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protocols::LoopRebuild Class Reference

The loop-rebuild protocol. More...

#include <looprelax_protocols.hh>

Inheritance diagram for protocols::LoopRebuild:
Inheritance graph
[legend]

Public Member Functions

 LoopRebuild (core::scoring::ScoreFunctionOP scorefxn, protocols::loops::Loops Loops_in)
 Construct te protocol object given a score function, list of loop segments to rebuild, and the fragment library to use. The skip rate of each loop is ignored (the decision of which loops to rebuild should be made outside the protocol). More...
 
 ~LoopRebuild () override
 
protocols::moves::MoverOP clone () const override
 Clone this object. More...
 
void set_default_settings ()
 sets all the standard settings for LoopBuild More...
 
protocols::moves::MonteCarloOP get_mc (core::pose::Pose &pose)
 Get the protocol's Monte Carlo object. More...
 
void set_default_mc (core::pose::Pose &pose)
 setting the mc object More...
 
void apply (core::pose::Pose &pose) override
 Apply the loop-rebuild protocol to the input pose. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool extended_loop ()
 Are we extending the loops before running loop-rebuild? More...
 
void set_extended_loop (bool val)
 Specify whether the protocol should extend the loops before running loop-rebuild. More...
 
bool get_success ()
 Were loops successfully built? More...
 
bool get_random_loop_flag ()
 
void set_random_loop_flag (bool setting=true)
 
int get_allowed_failure_before_extend ()
 
void set_allowed_failure_before_extend (int setting)
 
int get_allowed_failure_before_stop ()
 
void set_allowed_failure_before_stop (int setting)
 
bool get_abort_on_failed_loop ()
 
void set_abort_on_failed_loop (bool setting=true)
 
bool loop_model ()
 
bool get_ccd_closure_exist ()
 
bool get_desired_loops_exist ()
 
core::Size desired_loops ()
 
core::Real get_loop_combine_rate ()
 
bool get_combine_if_fail_exist ()
 
core::Real get_rmsd_tolerance ()
 Gets the RMSd tolerence, the most a loop may move during reconstruction. More...
 
core::Real get_chain_break_tolerance ()
 Gets the chainbreak tolerence, the largest the chainbreak score may be to accept a loop conformation. More...
 
- 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...
 

Public Attributes

int allowed_failure_before_stop
 

Private Member Functions

bool build_random_loops (core::pose::Pose &pose)
 Rebuild all loops in the pose, chosen in a random order. More...
 
void set_looprlx_allow_move_map (int const &loop_begin, int const &loop_end, core::kinematics::MoveMap &mm)
 
core::Real get_score_filter_cutoff ()
 Get the cutoff for score filtering loop conformations. CURRENTLY UNUSED IN THE PROTOCOL. More...
 
bool select_one_loop (int nres, int &selected_loop, std::vector< int > &folded_loops, std::vector< int > &inter_res, int &loop_begin, int &loop_end, int &cutpoint, bool &extend_this_loop, bool &are_loops_combined, int &combine_interval, int &loop_counter)
 Select a loop at random from the input list. More...
 
void barcode_extend_stems (core::pose::Pose &pose, int &barcst_extend_begin, int &barcst_extend_end, int &loop_begin, int &loop_end, int const &old_loop_begin, int const &old_loop_end, int const &nres, int const &selected_loop, int const &total_combine, int const &backward_combine)
 Extend the loop stems. More...
 
void extend_barcode_regions_if_chain_break (core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int &n_chain_break_fail, bool &is_chain_break, int &barcst_extend_begin, int &barcst_extend_end)
 If chainbreak score is greater than the tolerance, extend the loop. More...
 
bool shorten_long_terminal_loop ()
 
bool acceptable_rmsd_change (core::pose::Pose &pose1, core::pose::Pose &pose2)
 Is the RMS change between these two poses below the acceptible threshold? More...
 
core::Real get_looprlx_cycle_ratio ()
 
void build_loop_with_ccd_closure (core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int &cutpoint, bool const &extend_this_loop)
 frag insertion + ccd close + minimize More...
 
void fast_ccd_close_loops (core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int const &cutpoint, core::kinematics::MoveMap &mm)
 Apply ccd moves to close the specified loop. More...
 

