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protocols::abinitio::FoldConstraints Class Reference

extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles() More...

#include <FoldConstraints.hh>

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

typedef ClassicAbinitio Parent
 
- Public Types inherited from protocols::abinitio::ClassicAbinitio
enum  StageID {
  ALL_STAGES = 0, STAGE_1, STAGE_2, STAGE_3a,
  STAGE_3b, STAGE_4, STAGE_4rot, STAGE_5
}
 
- 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

 FoldConstraints (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)
 c'stor from Movers More...
 
 FoldConstraints (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)
 c'stor from FragSets — ClassicFragmentMover and SmoothFragmentMover will be created More...
 
 FoldConstraints (FoldConstraints const &src)
 Explicit copy constructor to handle OPs. More...
 
 ~FoldConstraints () override
 Explicit destructor to handle OPs. More...
 
moves::MoverOP clone () const override
 ... More...
 
void apply (core::pose::Pose &pose) override
 run the protocol More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_default_scores () override
 sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 More...
 
void set_constraint_weight (core::Real setting)
 
void set_default_options () override
 
void set_show_viol_level (core::Size setting)
 
- Public Member Functions inherited from 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. 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 () override
 Explicit destructor since this class contains OPs of other classes. More...
 
void init (core::pose::Pose const &pose) override
 setup moves, mc-object, scores More...
 
simple_moves::FragmentMoverOP smooth_move_small ()
 
simple_moves::FragmentMoverOP brute_move_small ()
 
simple_moves::FragmentMoverOP brute_move_large ()
 
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)
 
core::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
 
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
 
core::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 () 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 ()
 Why is this not being registered ? Probably not actually needed. More...
 
- Static Public Member Functions inherited from protocols::abinitio::ClassicAbinitio
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

bool prepare_stage1 (core::pose::Pose &pose) override
 
bool prepare_stage2 (core::pose::Pose &pose) override
 
bool prepare_stage4 (core::pose::Pose &pose) override
 
bool prepare_loop_in_stage3 (core::pose::Pose &pose, core::Size loop_iteration, core::Size total_iterations) override
 
bool prepare_loop_in_stage4 (core::pose::Pose &pose, core::Size loop_iteration, core::Size total_iterations) override
 
bool do_stage1_cycles (core::pose::Pose &pose) override
 
bool do_stage2_cycles (core::pose::Pose &pose) override
 
virtual void setup_default_min_move ()
 
void set_movemap (core::kinematics::MoveMapCOP mm) override
 
void set_min_move (protocols::minimization_packing::MinMoverOP mm)
 
protocols::minimization_packing::MinMovermin_move ()
 
void min_trial (core::pose::Pose &pose)
 
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 ()
 
void bIgnoreSequenceSeparation (bool setting)
 
bool bIgnoreSequenceSeparation ()
 
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)
 
- Protected Member Functions inherited from protocols::abinitio::ClassicAbinitio
virtual void update_moves ()
 
virtual void set_defaults (core::pose::Pose const &pose)
 
virtual void set_default_mc (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn)
 
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_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 stage4rot_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_stage3 (core::pose::Pose &pose)
 
virtual bool prepare_stage5 (core::pose::Pose &pose)
 
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...
 

Private Member Functions

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

Private Attributes

protocols::minimization_packing::MinMoverOP min_move_
 
constraints_additional::MaxSeqSepConstraintSetOP constraints_
 
core::Real constraint_weight_
 
bool bMinTrial_
 
bool bIgnoreSequenceSeparation_
 
core::Size run_
 
core::Real max_seq_sep_fudge_
 
core::Real seq_sep_stage1_
 
core::Real seq_sep_stage3_
 
core::Real seq_sep_stage4_
 
core::Real start_ramp_cstweight_
 
core::Size ramp_cst_cycles_
 
core::Size ramp_iterations_
 
bool bSkipOnNoViolation_
 
core::Size show_viol_level_
 
core::Size constraint_threshold_
 

Additional Inherited Members

- Public Attributes inherited from protocols::abinitio::ClassicAbinitio
bool bSkipStage1_
 
bool bSkipStage2_
 
bool bSkipStage3_
 
bool bSkipStage4_
 
bool bSkipStage5_
 
utility::vector1< StageIDrecover_low_stages_
 
- Protected Attributes inherited from protocols::abinitio::ClassicAbinitio
core::Size stage1_cycles_
 
core::Size stage2_cycles_
 
core::Size stage3_cycles_
 
core::Size stage4_cycles_
 
core::Size stage5_cycles_
 
core::Real stage4_cycles_pack_rate_
 

Detailed Description

extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles()

the other substantial difference to ClassicAbinitio is that minimizations are carried out. method min_trial() is called each time the max_seq_sep is changed. ( inhibit: -no_minimize )

Member Typedef Documentation

Constructor & Destructor Documentation

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

c'stor from Movers

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

protocols::abinitio::FoldConstraints::FoldConstraints ( core::fragment::FragSetCOP  fragset3mer,
core::fragment::FragSetCOP  fragset9mer,
core::kinematics::MoveMapCOP  movemap 
)

c'stor from FragSets — ClassicFragmentMover and SmoothFragmentMover will be created

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

protocols::abinitio::FoldConstraints::FoldConstraints ( FoldConstraints const &  src)
protocols::abinitio::FoldConstraints::~FoldConstraints ( )
overridedefault

Explicit destructor to handle OPs.

