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protocols::abinitio::MembraneAbinitio Class Reference

#include <MembraneAbinitio.hh>

Inheritance diagram for protocols::abinitio::MembraneAbinitio:
Inheritance graph
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Public Types

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

Public Member Functions

 MembraneAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_small_top25, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int)
 This constructor does not work – Fix it before using it. More...
 
 MembraneAbinitio (core::fragment::FragSetCOP fragset_small, core::fragment::FragSetCOP fragset_small_top25, core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap)
 constructor: supply fragsets for large and small fragment moves More...
 
void init (core::pose::Pose const &pose) override
 setup moves, mc-object, scores More...
 
moves::MoverOP clone () const override
 MembraneAbinitio 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...
 
simple_moves::FragmentMoverOP smooth_move_small ()
 
simple_moves::FragmentMoverOP brute_move_small_top25 ()
 
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 add_spanning_region (core::pose::Pose &pose)
 
void move_all_inserted (core::pose::Pose &pose)
 
void print_debug (core::pose::Pose &pose)
 
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)
 
core::Size total_trials () const
 
virtual void clear_checkpoints (void)
 for debugging, one wants to have access to the native pose. More...
 
virtual bool recover_checkpoint (core::pose::Pose &pose, std::string const &id)
 
virtual void checkpoint (core::pose::Pose &pose, std::string const &id)
 
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
 
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
 
void set_only_stage4 (bool value)
 
- Public Member Functions inherited from protocols::abinitio::Protocol
 Protocol ()
 
 ~Protocol () override=default
 
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 apply (core::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_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 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

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. More...
 

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 set_current_weight (core::scoring::ScoreType type, core::Real setting)
 
virtual int do_stage1_cycles (core::pose::Pose &pose)
 
virtual int do_stage2_cycles (core::pose::Pose &pose)
 
virtual int do_stage3_cycles (core::pose::Pose &pose)
 
virtual int do_stage3b_cycles (core::pose::Pose &pose)
 
virtual int do_stage4_cycles (core::pose::Pose &pose)
 
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 void set_trials ()
 
moves::TrialMoverOP trial_large ()
 
moves::TrialMoverOP trial_small ()
 
moves::TrialMoverOP trial_small_top25 ()
 
moves::TrialMoverOP trial_smooth ()
 
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)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix) override
 
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 Protocol Parent
 

Private Member Functions

core::Size get_tmh_inserted (core::pose::Pose const &pose) const
 
core::scoring::MembraneEmbed
const & 
MembraneEmbed_from_pose (core::pose::Pose const &) const
 
core::scoring::MembraneEmbednonconst_MembraneEmbed_from_pose (core::pose::Pose &) const
 
core::scoring::MembraneTopology
const & 
MembraneTopology_from_pose (core::pose::Pose const &) const
 
core::scoring::MembraneTopologynonconst_MembraneTopology_from_pose (core::pose::Pose &) const
 

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 only_stage4_
 
bool bQuickTest_
 
core::Real temperature_
 
core::kinematics::MoveMapCOP movemap_
 
moves::MonteCarloOP mc_
 
simple_moves::FragmentMoverOP brute_move_small_
 
simple_moves::FragmentMoverOP brute_move_small_top25_
 
simple_moves::FragmentMoverOP brute_move_large_
 
simple_moves::FragmentMoverOP smooth_move_small_
 
moves::TrialMoverOP trial_large_
 
moves::TrialMoverOP trial_small_
 
moves::TrialMoverOP trial_small_top25_
 
moves::TrialMoverOP smooth_trial_small_
 
std::vector< std::string > checkpoint_ids_
 
core::Size total_trials_
 
checkpoint::CheckPointer checkpoint_
 

Detailed Description

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

call MembraneAbinitio::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

Member Enumeration Documentation

Enumerator
ALL_STAGES 
STAGE_1 
STAGE_2 
STAGE_3a 
STAGE_3b 
STAGE_4 

Constructor & Destructor Documentation

protocols::abinitio::MembraneAbinitio::MembraneAbinitio ( simple_moves::FragmentMoverOP  brute_move_small,
simple_moves::FragmentMoverOP  brute_move_small_top25,
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 movemap_, and protocols::moves::Mover::type().

protocols::abinitio::MembraneAbinitio::MembraneAbinitio ( core::fragment::FragSetCOP  fragset_small,
core::fragment::FragSetCOP  fragset_small_top25,
core::fragment::FragSetCOP  fragset_large,
core::kinematics::MoveMapCOP  movemap 
)

constructor: supply fragsets for large and small fragment moves

References brute_move_large_, brute_move_small_, brute_move_small_top25_, movemap(), smooth_move_small_, and protocols::moves::Mover::type().

