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protocols::abinitio::ConstraintFragmentSampler Class Reference

#include <ConstraintFragmentSampler.hh>

Inheritance diagram for protocols::abinitio::ConstraintFragmentSampler:
Inheritance graph
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Public Member Functions

 ConstraintFragmentSampler (topology_broker::TopologyBrokerOP broker)
 This constructor does not work – Fix it before using it. More...
 
moves::MoverOP clone () const override
 ConstraintFragmentSampler 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...
 
- Public Member Functions inherited from protocols::abinitio::FragmentSampler
 ~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 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::FragmentSampler
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

void set_constraint_weight (core::Real setting)
 
void set_defaults ()
 
void do_stage1_cycles (core::pose::Pose &pose) override
 
void prepare_stage1 (core::pose::Pose &pose) override
 
void prepare_stage2 (core::pose::Pose &pose) override
 
void prepare_loop_in_stage3 (core::pose::Pose &, core::Size, core::Size) override
 
void prepare_loop_in_stage4 (core::pose::Pose &, core::Size, core::Size) override
 
void set_show_viol_level (core::Size setting)
 
virtual void set_max_seq_sep (core::pose::Pose &pose, core::Size setting)
 
core::Real max_seq_sep_fudge () const
 
void max_seq_sep_fudge (core::Real setting)
 
constraints_additional::MaxSeqSepConstraintSet
const & 
constraints ()
 
core::Size total_res (core::pose::Pose const &pose) const
 
void set_seq_sep_stage1 (core::Real setting)
 
void set_seq_sep_stage3 (core::Real setting)
 
void replace_scorefxn (core::pose::Pose &pose, StageID stage, core::Real intra_stage_progress) override
 
- Protected Member Functions inherited from protocols::abinitio::FragmentSampler
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)
 
void set_current_weight (core::scoring::ScoreType type, core::Real setting)
 
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_stage3 (core::pose::Pose &pose)
 
virtual void prepare_stage4 (core::pose::Pose &pose)
 
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...
 

Private Types

typedef FragmentSampler Parent
 
typedef moves::Mover BaseClass
 

Private Member Functions

core::Real evaluate_constraint_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &) const
 

Private Attributes

constraints_additional::MaxSeqSepConstraintSetOP constraints_
 
core::Real constraint_weight_
 
core::Real max_seq_sep_fudge_
 
core::Real seq_sep_stage1_
 
core::Real seq_sep_stage3_
 
core::Real seq_sep_stage4_
 
bool bSkipOnNoViolation_
 
core::Size show_viol_level_
 
bool bNoRecoverLowAtSwitch_
 
bool bRampChainbreaks_
 
bool bRampCoordConstraints_
 
bool bOverlapChainbreaks_
 

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
 
- Protected Attributes inherited from protocols::abinitio::FragmentSampler
core::Size stage1_cycles_
 
core::Size stage2_cycles_
 
core::Size stage3_cycles_
 
core::Size stage4_cycles_
 

Detailed Description

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

call ConstraintFragmentSampler::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::ConstraintFragmentSampler::ConstraintFragmentSampler ( 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().

Member Function Documentation

void protocols::abinitio::ConstraintFragmentSampler::apply ( core::pose::Pose )
overridevirtual
moves::MoverOP protocols::abinitio::ConstraintFragmentSampler::clone ( ) const
overridevirtual

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

Reimplemented from protocols::moves::Mover.

Referenced by set_max_seq_sep().

constraints_additional::MaxSeqSepConstraintSet const& protocols::abinitio::ConstraintFragmentSampler::constraints ( )
inlineprotected

References constraints_.

void protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles ( core::pose::Pose pose)
overrideprotectedvirtual
Real protocols::abinitio::ConstraintFragmentSampler::evaluate_constraint_energy ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  scfxn 
) const
inlineprivate
string protocols::abinitio::ConstraintFragmentSampler::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

core::Real protocols::abinitio::ConstraintFragmentSampler::max_seq_sep_fudge ( ) const
inlineprotected

References max_seq_sep_fudge_.

void protocols::abinitio::ConstraintFragmentSampler::max_seq_sep_fudge ( core::Real  setting)
inlineprotected

References max_seq_sep_fudge_.

void protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage3 ( core::pose::Pose pose,
core::Size  loop_iteration,
core::Size  total_iterations 
)
overrideprotectedvirtual
void protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage4 ( core::pose::Pose pose,
core::Size  loop_iteration,
core::Size  total_iterations 
)
overrideprotectedvirtual
void protocols::abinitio::ConstraintFragmentSampler::prepare_stage1 ( core::pose::Pose pose)
overrideprotectedvirtual
void protocols::abinitio::ConstraintFragmentSampler::prepare_stage2 ( core::pose::Pose pose)
overrideprotectedvirtual
void protocols::abinitio::ConstraintFragmentSampler::register_options ( )
static
void protocols::abinitio::ConstraintFragmentSampler::replace_scorefxn ( core::pose::Pose pose,
StageID  stage,
core::Real  intra_stage_progress 
)
overrideprotectedvirtual
void protocols::abinitio::ConstraintFragmentSampler::set_constraint_weight ( core::Real  setting)
inlineprotected
void protocols::abinitio::ConstraintFragmentSampler::set_defaults ( )
protected
void protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep ( core::pose::Pose pose,
core::Size  setting 
)
protectedvirtual
void protocols::abinitio::ConstraintFragmentSampler::set_seq_sep_stage1 ( core::Real  setting)
inlineprotected

References seq_sep_stage1_.

void protocols::abinitio::ConstraintFragmentSampler::set_seq_sep_stage3 ( core::Real  setting)
inlineprotected

References seq_sep_stage3_.

void protocols::abinitio::ConstraintFragmentSampler::set_show_viol_level ( core::Size  setting)
inlineprotected

References show_viol_level_.

Size protocols::abinitio::ConstraintFragmentSampler::total_res ( core::pose::Pose const &  pose) const
protected

Member Data Documentation

bool protocols::abinitio::ConstraintFragmentSampler::bNoRecoverLowAtSwitch_
private

Referenced by set_defaults(), and set_max_seq_sep().

bool protocols::abinitio::ConstraintFragmentSampler::bOverlapChainbreaks_
private

Referenced by replace_scorefxn(), and set_defaults().

bool protocols::abinitio::ConstraintFragmentSampler::bRampChainbreaks_
private

Referenced by replace_scorefxn(), and set_defaults().

bool protocols::abinitio::ConstraintFragmentSampler::bRampCoordConstraints_
private

Referenced by replace_scorefxn(), and set_defaults().

bool protocols::abinitio::ConstraintFragmentSampler::bSkipOnNoViolation_
private

Referenced by do_stage1_cycles(), and set_defaults().

core::Real protocols::abinitio::ConstraintFragmentSampler::constraint_weight_
private

Referenced by set_constraint_weight().

constraints_additional::MaxSeqSepConstraintSetOP protocols::abinitio::ConstraintFragmentSampler::constraints_
private
core::Real protocols::abinitio::ConstraintFragmentSampler::max_seq_sep_fudge_
private
core::Real protocols::abinitio::ConstraintFragmentSampler::seq_sep_stage1_
private
core::Real protocols::abinitio::ConstraintFragmentSampler::seq_sep_stage3_
private
core::Real protocols::abinitio::ConstraintFragmentSampler::seq_sep_stage4_
private

Referenced by replace_scorefxn(), and set_defaults().

core::Size protocols::abinitio::ConstraintFragmentSampler::show_viol_level_
private

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