Private Attributes

core::pose::PoseOP pose_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::kinematics::MoveMapOP movemap_
 
protocols::moves::MonteCarloOP mc_
 
protocols::loops::Loops Loops_in_
 
std::vector
< core::fragment::FragSetOP
frag_libs_
 
bool extend_loops
 
bool use_default_extend_loops
 
bool random_loop_flag_
 
int allowed_failure_before_extend_
 
int allowed_failure_before_stop_
 
bool abort_on_failed_loop_
 
core::Real m_Temperature_
 
bool mc_created
 
bool success
 

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
 
- 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 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...
 

Detailed Description

The loop-rebuild protocol.

Constructor & Destructor Documentation

protocols::LoopRebuild::LoopRebuild ( core::scoring::ScoreFunctionOP  scorefxn,
protocols::loops::Loops  Loops_in 
)

Construct te protocol object given a score function, list of loop segments to rebuild, and the fragment library to use. The skip rate of each loop is ignored (the decision of which loops to rebuild should be made outside the protocol).

References frag_libs_, protocols::loops::read_loop_fragments(), and set_default_settings().

protocols::LoopRebuild::~LoopRebuild ( )
overridedefault

Member Function Documentation

bool protocols::LoopRebuild::acceptable_rmsd_change ( core::pose::Pose pose1,
core::pose::Pose pose2 
)
private

Is the RMS change between these two poses below the acceptible threshold?

References get_rmsd_tolerance(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by build_random_loops().

void protocols::LoopRebuild::apply ( core::pose::Pose pose)
overridevirtual

Apply the loop-rebuild protocol to the input pose.

Apply the loop rebuilding protocol to a pose. The loops to be rebuilt and fragments are defined upon object construction.

Implements protocols::moves::Mover.

References build_random_loops(), Loops_in_, mc_created, set_default_mc(), protocols::loops::set_secstruct_from_psipred_ss2(), protocols::loops::Loops::size(), success, protocols::TR(), and protocols::loops::Loops::verify_against().

Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().

void protocols::LoopRebuild::barcode_extend_stems ( core::pose::Pose pose,
int &  barcst_extend_begin,
int &  barcst_extend_end,
int &  loop_begin,
int &  loop_end,
int const &  old_loop_begin,
int const &  old_loop_end,
int const &  nres,
int const &  selected_loop,
int const &  total_combine,
int const &  backward_combine 
)
private
void protocols::LoopRebuild::build_loop_with_ccd_closure ( core::pose::Pose pose,
int const &  loop_begin,
int const &  loop_end,
int &  cutpoint,
bool const &  extend_this_loop 
)
private
bool protocols::LoopRebuild::build_random_loops ( core::pose::Pose pose)
private
protocols::moves::MoverOP protocols::LoopRebuild::clone ( ) const
overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

core::Size protocols::LoopRebuild::desired_loops ( )

References core::init::init().

Referenced by build_random_loops().

void protocols::LoopRebuild::extend_barcode_regions_if_chain_break ( core::pose::Pose pose,
int const &  loop_begin,
int const &  loop_end,
int &  n_chain_break_fail,
bool is_chain_break,
int &  barcst_extend_begin,
int &  barcst_extend_end 
)
private
bool protocols::LoopRebuild::extended_loop ( )

Are we extending the loops before running loop-rebuild?

References extend_loops, and use_default_extend_loops.

Referenced by build_loop_with_ccd_closure(), and select_one_loop().

void protocols::LoopRebuild::fast_ccd_close_loops ( core::pose::Pose pose,
int const &  loop_begin,
int const &  loop_end,
int const &  cutpoint,
core::kinematics::MoveMap mm 
)
private

Apply ccd moves to close the specified loop.

CCD close the loop [loop_begin,loop_end]. Wraps protocols::loops::loop_closure::ccd::CCDLoopClosureMover.apply() using most of its default options. rama scores are not checked, however, and the secondary structure is "fixed" afterward.

Remarks
This is a misnomer; it actually closes a single loop only. ~Labonte

References protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::check_rama_scores(), core::pose::Pose::conformation(), core::conformation::Conformation::secstruct(), and core::pose::Pose::set_secstruct().

Referenced by build_loop_with_ccd_closure().

bool protocols::LoopRebuild::get_abort_on_failed_loop ( )
inline

References abort_on_failed_loop_.

Referenced by build_random_loops().

int protocols::LoopRebuild::get_allowed_failure_before_extend ( )
inline
int protocols::LoopRebuild::get_allowed_failure_before_stop ( )
inline
bool protocols::LoopRebuild::get_ccd_closure_exist ( )
core::Real protocols::LoopRebuild::get_chain_break_tolerance ( )

Gets the chainbreak tolerence, the largest the chainbreak score may be to accept a loop conformation.

