Rosetta 3.4
Public Member Functions | Protected Member Functions | Protected Attributes
protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD Class Reference

LoopMover utilizing fragment insertion, ccd loop closure, and minimization. More...

#include <LoopMover_QuickCCD.hh>

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List of all members.

Public Member Functions

 LoopMover_Perturb_QuickCCD ()
 Loops constructor.
 LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in)
 Loops constructor.
 LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn)
 Loops & ScoreFunction constructor.
 LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn, core::fragment::FragSetOP fragset)
 Loops & ScoreFunction constructor.
 ~LoopMover_Perturb_QuickCCD ()
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual protocols::moves::MoverOP clone () const
 clone this object
bool randomize_loop () const
 randomize loops prior to loop modeling?
void randomize_loop (bool const flag)
 indicate whether loops should be randomized prior to modeling
void set_default_settings ()
 set default settings

Protected Member Functions

virtual LoopResult model_loop (core::pose::Pose &pose, protocols::loops::Loop const &loop)
 loop modeling protocol implementation
virtual basic::Tracer & tr () const

Protected Attributes

bool randomize_loop_
 randomize loops prior to performing loop modeling?

Detailed Description

LoopMover utilizing fragment insertion, ccd loop closure, and minimization.


Constructor & Destructor Documentation

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( )
protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( protocols::loops::LoopsOP  loops_in)

Loops constructor.

Parameters:
[in]loops_inthe set of loops to model
Remarks:
Will be initialized with centroid level score function 'score4L'.

References protocols::loops::get_cen_scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( protocols::loops::LoopsOP  loops_in,
core::scoring::ScoreFunctionOP  scorefxn 
)

Loops & ScoreFunction constructor.

Parameters:
[in]loops_inthe set of loops to model
[in]scorefxndesired ScoreFunction

References protocols::loops::get_cen_scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( protocols::loops::LoopsOP  loops_in,
core::scoring::ScoreFunctionOP  scorefxn,
core::fragment::FragSetOP  fragset 
)

Loops & ScoreFunction constructor.

Parameters:
[in]loops_inthe set of loops to model
[in]scorefxndesired ScoreFunction
[in]fragsetis the FragSet to be used line?

References protocols::loops::loop_mover::LoopMover::add_fragments(), protocols::loops::get_cen_scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::~LoopMover_Perturb_QuickCCD ( )

Member Function Documentation

protocols::moves::MoverOP protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::clone ( ) const [virtual]
std::string protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::get_name ( ) const [virtual]

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

Reimplemented from protocols::loops::loop_mover::IndependentLoopMover.

Reimplemented in protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves.

LoopResult protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop ( core::pose::Pose pose,
protocols::loops::Loop const &  loop 
) [protected, virtual]

loop modeling protocol implementation

Implements protocols::loops::loop_mover::IndependentLoopMover.

Reimplemented in protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves.

References core::pose::add_variant_type_to_pose_residue(), core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pack::interaction_graph::debug, protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(), core::pose::Pose::energies(), protocols::loops::loop_mover::ExtendFailure, protocols::loops::loop_mover::Failure, protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), core::pose::Pose::fold_tree(), protocols::loops::loop_mover::LoopMover::frag_libs(), protocols::loops::idealize_loop(), protocols::loops::Loop::is_extended(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, core::pose::symmetry::make_symmetric_movemap(), protocols::rigid::random, randomize_loop_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), protocols::loops::loop_mover::LoopMover::scorefxn(), protocols::simple_moves::ClassicFragmentMover::set_check_ss(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_move_map_for_centroid_loop(), protocols::loops::set_single_loop_fold_tree(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::loop_mover::Success, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), and tr().

void protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::randomize_loop ( bool const  flag) [inline]

indicate whether loops should be randomized prior to modeling

References randomize_loop_.

bool protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::randomize_loop ( ) const [inline]

randomize loops prior to loop modeling?

References randomize_loop_.

void protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::set_default_settings ( ) [inline]

set default settings

default settings are as follows:

References randomize_loop_.

Referenced by LoopMover_Perturb_QuickCCD().

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

Member Data Documentation


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