Member Function Documentation

void protocols::abinitio::MembraneAbinitio::add_spanning_region ( core::pose::Pose pose)
void protocols::abinitio::MembraneAbinitio::apply ( core::pose::Pose )
overridevirtual
bool protocols::abinitio::MembraneAbinitio::bQuickTest ( ) const
inline

References bQuickTest_.

Referenced by set_default_options().

simple_moves::FragmentMoverOP protocols::abinitio::MembraneAbinitio::brute_move_large ( )

References brute_move_large_.

Referenced by do_stage1_cycles(), and set_moves().

simple_moves::FragmentMoverOP protocols::abinitio::MembraneAbinitio::brute_move_small ( )

References brute_move_small_.

Referenced by set_moves().

simple_moves::FragmentMoverOP protocols::abinitio::MembraneAbinitio::brute_move_small_top25 ( )
void protocols::abinitio::MembraneAbinitio::checkpoint ( core::pose::Pose pose,
std::string const &  id 
)
virtual
void protocols::abinitio::MembraneAbinitio::clear_checkpoints ( void  )
virtual

for debugging, one wants to have access to the native pose.

References checkpoint_, and protocols::checkpoint::CheckPointer::clear_checkpoints().

Referenced by apply().

moves::MoverOP protocols::abinitio::MembraneAbinitio::clone ( ) const
overridevirtual

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

Reimplemented from protocols::moves::Mover.

Referenced by set_current_weight().

scoring::ScoreFunction const & protocols::abinitio::MembraneAbinitio::current_scorefxn ( ) const
protected
void protocols::abinitio::MembraneAbinitio::current_scorefxn ( core::scoring::ScoreFunction const &  scorefxn)
protected
int protocols::abinitio::MembraneAbinitio::do_stage1_cycles ( core::pose::Pose pose)
protectedvirtual
int protocols::abinitio::MembraneAbinitio::do_stage2_cycles ( core::pose::Pose pose)
protectedvirtual
int protocols::abinitio::MembraneAbinitio::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::RepeatMover::apply(), checkpoint(), core::scoring::linear_chainbreak, mc_, prepare_loop_in_stage3(), recover_checkpoint(), score_stage3a_, score_stage3b_, stage3_cycles(), stage3_mover(), tr(), trial_large(), and trial_small_top25().

Referenced by apply().

int protocols::abinitio::MembraneAbinitio::do_stage3b_cycles ( core::pose::Pose pose)
protectedvirtual
int protocols::abinitio::MembraneAbinitio::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(), checkpoint(), just_smooth_cycles_, core::scoring::linear_chainbreak, mc_, prepare_loop_in_stage4(), recover_checkpoint(), score_stage4_, stage4_cycles(), stage4_mover(), tr(), trial_small(), trial_small_top25(), and trial_smooth().

Referenced by apply().

std::string protocols::abinitio::MembraneAbinitio::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Size protocols::abinitio::MembraneAbinitio::get_tmh_inserted ( core::pose::Pose const &  pose) const
private
void protocols::abinitio::MembraneAbinitio::init ( core::pose::Pose const &  pose)
overridevirtual

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().

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

References just_smooth_cycles_.

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

References mc_.

moves::MonteCarloOP protocols::abinitio::MembraneAbinitio::mc_ptr ( )
inlineprotected

References mc_.

