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

#include <LoopMoverFromCommandLine.hh>

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List of all members.

Public Member Functions

 LoopMoverFromCommandLine ()
 LoopMoverFromCommandLine (std::string const protocol, bool const perturb, bool const refine, core::scoring::ScoreFunctionOP &hires_score, core::scoring::ScoreFunctionOP &lores_score, std::string const loop_file_name, protocols::loops::LoopsCOP loops)
bool perturb () const
void perturb (bool const setting)
bool refine () const
void refine (bool const setting)
void refine (std::string const setting)
std::string string_refine () const
void intermedrelax (std::string const setting)
std::string intermedrelax () const
void relax (std::string const setting)
std::string relax () const
void remodel (std::string const setting)
std::string remodel () const
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 ~LoopMoverFromCommandLine ()

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::LoopMoverFromCommandLine::LoopMoverFromCommandLine ( )
protocols::protein_interface_design::movers::LoopMoverFromCommandLine::LoopMoverFromCommandLine ( std::string const  protocol,
bool const  perturb,
bool const  refine,
core::scoring::ScoreFunctionOP hires_score,
core::scoring::ScoreFunctionOP lores_score,
std::string const  loop_file_name,
protocols::loops::LoopsCOP  loops 
)
protocols::protein_interface_design::movers::LoopMoverFromCommandLine::~LoopMoverFromCommandLine ( ) [virtual]

Member Function Documentation

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::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::loops::loop_mover::LoopMover::add_fragments(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::allsc(), 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::comparative_modeling::LoopRelaxMover::apply(), core::chemical::CENTROID, core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::comparative_modeling::LoopRelaxMover::frag_libs(), core::scoring::dssp::Dssp::insert_ss_into_pose(), intermedrelax(), protocols::comparative_modeling::LoopRelaxMover::intermedrelax(), protocols::comparative_modeling::LoopRelaxMover::loops(), perturb(), protocols::loops::read_loop_fragments(), refine(), protocols::comparative_modeling::LoopRelaxMover::refine(), relax(), protocols::comparative_modeling::LoopRelaxMover::relax(), remodel(), protocols::comparative_modeling::LoopRelaxMover::remodel(), protocols::comparative_modeling::LoopRelaxMover::scorefxns(), core::pose::Pose::secstruct(), core::pose::Pose::sequence(), 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::set_secstruct_from_psipred_ss2(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), string_refine(), core::util::switch_to_residue_type_set(), protocols::simple_moves::DesignRepackMover::task_factory(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopMoverFromCommandLine::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.

References LoopMoverFromCommandLine().

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopMoverFromCommandLine::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::LoopMoverFromCommandLine::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::LoopMoverFromCommandLineCreator::mover_name().

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::intermedrelax ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::intermedrelax ( std::string const  setting) [inline]
void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::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::moves::DataMap::get(), intermedrelax(), protocols::rosetta_scripts::parse_task_operations(), refine(), relax(), remodel(), and protocols::simple_moves::DesignRepackMover::task_factory().

bool protocols::protein_interface_design::movers::LoopMoverFromCommandLine::perturb ( ) const [inline]

Referenced by apply().

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

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::refine ( bool const  setting) [inline]
void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::refine ( std::string const  setting) [inline]
void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::relax ( std::string const  setting) [inline]
std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::relax ( ) const [inline]

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::movers::LoopMoverFromCommandLine::remodel ( std::string const  setting) [inline]
std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::remodel ( ) const [inline]

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::LoopMoverFromCommandLine::string_refine ( ) const [inline]

Referenced by apply().


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