Member Function Documentation

void protocols::abinitio::FoldConstraints::apply ( core::pose::Pose pose)
overridevirtual
void protocols::abinitio::FoldConstraints::bIgnoreSequenceSeparation ( bool  setting)
inlineprotected
bool protocols::abinitio::FoldConstraints::bIgnoreSequenceSeparation ( )
inlineprotected

References bIgnoreSequenceSeparation_.

Referenced by apply(), and set_max_seq_sep().

moves::MoverOP protocols::abinitio::FoldConstraints::clone ( ) const
overridevirtual
constraints_additional::MaxSeqSepConstraintSet const& protocols::abinitio::FoldConstraints::constraints ( )
inlineprotected
bool protocols::abinitio::FoldConstraints::do_stage1_cycles ( core::pose::Pose pose)
overrideprotectedvirtual
bool protocols::abinitio::FoldConstraints::do_stage2_cycles ( core::pose::Pose pose)
overrideprotectedvirtual
core::Real protocols::abinitio::FoldConstraints::evaluate_constraint_energy ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  scfxn 
) const
inlineprivate
std::string protocols::abinitio::FoldConstraints::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::abinitio::ClassicAbinitio.

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

core::Real protocols::abinitio::FoldConstraints::max_seq_sep_fudge ( ) const
inlineprotected
void protocols::abinitio::FoldConstraints::max_seq_sep_fudge ( core::Real  setting)
inlineprotected

References max_seq_sep_fudge_.

protocols::minimization_packing::MinMover& protocols::abinitio::FoldConstraints::min_move ( )
inlineprotected

References min_move_.

void protocols::abinitio::FoldConstraints::min_trial ( core::pose::Pose pose)
protected
bool protocols::abinitio::FoldConstraints::prepare_loop_in_stage3 ( core::pose::Pose pose,
core::Size  loop_iteration,
core::Size  total_iterations 
)
overrideprotectedvirtual
bool protocols::abinitio::FoldConstraints::prepare_loop_in_stage4 ( core::pose::Pose pose,
core::Size  loop_iteration,
core::Size  total_iterations 
)
overrideprotectedvirtual
bool protocols::abinitio::FoldConstraints::prepare_stage1 ( core::pose::Pose pose)
overrideprotectedvirtual
bool protocols::abinitio::FoldConstraints::prepare_stage2 ( core::pose::Pose pose)
overrideprotectedvirtual
bool protocols::abinitio::FoldConstraints::prepare_stage4 ( core::pose::Pose pose)
overrideprotectedvirtual
void protocols::abinitio::FoldConstraints::register_options ( )
static

Why is this not being registered ? Probably not actually needed.

References protocols::abinitio::ClassicAbinitio::register_options().

void protocols::abinitio::FoldConstraints::set_constraint_weight ( core::Real  setting)
inline
void protocols::abinitio::FoldConstraints::set_default_options ( )
overridevirtual
void protocols::abinitio::FoldConstraints::set_default_scores ( )
overridevirtual
void protocols::abinitio::FoldConstraints::set_max_seq_sep ( core::pose::Pose pose,
core::Size  setting 
)
protectedvirtual
void protocols::abinitio::FoldConstraints::set_min_move ( protocols::minimization_packing::MinMoverOP  mm)
protected

References min_move_.

void protocols::abinitio::FoldConstraints::set_movemap ( core::kinematics::MoveMapCOP  mm)
overrideprotectedvirtual
void protocols::abinitio::FoldConstraints::set_seq_sep_stage1 ( core::Real  setting)
inlineprotected
void protocols::abinitio::FoldConstraints::set_seq_sep_stage3 ( core::Real  setting)
inlineprotected
void protocols::abinitio::FoldConstraints::set_show_viol_level ( core::Size  setting)
inline

References show_viol_level_.

void protocols::abinitio::FoldConstraints::setup_default_min_move ( )
protectedvirtual
Size protocols::abinitio::FoldConstraints::total_res ( core::pose::Pose const &  pose) const
protected

Member Data Documentation

bool protocols::abinitio::FoldConstraints::bIgnoreSequenceSeparation_
private
bool protocols::abinitio::FoldConstraints::bMinTrial_
private
bool protocols::abinitio::FoldConstraints::bSkipOnNoViolation_
private
core::Size protocols::abinitio::FoldConstraints::constraint_threshold_
private
core::Real protocols::abinitio::FoldConstraints::constraint_weight_
private
constraints_additional::MaxSeqSepConstraintSetOP protocols::abinitio::FoldConstraints::constraints_
private
core::Real protocols::abinitio::FoldConstraints::max_seq_sep_fudge_
private
protocols::minimization_packing::MinMoverOP protocols::abinitio::FoldConstraints::min_move_
private
core::Size protocols::abinitio::FoldConstraints::ramp_cst_cycles_
private
core::Size protocols::abinitio::FoldConstraints::ramp_iterations_
private
core::Size protocols::abinitio::FoldConstraints::run_
private

Referenced by apply(), and FoldConstraints().

core::Real protocols::abinitio::FoldConstraints::seq_sep_stage1_
private
core::Real protocols::abinitio::FoldConstraints::seq_sep_stage3_
private
core::Real protocols::abinitio::FoldConstraints::seq_sep_stage4_
private
core::Size protocols::abinitio::FoldConstraints::show_viol_level_
private
core::Real protocols::abinitio::FoldConstraints::start_ramp_cstweight_
private

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