Referenced by do_stage2_cycles().

core::scoring::MembraneEmbed const & protocols::abinitio::MembraneAbinitio::MembraneEmbed_from_pose ( core::pose::Pose const &  pose) const
private

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.

core::scoring::MembraneTopology const & protocols::abinitio::MembraneAbinitio::MembraneTopology_from_pose ( core::pose::Pose const &  pose) const
private

Pose must already contain a cenlist object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

Referenced by apply(), get_tmh_inserted(), and print_debug().

void protocols::abinitio::MembraneAbinitio::move_all_inserted ( core::pose::Pose pose)
core::kinematics::MoveMapCOP protocols::abinitio::MembraneAbinitio::movemap ( )
core::scoring::MembraneEmbed & protocols::abinitio::MembraneAbinitio::nonconst_MembraneEmbed_from_pose ( core::pose::Pose pose) const
private

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_EMBED.

core::scoring::MembraneTopology & protocols::abinitio::MembraneAbinitio::nonconst_MembraneTopology_from_pose ( core::pose::Pose pose) const
private

Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

Referenced by add_spanning_region(), apply(), and move_all_inserted().

void protocols::abinitio::MembraneAbinitio::output_debug_structure ( core::pose::Pose pose,
std::string  prefix 
)
overrideprotectedvirtual
void protocols::abinitio::MembraneAbinitio::prepare_loop_in_stage3 ( core::pose::Pose ,
core::Size  ,
core::Size   
)
protectedvirtual

References mc_, and temperature_.

Referenced by do_stage3_cycles(), and do_stage3b_cycles().

void protocols::abinitio::MembraneAbinitio::prepare_loop_in_stage4 ( core::pose::Pose ,
core::Size  ,
core::Size   
)
protectedvirtual

References mc_, and temperature_.

Referenced by do_stage4_cycles().

void protocols::abinitio::MembraneAbinitio::prepare_stage1 ( core::pose::Pose pose)
protectedvirtual

References mc_, movemap(), score_stage1_, set_movemap(), and temperature_.

Referenced by apply().

void protocols::abinitio::MembraneAbinitio::prepare_stage2 ( core::pose::Pose pose)
protectedvirtual

References mc_, score_stage2_, and temperature_.

Referenced by apply().

void protocols::abinitio::MembraneAbinitio::prepare_stage3 ( core::pose::Pose pose)
protectedvirtual

References mc_, score_stage3a_, and temperature_.

Referenced by apply().

void protocols::abinitio::MembraneAbinitio::prepare_stage4 ( core::pose::Pose pose)
protectedvirtual

References mc_, score_stage4_, and temperature_.

Referenced by apply().

void protocols::abinitio::MembraneAbinitio::print_debug ( core::pose::Pose pose)
bool protocols::abinitio::MembraneAbinitio::recover_checkpoint ( core::pose::Pose pose,
std::string const &  id 
)
virtual
void protocols::abinitio::MembraneAbinitio::register_options ( )
static

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

References core::pack::interaction_graph::debug.

void protocols::abinitio::MembraneAbinitio::set_current_weight ( core::scoring::ScoreType  type,
core::Real  setting 
)
protected
void protocols::abinitio::MembraneAbinitio::set_cycles ( core::Real  increase_cycles = 1.0)
virtual
void protocols::abinitio::MembraneAbinitio::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::MembraneAbinitio::set_default_options ( )
protectedvirtual
void protocols::abinitio::MembraneAbinitio::set_default_scores ( )
protectedvirtual
void protocols::abinitio::MembraneAbinitio::set_defaults ( core::pose::Pose const &  pose)
protectedvirtual
void protocols::abinitio::MembraneAbinitio::set_mc ( moves::MonteCarloOP  mc_in)
void protocols::abinitio::MembraneAbinitio::set_movemap ( core::kinematics::MoveMapCOP  mm)
virtual
void protocols::abinitio::MembraneAbinitio::set_moves ( simple_moves::FragmentMoverOP  brute_move_small,
simple_moves::FragmentMoverOP  brute_move_large,
simple_moves::FragmentMoverOP  smooth_move_small 
)
void protocols::abinitio::MembraneAbinitio::set_only_stage4 ( bool  value)
inline

References only_stage4_.

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

for debugging, one wants to have access to the native pose.

sets a score weight for all stages of abinitio

References ALL_STAGES, core::scoring::name_from_score_type(), score_stage1_, score_stage2_, score_stage3a_, score_stage3b_, score_stage4_, STAGE_1, STAGE_2, STAGE_3a, STAGE_3b, STAGE_4, and tr().

void protocols::abinitio::MembraneAbinitio::set_stage4_cycles ( core::Size  stage4_cycles_new)
inline

References stage4_cycles_.

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

References smooth_move_small_.

Referenced by set_moves().

core::Size protocols::abinitio::MembraneAbinitio::stage1_cycles ( ) const
inline

References stage1_cycles_.

