool apply_large_frags_
 
bool short_insert_region_
 
bool just_smooth_cycles_
 
bool bQuickTest_
 
bool close_chbrk_
 
core::Real temperature_
 
core::kinematics::MoveMapCOP movemap_
 
moves::MonteCarloOP mc_
 
simple_moves::FragmentMoverOP brute_move_small_
 
simple_moves::FragmentMoverOP brute_move_large_
 
simple_moves::FragmentMoverOP smooth_move_small_
 
moves::TrialMoverOP trial_large_
 
moves::TrialMoverOP trial_small_
 
moves::TrialMoverOP smooth_trial_small_
 
Size total_trials_
 

Detailed Description

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

call ClassicAbinitio::register_options() before core::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

Member Enumeration Documentation

Enumerator
ALL_STAGES 
STAGE_1 
STAGE_2 
STAGE_3a 
STAGE_3b 
STAGE_4 
STAGE_5 

Constructor & Destructor Documentation

protocols::abinitio::ClassicAbinitio::ClassicAbinitio ( simple_moves::FragmentMoverOP  brute_move_small,
simple_moves::FragmentMoverOP  brute_move_large,
simple_moves::FragmentMoverOP  smooth_move_small,
int   
)

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

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

References bSkipStage1_, bSkipStage2_, close_chbrk_, protocols::abinitio::Protocol::get_checkpoints(), movemap_, protocols::checkpoint::CheckPointer::set_type(), and protocols::moves::Mover::type().

Referenced by clone().

protocols::abinitio::ClassicAbinitio::ClassicAbinitio ( core::fragment::FragSetCOP  fragset_small,
core::fragment::FragSetCOP  fragset_large,
core::kinematics::MoveMapCOP  movemap 
)
protocols::abinitio::ClassicAbinitio::ClassicAbinitio ( ClassicAbinitio const &  src)

Explicit copy constructor since this class contains OPs of other classes.

Call parent's copy constructor and perform a shallow copy of all the data. NOTE: Shallow copy is only to preserve behavior pre 9/7/2009 when the compiler-provided copy constructor was being invoked.

References apply_large_frags_, bQuickTest_, brute_move_large_, brute_move_small_, bSkipStage1_, bSkipStage2_, bSkipStage3_, bSkipStage4_, bSkipStage5_, close_chbrk_, just_smooth_cycles_, mc_, movemap_, recover_low_stages_, score_stage1_, score_stage2_, score_stage3a_, score_stage3b_, score_stage4_, score_stage5_, short_insert_region_, smooth_move_small_, smooth_trial_small_, stage1_cycles_, stage2_cycles_, stage3_cycles_, stage4_cycles_, stage5_cycles_, temperature_, total_trials_, trial_large_, and trial_small_.

protocols::abinitio::ClassicAbinitio::~ClassicAbinitio ( )

Explicit destructor since this class contains OPs of other classes.

Explicit destructor is needed to destroy all the OPs The compiler does all the work, but it requires that we place the destructor in the .cc file.

Member Function Documentation

void protocols::abinitio::ClassicAbinitio::apply ( core::pose::Pose pose)
virtual

Reimplemented from protocols::abinitio::Protocol.

Reimplemented in protocols::abinitio::Stage1Sampler, protocols::abinitio::JumpingFoldConstraintsWrapper, protocols::abinitio::FoldConstraints, protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraints.