References core::init::init().

Referenced by extend_barcode_regions_if_chain_break().

bool protocols::LoopRebuild::get_combine_if_fail_exist ( )

References core::init::init().

Referenced by build_random_loops().

bool protocols::LoopRebuild::get_desired_loops_exist ( )

References core::init::init().

Referenced by build_random_loops().

core::Real protocols::LoopRebuild::get_loop_combine_rate ( )

References core::init::init().

Referenced by select_one_loop().

core::Real protocols::LoopRebuild::get_looprlx_cycle_ratio ( )
private
moves::MonteCarloOP protocols::LoopRebuild::get_mc ( core::pose::Pose pose)

Get the protocol's Monte Carlo object.

returns mc object

References mc_, mc_created, and set_default_mc().

std::string protocols::LoopRebuild::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::LoopRebuild::get_random_loop_flag ( )
inline
core::Real protocols::LoopRebuild::get_rmsd_tolerance ( )

Gets the RMSd tolerence, the most a loop may move during reconstruction.

References core::init::init().

Referenced by acceptable_rmsd_change().

core::Real protocols::LoopRebuild::get_score_filter_cutoff ( )
private

Get the cutoff for score filtering loop conformations. CURRENTLY UNUSED IN THE PROTOCOL.

References core::init::init().

bool protocols::LoopRebuild::get_success ( )
inline

Were loops successfully built?

References success.

bool protocols::LoopRebuild::loop_model ( )
bool protocols::LoopRebuild::select_one_loop ( int  nres,
int &  selected_loop,
std::vector< int > &  folded_loops,
std::vector< int > &  inter_res,
int &  loop_begin,
int &  loop_end,
int &  cutpoint,
bool extend_this_loop,
bool are_loops_combined,
int &  combine_interval,
int &  loop_counter 
)
private
void protocols::LoopRebuild::set_abort_on_failed_loop ( bool  setting = true)
inline

References abort_on_failed_loop_.

void protocols::LoopRebuild::set_allowed_failure_before_extend ( int  setting)
inline
void protocols::LoopRebuild::set_allowed_failure_before_stop ( int  setting)
inline
void protocols::LoopRebuild::set_default_mc ( core::pose::Pose pose)

setting the mc object

sets mc object

References m_Temperature_, mc_, and scorefxn_.

Referenced by apply(), and get_mc().

void protocols::LoopRebuild::set_default_settings ( )
void protocols::LoopRebuild::set_extended_loop ( bool  val)

Specify whether the protocol should extend the loops before running loop-rebuild.

References extend_loops, use_default_extend_loops, and protocols::hybridization::val.

void protocols::LoopRebuild::set_looprlx_allow_move_map ( int const &  loop_begin,
int const &  loop_end,
core::kinematics::MoveMap mm 
)
private
void protocols::LoopRebuild::set_random_loop_flag ( bool  setting = true)
inline

References random_loop_flag_.

bool protocols::LoopRebuild::shorten_long_terminal_loop ( )
private

References core::init::init().

Referenced by barcode_extend_stems().

Member Data Documentation

bool protocols::LoopRebuild::abort_on_failed_loop_
private
int protocols::LoopRebuild::allowed_failure_before_extend_
private
int protocols::LoopRebuild::allowed_failure_before_stop
int protocols::LoopRebuild::allowed_failure_before_stop_
private
bool protocols::LoopRebuild::extend_loops
private

Referenced by extended_loop(), and set_extended_loop().

std::vector< core::fragment::FragSetOP > protocols::LoopRebuild::frag_libs_
private
protocols::loops::Loops protocols::LoopRebuild::Loops_in_
private
core::Real protocols::LoopRebuild::m_Temperature_
private

Referenced by set_default_mc().

protocols::moves::MonteCarloOP protocols::LoopRebuild::mc_
private
bool protocols::LoopRebuild::mc_created
private

Referenced by apply(), get_mc(), and set_default_settings().

core::kinematics::MoveMapOP protocols::LoopRebuild::movemap_
private
core::pose::PoseOP protocols::LoopRebuild::pose_
private
bool protocols::LoopRebuild::random_loop_flag_
private
core::scoring::ScoreFunctionOP protocols::LoopRebuild::scorefxn_
private
bool protocols::LoopRebuild::success
private

Referenced by apply(), and get_success().

bool protocols::LoopRebuild::use_default_extend_loops
private

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