Referenced by apply(), and do_stage1_cycles().

core::Size protocols::abinitio::MembraneAbinitio::stage2_cycles ( ) const
inline

References stage2_cycles_.

Referenced by apply(), and do_stage2_cycles().

moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::stage2_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
)
protectedvirtual
core::Size protocols::abinitio::MembraneAbinitio::stage3_cycles ( ) const
inline
moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::stage3_mover ( core::pose::Pose pose,
int  lct1,
int  lct2,
moves::TrialMoverOP  trials_in 
)
protectedvirtual
core::Size protocols::abinitio::MembraneAbinitio::stage4_cycles ( ) const
inline

References stage4_cycles_.

Referenced by apply(), and do_stage4_cycles().

moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::stage4_mover ( core::pose::Pose pose,
int  kk,
moves::TrialMoverOP  trials_in 
)
protectedvirtual

Referenced by do_stage4_cycles().

core::Size protocols::abinitio::MembraneAbinitio::total_trials ( ) const
inline

References total_trials_.

moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::trial_large ( )
inlineprotected
moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::trial_small ( )
inlineprotected

References trial_small_.

Referenced by do_stage4_cycles().

moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::trial_small_top25 ( )
inlineprotected
moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::trial_smooth ( )
inlineprotected

References smooth_trial_small_.

Referenced by do_stage4_cycles().

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

References set_trials().

Referenced by set_defaults(), and set_moves().

Member Data Documentation

bool protocols::abinitio::MembraneAbinitio::apply_large_frags_
private

Referenced by set_default_options(), and trial_large().

bool protocols::abinitio::MembraneAbinitio::bQuickTest_
private

Referenced by bQuickTest(), and set_default_options().

simple_moves::FragmentMoverOP protocols::abinitio::MembraneAbinitio::brute_move_large_
private
simple_moves::FragmentMoverOP protocols::abinitio::MembraneAbinitio::brute_move_small_
private
simple_moves::FragmentMoverOP protocols::abinitio::MembraneAbinitio::brute_move_small_top25_
private
checkpoint::CheckPointer protocols::abinitio::MembraneAbinitio::checkpoint_
private
std::vector< std::string > protocols::abinitio::MembraneAbinitio::checkpoint_ids_
private
bool protocols::abinitio::MembraneAbinitio::just_smooth_cycles_
private
moves::MonteCarloOP protocols::abinitio::MembraneAbinitio::mc_
private
core::kinematics::MoveMapCOP protocols::abinitio::MembraneAbinitio::movemap_
private
bool protocols::abinitio::MembraneAbinitio::only_stage4_
private
core::scoring::ScoreFunctionOP protocols::abinitio::MembraneAbinitio::score_stage1_
private
core::scoring::ScoreFunctionOP protocols::abinitio::MembraneAbinitio::score_stage2_
private
core::scoring::ScoreFunctionOP protocols::abinitio::MembraneAbinitio::score_stage3a_
private
core::scoring::ScoreFunctionOP protocols::abinitio::MembraneAbinitio::score_stage3b_
private
core::scoring::ScoreFunctionOP protocols::abinitio::MembraneAbinitio::score_stage4_
private
bool protocols::abinitio::MembraneAbinitio::short_insert_region_
private

Referenced by set_default_options().

simple_moves::FragmentMoverOP protocols::abinitio::MembraneAbinitio::smooth_move_small_
private
moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::smooth_trial_small_
private

Referenced by set_mc(), set_trials(), and trial_smooth().

core::Size protocols::abinitio::MembraneAbinitio::stage1_cycles_
protected

Referenced by set_cycles(), and stage1_cycles().

core::Size protocols::abinitio::MembraneAbinitio::stage2_cycles_
protected

Referenced by set_cycles(), and stage2_cycles().

core::Size protocols::abinitio::MembraneAbinitio::stage3_cycles_
protected

Referenced by set_cycles(), and stage3_cycles().

core::Size protocols::abinitio::MembraneAbinitio::stage4_cycles_
protected
core::Real protocols::abinitio::MembraneAbinitio::temperature_
private
core::Size protocols::abinitio::MembraneAbinitio::total_trials_
private

Referenced by apply(), and total_trials().

moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::trial_large_
private
moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::trial_small_
private
moves::TrialMoverOP protocols::abinitio::MembraneAbinitio::trial_small_top25_
private

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