References protocols::abinitio::Protocol::apply(), bSkipStage1_, bSkipStage2_, bSkipStage3_, bSkipStage4_, bSkipStage5_, protocols::checkpoint::CheckPointer::checkpoint(), close_chbrk_, core::pose::Pose::constraint_set(), current_scorefxn(), core::pack::interaction_graph::debug, protocols::checkpoint::CheckPointer::debug(), do_stage1_cycles(), do_stage2_cycles(), do_stage3_cycles(), do_stage4_cycles(), do_stage5_cycles(), protocols::moves::FAIL_RETRY, protocols::checkpoint::CheckPointer::flush_checkpoints(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_tag(), core::scoring::linear_chainbreak, mc(), output_debug_structure(), prepare_stage1(), prepare_stage2(), prepare_stage3(), prepare_stage4(), prepare_stage5(), recover_low(), protocols::moves::MonteCarlo::reset_counters(), protocols::moves::Mover::set_last_move_status(), set_score_weight(), core::scoring::ScoreFunction::show(), protocols::moves::MonteCarlo::show_counters(), stage1_cycles(), stage2_cycles(), stage3_cycles(), stage4_cycles(), stage5_cycles(), STAGE_1, STAGE_2, STAGE_3b, STAGE_4, STAGE_5, protocols::moves::MonteCarlo::total_trials(), total_trials_, and tr().

Referenced by protocols::surface_docking::SurfaceDockingProtocol::abinitio(), protocols::abinitio::DomainAssembly::apply(), and protocols::abinitio::FoldConstraints::apply().

bool protocols::abinitio::ClassicAbinitio::bQuickTest ( ) const
inline
simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::brute_move_large ( )
simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::brute_move_small ( )
moves::MoverOP protocols::abinitio::ClassicAbinitio::clone ( ) const
virtual
scoring::ScoreFunction const & protocols::abinitio::ClassicAbinitio::current_scorefxn ( ) const
protected
void protocols::abinitio::ClassicAbinitio::current_scorefxn ( core::scoring::ScoreFunction const &  scorefxn)
protected
bool protocols::abinitio::ClassicAbinitio::do_stage1_cycles ( core::pose::Pose pose)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::do_stage2_cycles ( core::pose::Pose pose)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::do_stage3_cycles ( core::pose::Pose pose)
protectedvirtual

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::WhileMover::apply(), protocols::moves::RepeatMover::apply(), protocols::checkpoint::CheckPointer::checkpoint(), current_scorefxn(), protocols::checkpoint::CheckPointer::debug(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_tag(), prepare_loop_in_stage3(), recover_low(), short_insert_region_, stage3_cycles(), stage3_mover(), STAGE_3a, STAGE_3b, tr(), trial_large(), and trial_small().

Referenced by apply().

bool protocols::abinitio::ClassicAbinitio::do_stage4_cycles ( core::pose::Pose pose)
protectedvirtual

stage4 cycles: nloop_stage4: iterations stage4_cycle : trials per iteration

first iteration: use trial_small() following iterations: use trial_smooth() only trial_smooth() if just_smooth_cycles==true

prepare_loop_in_stage4() is called each time before the stage4_cycles_ of trials are started.

start each iteration with the lowest_score_pose. ( mc->recover_low() in prepare_loop_in_stage4() )

References protocols::moves::RepeatMover::apply(), protocols::checkpoint::CheckPointer::checkpoint(), current_scorefxn(), protocols::checkpoint::CheckPointer::debug(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_tag(), just_smooth_cycles_, prepare_loop_in_stage4(), recover_low(), stage4_cycles(), stage4_mover(), STAGE_4, tr(), trial_small(), and trial_smooth().

Referenced by apply().

bool protocols::abinitio::ClassicAbinitio::do_stage5_cycles ( core::pose::Pose pose)
protectedvirtual
std::string protocols::abinitio::ClassicAbinitio::get_name ( ) const
virtual

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

Reimplemented from protocols::abinitio::Protocol.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper, protocols::abinitio::FoldConstraints, and protocols::abinitio::KinematicAbinitio.

void protocols::abinitio::ClassicAbinitio::init ( core::pose::Pose const &  pose)
virtual

setup moves, mc-object, scores

can't call this from constructor; virtual functions don't operate until construction has completed.

Reimplemented from protocols::abinitio::Protocol.

References set_defaults().

