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

#include <LoopMover_KIC.hh>

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List of all members.

Public Member Functions

 LoopMover_Refine_KIC ()
 LoopMover_Refine_KIC (protocols::loops::LoopsOP loops_in)
 LoopMover_Refine_KIC (protocols::loops::LoopsOP const loops_in, core::scoring::ScoreFunctionCOP scorefxn)
 ~LoopMover_Refine_KIC ()
void init (core::scoring::ScoreFunctionCOP scorefxn)
void set_default_settings ()
void set_redesign_loop (bool value=true)
bool get_redesign_loop ()
void set_task_factory (core::pack::task::TaskFactoryOP value)
bool get_task_factory ()
virtual protocols::moves::MoverOP clone () const
 Clone this object.
void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void update_movemap_vectors (core::pose::Pose &pose, utility::vector1< core::kinematics::MoveMap > &move_maps)
 update the vector of movemaps, one for each loop in loops_
void update_allow_sc_vectors (core::pose::Pose &pose, utility::vector1< utility::vector1< bool > > &allow_sc_vectors)
 update the vector of vectors of moveable side-chain positions, one for each loop in loops_
void set_rottrials_from_kic_segment (core::pose::Pose &pose, core::pack::task::PackerTaskOP &rottrials_packer_task, Size kic_start, Size kic_end)
void set_movemap_from_kic_segment (core::pose::Pose &pose, core::kinematics::MoveMap &cur_mm, Size kic_start, Size kic_end)

Protected Member Functions

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_KIC::LoopMover_Refine_KIC ( )
protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC ( protocols::loops::LoopsOP  loops_in)
protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC ( protocols::loops::LoopsOP const  loops_in,
core::scoring::ScoreFunctionCOP  scorefxn 
)

References init().

protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::~LoopMover_Refine_KIC ( )

Member Function Documentation

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

detailed Refines the polypeptide segments in the LoopMover_Refine_KIC::loops_ class variable from their current conformations. Uses Rosetta's all-atom respresentation and high-resolution scoring function (score12 with an upweighted chain break term). At the beginning of this stage, unless the flag -loops:fix_natsc has been set, all residues within the neighbor distance of a loop (defined by -loops:neighbor_dist) are repacked and then subject to rotamer trials. The backbones of all loop residues, and the side-chains of all loop residues and neighbors are then subject to DFPmin. If -loops:fix_natsc is set, only the loop residues (and not the neighbors) will be subject to repacking, rotamer trials, and minimization. Consequently, if this stage has been preceeded by LoopMover_Perturb_KIC:model_loop, and the -loops:fix_natsc flag is omitted, the side-chains surrounding the loop will be optimized for the perturbed loop conformation, rather than the starting conformation that preceded the call to model_loop.

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

References protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), protocols::loops::Loops::begin(), make_table_of_pilot_apps::begin, protocols::moves::MonteCarlo::boltzmann(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pack::interaction_graph::debug, core::pose::Pose::dump_pdb(), core::sequence::end, make_table_of_pilot_apps::f, core::scoring::fa_sol, protocols::loops::get_fa_scorefxn(), protocols::moves::Mover::get_native_pose(), core::conformation::Residue::has_variant_type(), core::pose::symmetry::is_symmetric(), protocols::moves::MonteCarlo::last_accepted_pose(), protocols::loops::loop_rmsd(), protocols::loops::loop_mover::LoopMover::loops(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), protocols::loops::loops_set_move_map(), protocols::moves::MonteCarlo::lowest_score_pose(), core::pose::symmetry::make_residue_mask_symmetric(), make_table_of_pilot_apps::name, core::scoring::occ_sol_exact, core::pack::pack_rotamers(), protocols::moves::MonteCarlo::recover_low(), redesign_loop_, core::pose::Pose::residue(), protocols::loops::loop_mover::refine::RG(), core::pack::rotamer_trials(), protocols::moves::MonteCarlo::score_function(), protocols::loops::loop_mover::LoopMover::scorefxn(), protocols::loops::select_loop_residues(), core::pose::Pose::sequence(), set_movemap_from_kic_segment(), set_rottrials_from_kic_segment(), protocols::moves::MonteCarlo::set_temperature(), protocols::moves::MonteCarlo::show_counters(), protocols::moves::MonteCarlo::show_scores(), task_factory, core::pose::Pose::total_residue(), tr(), update_allow_sc_vectors(), update_movemap_vectors(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::abinitio::AbrelaxApplication::fold(), and protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub().

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

Clone this object.

Reimplemented from protocols::moves::Mover.

References LoopMover_Refine_KIC().

std::string protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::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_KIC::get_redesign_loop ( ) [inline]

References redesign_loop_.

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_task_factory ( )

References task_factory.

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::init ( core::scoring::ScoreFunctionCOP  scorefxn)
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_default_settings ( )

References redesign_loop_.

Referenced by init().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment ( core::pose::Pose pose,
core::kinematics::MoveMap cur_mm,
Size  kic_start,
Size  kic_end 
)

detailed Sets the MoveMap for minimization used in LoopMover_Refine_KIC::apply() to only minimize the neighborhood around KIC segment that moved. May slightly hurt performance in de novo loop reconstruction, but may yield a speedup of 2X or more in cases of modeling very large or multiple segments (loop definitions), in conjunction with set_movemap_from_kic_segment(), which are both used when optimize_only_kic_region_sidechains_after_move_ is set to true.

References protocols::loops::Loops::add_loop(), and protocols::loops::loops_set_move_map().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_redesign_loop ( bool  value = true) [inline]
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_rottrials_from_kic_segment ( core::pose::Pose pose,
core::pack::task::PackerTaskOP rottrials_packer_task,
Size  kic_start,
Size  kic_end 
)

detailed Sets the rotamer trials packer task used in LoopMover_Refine_KIC::apply() to only rotamer trial the neighborhood around KIC segment that moved. May slightly hurt performance in de novo loop reconstruction, but may yield a speedup of 2X or more in cases of modeling very large or multiple segments (loop definitions), in conjunction with set_movemap_from_kic_segment(), which are both used when optimize_only_kic_region_sidechains_after_move_ is set to true.

References protocols::loops::select_loop_residues(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_task_factory ( core::pack::task::TaskFactoryOP  value)
basic::Tracer & protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::tr ( ) const [protected, virtual]
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_allow_sc_vectors ( core::pose::Pose pose,
utility::vector1< utility::vector1< bool > > &  allow_sc_vectors 
)

update the vector of vectors of moveable side-chain positions, one for each loop in loops_

detailed Update the allow_sc_vectors that define, for each loop in loops_, which residue side-chains may be subject to rotamer trials. Allows for rotamer trials to apply only to the neighborhood around the segment that KIC moved, in cases where multiple segments (loops) are defined.

References protocols::loops::Loops::add_loop(), protocols::loops::loop_mover::LoopMover::loops(), protocols::loops::select_loop_residues(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors ( core::pose::Pose pose,
utility::vector1< core::kinematics::MoveMap > &  move_maps 
)

update the vector of movemaps, one for each loop in loops_

detailed Update the MoveMaps that define, for each loop in loops_, which residues may be minimized. Allows for minimization to apply only to the neighborhood around the segment that KIC moved, in cases where multiple segments (loops) are defined.

References protocols::loops::Loops::add_loop(), protocols::loops::loop_mover::LoopMover::loops(), and protocols::loops::loops_set_move_map().

Referenced by apply().


Member Data Documentation


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