Rosetta 3.4
Public Member Functions | Protected Member Functions | Protected Attributes
protocols::loops::loop_mover::refine::LoopMover_Refine_CCD Class Reference

#include <LoopMover_CCD.hh>

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List of all members.

Public Member Functions

 LoopMover_Refine_CCD ()
 LoopMover_Refine_CCD (protocols::loops::LoopsOP loops_in)
 LoopMover_Refine_CCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn)
 ~LoopMover_Refine_CCD ()
virtual protocols::moves::MoverOP clone () const
 Clone this object.
void set_default_settings ()
void set_redesign_loop (bool value=true)
bool get_redesign_loop ()
void set_task_factory (core::pack::task::TaskFactoryCOP task_factory_in)
core::pack::task::TaskFactoryCOP get_task_factory () const
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, 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.
void apply (core::pose::Pose &pose)
 Apply the loop-build protocol to the input pose.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void outer_cycles (core::Size value)
void max_inner_cycles (core::Size value)
void repack_period (core::Size value)
void temp_initial (core::Real value)
void temp_final (core::Real value)
void set_fold_tree_from_loops (bool const s)
bool set_fold_tree_from_loops () const
core::kinematics::MoveMapOP move_map () const
void move_map (core::kinematics::MoveMapOP mm)

Protected Member Functions

void read_options ()
void setup_movemap (core::pose::Pose const &pose, protocols::loops::Loops const &loops, utility::vector1< bool > const &allow_repack, core::kinematics::MoveMapOP &movemap)
 setup an appropriate movemap for the given loops
virtual basic::Tracer & tr () const

Protected Attributes

core::pack::task::TaskFactoryOP task_factory_
bool redesign_loop_

Constructor & Destructor Documentation

protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD ( )
protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD ( protocols::loops::LoopsOP  loops_in)
protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD ( protocols::loops::LoopsOP  loops_in,
core::scoring::ScoreFunctionOP  scorefxn 
)
protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::~LoopMover_Refine_CCD ( )

Member Function Documentation

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply ( core::pose::Pose ) [virtual]

Apply the loop-build protocol to the input pose.

Reimplemented from protocols::loops::loop_mover::LoopMover.

References protocols::loops::add_cutpoint_variants(), protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), protocols::simple_moves::BackboneMover::apply(), make_table_of_pilot_apps::begin, protocols::loops::ccd_close_loops(), core::scoring::chainbreak, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pack::interaction_graph::debug, core::pose::Pose::dump_pdb(), core::sequence::end, core::pose::Pose::energies(), make_table_of_pilot_apps::f, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::loops::get_fa_scorefxn(), protocols::moves::Mover::get_native_pose(), core::conformation::Residue::has_variant_type(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_upper_terminus(), protocols::loops::loop_rmsd(), protocols::loops::loop_mover::LoopMover::loops(), core::pose::symmetry::make_residue_mask_symmetric(), core::pack::pack_rotamers(), redesign_loop_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), core::pack::rotamer_trials(), protocols::loops::loop_mover::LoopMover::scorefxn(), protocols::loops::select_loop_residues(), protocols::loops::loop_mover::LoopMover::set_loops_from_pose_observer_cache(), setup_movemap(), task_factory_, core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), tr(), protocols::loops::loop_mover::LoopMover::use_loops_from_observer_cache(), and core::scoring::EMapVector::weighted_string_of().

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::LoopRefine::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), and protocols::forge::remodel::RemodelMover::confirm_sequence().

protocols::moves::MoverOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::clone ( ) const [virtual]

Clone this object.

Reimplemented from protocols::moves::Mover.

References LoopMover_Refine_CCD().

std::string protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_name ( ) const [virtual]

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

Reimplemented from protocols::loops::loop_mover::LoopMover.

bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_redesign_loop ( ) [inline]

References redesign_loop_.

core::pack::task::TaskFactoryCOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_task_factory ( ) const

References task_factory_.

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::max_inner_cycles ( core::Size  value) [inline]
loop_mover::LoopMover::MoveMapOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map ( ) const
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map ( core::kinematics::MoveMapOP  mm)
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::outer_cycles ( core::Size  value) [inline]

Referenced by read_options().

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::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::moves::Mover.

References protocols::moves::DataMap::get(), protocols::loops::loop_mover::LoopMover::loops(), protocols::loops::loops_from_string(), protocols::rosetta_scripts::parse_movemap(), protocols::rosetta_scripts::parse_task_operations(), set_fold_tree_from_loops(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), set_task_factory(), protocols::loops::loop_mover::LoopMover::set_use_loops_from_observer_cache(), task_factory_, temp_final(), and temp_initial().

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::read_options ( ) [protected]

References outer_cycles().

Referenced by LoopMover_Refine_CCD().

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period ( core::Size  value) [inline]
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_default_settings ( )

References redesign_loop_.

Referenced by LoopMover_Refine_CCD().

bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops ( ) const [inline]

Referenced by parse_my_tag().

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops ( bool const  s) [inline]
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_redesign_loop ( bool  value = true) [inline]
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory ( core::pack::task::TaskFactoryCOP  task_factory_in)
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  loops,
utility::vector1< bool > const &  allow_repack,
core::kinematics::MoveMapOP movemap 
) [protected]

setup an appropriate movemap for the given loops

Parameters:
[in]loopsThe loops to model.
[in]allow_repackIndicates whether or not to allow a position to repack.
[out]movemapOutput movemap, all settings added here.
Remarks:
will enforce the false movemap

References protocols::loops::loop_mover::LoopMover::enforce_false_movemap(), core::pose::symmetry::is_symmetric(), protocols::loops::loops_set_move_map(), and core::pose::symmetry::make_symmetric_movemap().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_final ( core::Real  value) [inline]

Referenced by parse_my_tag().

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_initial ( core::Real  value) [inline]

Referenced by parse_my_tag().

basic::Tracer & protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::tr ( ) const [protected, virtual]

Member Data Documentation


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