Referenced by protocols::surface_docking::SurfaceDockingProtocol::abinitio(), and protocols::abinitio::DomainAssembly::apply().

bool protocols::abinitio::ClassicAbinitio::just_smooth_cycles ( ) const
inline

References just_smooth_cycles_.

moves::MonteCarlo& protocols::abinitio::ClassicAbinitio::mc ( )
inline
moves::MonteCarlo const& protocols::abinitio::ClassicAbinitio::mc ( ) const
inline

References mc_.

moves::MonteCarloOP protocols::abinitio::ClassicAbinitio::mc_ptr ( )
protected
core::kinematics::MoveMapCOP protocols::abinitio::ClassicAbinitio::movemap ( )
ClassicAbinitio const& protocols::abinitio::ClassicAbinitio::operator= ( ClassicAbinitio const &  src)
private

Private, unimplemented assignment operator to prevent assignment of this class. Copy-constructor copying only.

void protocols::abinitio::ClassicAbinitio::output_debug_structure ( core::pose::Pose pose,
std::string  prefix 
)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::prepare_loop_in_stage3 ( core::pose::Pose pose,
Size  iteration,
Size  total 
)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::prepare_loop_in_stage4 ( core::pose::Pose pose,
Size  iteration,
Size  total 
)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::prepare_stage1 ( core::pose::Pose pose)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::prepare_stage2 ( core::pose::Pose pose)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::prepare_stage3 ( core::pose::Pose pose)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::prepare_stage4 ( core::pose::Pose pose)
protectedvirtual
bool protocols::abinitio::ClassicAbinitio::prepare_stage5 ( core::pose::Pose pose)
protectedvirtual

References replace_scorefxn(), and STAGE_5.

Referenced by apply().

void protocols::abinitio::ClassicAbinitio::recover_low ( core::pose::Pose pose,
StageID  stage 
)
protected
void protocols::abinitio::ClassicAbinitio::register_options ( )
static
void protocols::abinitio::ClassicAbinitio::replace_scorefxn ( core::pose::Pose pose,
StageID  stage,
core::Real  intra_stage_progress 
)
protectedvirtual
void protocols::abinitio::ClassicAbinitio::set_current_weight ( core::scoring::ScoreType  type,
core::Real  setting 
)
protected
void protocols::abinitio::ClassicAbinitio::set_cycles ( core::Real  increase_cycles = 1.0)
virtual
void protocols::abinitio::ClassicAbinitio::set_default_mc ( core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  scorefxn 
)
protectedvirtual

References set_mc(), and temperature_.

Referenced by set_defaults().

void protocols::abinitio::ClassicAbinitio::set_default_options ( )
protectedvirtual
void protocols::abinitio::ClassicAbinitio::set_default_scores ( )
protectedvirtual
void protocols::abinitio::ClassicAbinitio::set_defaults ( core::pose::Pose const &  pose)
protectedvirtual
void protocols::abinitio::ClassicAbinitio::set_mc ( moves::MonteCarloOP  mc_in)
void protocols::abinitio::ClassicAbinitio::set_movemap ( core::kinematics::MoveMapCOP  mm)
virtual
void protocols::abinitio::ClassicAbinitio::set_moves ( simple_moves::FragmentMoverOP  brute_move_small,
simple_moves::FragmentMoverOP  brute_move_large,
simple_moves::FragmentMoverOP  smooth_move_small 
)
void protocols::abinitio::ClassicAbinitio::set_score_weight ( core::scoring::ScoreType  type,
core::Real  setting,
StageID  stage = ALL_STAGES 
)
virtual
void protocols::abinitio::ClassicAbinitio::set_skip_stage1 ( bool  setting)
inline
void protocols::abinitio::ClassicAbinitio::set_skip_stage2 ( bool  setting)
inline
void protocols::abinitio::ClassicAbinitio::set_stage4_cycles ( Size  stage4_cycles_new)
inline

References stage4_cycles_.

void protocols::abinitio::ClassicAbinitio::set_trials ( )
protectedvirtual
simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::smooth_move_small ( )

References smooth_move_small_.

Referenced by set_moves().

