Rosetta 3.4
Public Member Functions
protocols::protein_interface_design::movers::LoopRemodel Class Reference

#include <LoopRemodel.hh>

Inheritance diagram for protocols::protein_interface_design::movers::LoopRemodel:
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Collaboration diagram for protocols::protein_interface_design::movers::LoopRemodel:
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List of all members.

Public Member Functions

 LoopRemodel ()
 LoopRemodel (std::string const protocol, core::Size const loop_start, core::Size const loop_end, core::Size const cycles, bool const auto_loops, bool const perturb, bool const refine, bool const hurry, core::scoring::ScoreFunctionOP hires_score, core::scoring::ScoreFunctionOP lores_score, protocols::loops::LoopsCOP loops, core::fragment::FragSetOP frag1, core::fragment::FragSetOP frag3, core::fragment::FragSetOP frag9)
bool perturb ()
void perturb (bool const setting)
bool refine ()
void refine (bool const setting)
bool hurry ()
void hurry (bool const setting)
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
protocols::moves::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).
void apply (core::pose::Pose &pose)
 a dummy apply so that instantiation of this baseclass would be possible.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
virtual ~LoopRemodel ()

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::LoopRemodel::LoopRemodel ( )
protocols::protein_interface_design::movers::LoopRemodel::LoopRemodel ( std::string const  protocol,
core::Size const  loop_start,
core::Size const  loop_end,
core::Size const  cycles,
bool const  auto_loops,
bool const  perturb,
bool const  refine,
bool const  hurry,
core::scoring::ScoreFunctionOP  hires_score,
core::scoring::ScoreFunctionOP  lores_score,
protocols::loops::LoopsCOP  loops,
core::fragment::FragSetOP  frag1,
core::fragment::FragSetOP  frag3,
core::fragment::FragSetOP  frag9 
)
protocols::protein_interface_design::movers::LoopRemodel::~LoopRemodel ( ) [virtual]

Member Function Documentation

void protocols::protein_interface_design::movers::LoopRemodel::apply ( core::pose::Pose ) [virtual]

a dummy apply so that instantiation of this baseclass would be possible.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References core::util::add_cutpoint_variants(), protocols::forge::remodel::RemodelLoopMover::add_fragments(), protocols::loops::loop_mover::LoopMover::add_fragments(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::allsc(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply(), protocols::moves::MonteCarlo::boltzmann(), core::chemical::CENTROID, core::scoring::chainbreak, protocols::simple_moves::DesignRepackMover::design(), core::chemical::FA_STANDARD, protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::moves::Mover::get_last_move_status(), core::scoring::dssp::Dssp::insert_ss_into_pose(), protocols::moves::MonteCarlo::last_accepted_pose(), protocols::loops::loops_set_move_map(), protocols::moves::MS_SUCCESS, core::scoring::omega, perturb(), protocols::simple_moves::DesignRepackMover::prevent_repacking(), protocols::moves::MonteCarlo::recover_low(), refine(), core::util::remove_cutpoint_variants(), core::pack::task::operation::OperateOnCertainResidues::residue_indices(), protocols::forge::remodel::RemodelLoopMover::scorefunction(), core::pose::Pose::secstruct(), core::pose::Pose::sequence(), protocols::moves::MonteCarlo::set_autotemp(), protocols::moves::Mover::set_last_move_status(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_redesign_loop(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_redesign_loop(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), protocols::moves::MonteCarlo::show_counters(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::util::switch_to_residue_type_set(), protocols::simple_moves::DesignRepackMover::task(), protocols::simple_moves::DesignRepackMover::task_factory(), protocols::moves::MonteCarlo::temperature(), core::pose::Pose::total_residue(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopRemodel::clone ( ) const [virtual]

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Implements protocols::simple_moves::DesignRepackMover.

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopRemodel::fresh_instance ( ) const [inline, virtual]

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).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Implements protocols::simple_moves::DesignRepackMover.

std::string protocols::protein_interface_design::movers::LoopRemodel::get_name ( ) const [virtual]

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::protein_interface_design::movers::LoopRemodelCreator::mover_name().

bool protocols::protein_interface_design::movers::LoopRemodel::hurry ( ) [inline]
void protocols::protein_interface_design::movers::LoopRemodel::hurry ( bool const  setting) [inline]
void protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
) [virtual]

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::simple_moves::DesignRepackMover::design(), protocols::moves::DataMap::get(), protocols::rosetta_scripts::get_resnum(), protocols::moves::DataMap::has(), protocols::rosetta_scripts::parse_task_operations(), protocols::simple_moves::DesignRepackMover::task_factory(), core::pose::Pose::total_residue(), and protocols::protein_interface_design::movers::TR().

void protocols::protein_interface_design::movers::LoopRemodel::perturb ( bool const  setting) [inline]
bool protocols::protein_interface_design::movers::LoopRemodel::perturb ( ) [inline]

Referenced by apply().

void protocols::protein_interface_design::movers::LoopRemodel::refine ( bool const  setting) [inline]
bool protocols::protein_interface_design::movers::LoopRemodel::refine ( ) [inline]

Referenced by apply().


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