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

#include <LoopMover_CCD.hh>

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List of all members.

Public Member Functions

 LoopMover_Perturb_CCD ()
 LoopMover_Perturb_CCD (protocols::loops::LoopsOP loops_in)
 LoopMover_Perturb_CCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn)
 LoopMover_Perturb_CCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn, core::fragment::FragSetOP fragset)
 ~LoopMover_Perturb_CCD ()
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.
void set_default_settings ()

Protected Member Functions

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

Protected Attributes

std::vector
< core::fragment::FragSetOP
frag_libs_

Detailed Description

the main function to model one single loop in centroid mode. The modeling algorithm is fragment_ccd_min_trial, which consists of perturbing the loop conformation by fragment insertion , then close the loop by CCD loop closure, then minimize the loop conformation and finally subject it to Monte Carlo acceptance or rejection. The loop conformation will be initialized as extended conformation if it is specified in the loop definition, resembling ab initio loop modeling in real practice. The loop has to be long enough for inserting certain length of fragments.


Constructor & Destructor Documentation

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

Member Function Documentation

protocols::moves::MoverOP protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::clone ( ) const [virtual]

Clone this object.

Reimplemented from protocols::moves::Mover.

References LoopMover_Perturb_CCD().

std::string protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::get_name ( ) const [virtual]

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

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

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

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

References protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), protocols::moves::MonteCarlo::boltzmann(), protocols::loops::ccd_close_loops(), core::pose::Pose::conformation(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pack::interaction_graph::debug, core::pose::Pose::dump_pdb(), protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(), core::pose::Pose::energies(), make_table_of_pilot_apps::f, core::pose::Pose::fold_tree(), frag_libs_, protocols::moves::Mover::get_native_pose(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::Residue::is_bonded(), core::kinematics::FoldTree::is_cutpoint(), protocols::loops::Loop::is_extended(), core::pose::symmetry::is_symmetric(), protocols::loops::Loop::is_terminal(), protocols::loops::loop_rmsd(), protocols::loops::loops_set_move_map(), protocols::moves::MonteCarlo::lowest_score_pose(), protocols::moves::MonteCarlo::recover_low(), core::pose::Pose::residue(), protocols::loops::loop_mover::LoopMover::scorefxn(), protocols::simple_moves::ClassicFragmentMover::set_check_ss(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::set_temperature(), protocols::moves::MonteCarlo::show_scores(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::loop_mover::Success, core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), tr(), and core::scoring::EMapVector::weighted_string_of().

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

Referenced by LoopMover_Perturb_CCD().

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

Member Data Documentation

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

Referenced by model_loop().


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