Size protocols::abinitio::ClassicAbinitio::stage1_cycles ( ) const
inline
moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage1_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
)
protectedvirtual
Size protocols::abinitio::ClassicAbinitio::stage2_cycles ( ) const
inline

References stage2_cycles_.

Referenced by apply(), and do_stage2_cycles().

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage2_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
)
protectedvirtual
Size protocols::abinitio::ClassicAbinitio::stage3_cycles ( ) const
inline

References stage3_cycles_.

Referenced by apply(), and do_stage3_cycles().

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage3_mover ( core::pose::Pose pose,
int  lct1,
int  lct2,
moves::TrialMoverOP  trials_in 
)
protectedvirtual
Size protocols::abinitio::ClassicAbinitio::stage4_cycles ( ) const
inline

References stage4_cycles_.

Referenced by apply(), and do_stage4_cycles().

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage4_mover ( core::pose::Pose pose,
int  kk,
moves::TrialMoverOP  trials_in 
)
protectedvirtual
Size protocols::abinitio::ClassicAbinitio::stage5_cycles ( ) const
inline

References stage5_cycles_.

Referenced by apply(), and do_stage5_cycles().

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::stage5_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
)
protectedvirtual

Referenced by do_stage5_cycles().

Size protocols::abinitio::ClassicAbinitio::total_trials ( ) const
inline

References total_trials_.

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_large ( )
protected
moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_small ( )
protected

References trial_small_.

Referenced by do_stage3_cycles(), and do_stage4_cycles().

moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_smooth ( )
protected

References smooth_trial_small_.

Referenced by do_stage4_cycles().

void protocols::abinitio::ClassicAbinitio::update_moves ( )
protectedvirtual

References set_trials().

Referenced by set_defaults(), and set_moves().

Member Data Documentation

bool protocols::abinitio::ClassicAbinitio::apply_large_frags_
private
bool protocols::abinitio::ClassicAbinitio::bQuickTest_
private
simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::brute_move_large_
private
simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::brute_move_small_
private
bool protocols::abinitio::ClassicAbinitio::bSkipStage1_
bool protocols::abinitio::ClassicAbinitio::bSkipStage2_
bool protocols::abinitio::ClassicAbinitio::bSkipStage3_
bool protocols::abinitio::ClassicAbinitio::bSkipStage4_
bool protocols::abinitio::ClassicAbinitio::bSkipStage5_
bool protocols::abinitio::ClassicAbinitio::close_chbrk_
private
bool protocols::abinitio::ClassicAbinitio::just_smooth_cycles_
private
moves::MonteCarloOP protocols::abinitio::ClassicAbinitio::mc_
private
core::kinematics::MoveMapCOP protocols::abinitio::ClassicAbinitio::movemap_
private
utility::vector1< StageID > protocols::abinitio::ClassicAbinitio::recover_low_stages_
core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage1_
private
core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage2_
private
core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage3a_
private
core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage3b_
private
core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage4_
private
core::scoring::ScoreFunctionOP protocols::abinitio::ClassicAbinitio::score_stage5_
private
bool protocols::abinitio::ClassicAbinitio::short_insert_region_
private
simple_moves::FragmentMoverOP protocols::abinitio::ClassicAbinitio::smooth_move_small_
private
moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::smooth_trial_small_
private
Size protocols::abinitio::ClassicAbinitio::stage1_cycles_
protected
Size protocols::abinitio::ClassicAbinitio::stage2_cycles_
protected
Size protocols::abinitio::ClassicAbinitio::stage3_cycles_
protected
Size protocols::abinitio::ClassicAbinitio::stage4_cycles_
protected
Size protocols::abinitio::ClassicAbinitio::stage5_cycles_
protected
core::Real protocols::abinitio::ClassicAbinitio::temperature_
private
Size protocols::abinitio::ClassicAbinitio::total_trials_
private
moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_large_
private
moves::TrialMoverOP protocols::abinitio::ClassicAbinitio::trial_small_
private

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