Rosetta 3.4
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions
protocols::forge::remodel::RemodelLoopMover Class Reference

Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++. More...

#include <RemodelLoopMover.hh>

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List of all members.

Public Types

typedef core::Real Real
typedef core::Size Size
typedef std::string String
typedef core::kinematics::MoveMap MoveMap
typedef core::fragment::FragSetCOP FragSetCOP
typedef core::fragment::FragSetOP FragSetOP
typedef core::pose::Pose Pose
typedef core::pose::PoseOP PoseOP
typedef
core::scoring::ScoreFunction 
ScoreFunction
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
typedef
protocols::simple_moves::ClassicFragmentMoverOP 
ClassicFragmentMoverOP
typedef
protocols::simple_moves::FragmentMoverOP 
FragmentMoverOP
typedef protocols::loops::Loop Loop
typedef protocols::loops::Loops Loops
typedef
protocols::moves::MonteCarlo 
MonteCarlo
typedef protocols::moves::MoverOP MoverOP
typedef utility::vector1
< FragSetOP
FragSetOPs
typedef utility::vector1
< FragmentMoverOP
FragmentMoverOPs
typedef utility::tag::TagPtr TagPtr
typedef
protocols::filters::Filters_map 
Filters_map
typedef protocols::moves::DataMap DataMap
typedef
protocols::moves::Movers_map 
Movers_map

Public Member Functions

 RemodelLoopMover ()
 default constructor
 RemodelLoopMover (loops::LoopsOP const loops)
 loops constructor
 RemodelLoopMover (RemodelLoopMover const &rval)
 copy constructor
virtual ~RemodelLoopMover ()
 default destructor
void set_param_from_options ()
 set parameters from options
virtual MoverOP clone () const
 clone this object
virtual MoverOP fresh_instance () const
 create this type of object
ScoreFunction const & scorefunction () const
 the ScoreFunction to use during modeling;
MoveMap const & false_movemap () const
 get the false movemap
Real max_linear_chainbreak () const
 if linear chainbreak is <= this value, loop is considered closed (default 0.07)
bool randomize_loops () const
 randomize loops prior to running main protocol? (default true)
Size allowed_closure_attempts () const
 the allowed number of overall closure attempts before apply() exits (default 3)
Size simultaneous_cycles () const
 the number of simultaneous closure cycles to perform (default 2)
Size independent_cycles () const
 the number of independent closure cycles to perform (default 8)
Size boost_closure_cycles () const
 the maximum number of possible lockdown closure cycles to perform (default 30)
Size total_standard_cycles () const
 the total number of "standard" (equal to simul + independent) to perform
Real temperature () const
 temperature for mc ( default 2.0 )
void repeat_generation_with_additional_residue (Pose &pose, Pose &repeat_pose)
void repeat_generation (Pose &pose, Pose &repeat_pose)
void repeat_propagation (Pose &pose, Pose &repeat_pose, Size repeat_number)
void scorefunction (ScoreFunction const &sfx)
 the ScoreFunction to use during modeling
void false_movemap (MoveMap const &movemap)
 set the false movemap to use
void max_linear_chainbreak (Real const val)
 if linear chainbreak is <= this value, loop is considered closed
void randomize_loops (bool const flag)
 randomize loops prior to running main protocol?
void allowed_closure_attempts (Size const attempts)
 the allowed number of overall closure attempts before apply() exits
void simultaneous_cycles (Size const cycles)
 the number of simultaneous closure cycles to perform
void independent_cycles (Size const cycles)
 the number of independent closure cycles to perform
void boost_closure_cycles (Size const cycles)
 the maximum number of possible lockdown closure cycles to perform
void temperature (Real const temp)
 temperature for mc
void set_repeat_tail_length (Size const length)
loops::LoopsOP const loops () const
 the loops to model
void loops (loops::LoopsOP const loops)
 set the loops to model
void add_loop (Loop const loop)
 add a loop to model
void add_fragments (FragSetCOP fragset)
 add a fragment set
void clear_fragments ()
 clear all fragment sets
virtual void apply (Pose &pose)
 apply defined moves to given Pose
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void randomize_stage (Pose &pose)
 randomize loops

Static Public Member Functions

static void register_options ()
 options

Protected Member Functions

void insert_random_smallestmer_per_loop (Pose &pose, bool const only_broken_loops=true)
 find the smallest fragment size and insert a single such smallmer into each loop; for breaking up trapped trajectories
void simultaneous_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
 simultaneous stage: multiple loop movement prior to MC accept/reject
void independent_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
 independent stage: single loop movement prior to MC accept/reject
void boost_closure_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
 lockdown stage: close loops within some threshold w/ smallest-mer (typically 1-mer) + ccd_move only
loops::LoopsOP determine_loops_to_model (Pose &pose)
 determine which loops need modeling wrt to given Pose
bool check_closure_criteria (Pose &pose, bool const show_in_tracer=false)
 check all loops for closure criteria
FragmentMoverOPs create_fragment_movers (MoveMap const &movemap, Size const largest_frag_size=0)
 return fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set
void create_fragment_movers (MoveMap const &movemap, FragmentMoverOPs &frag_movers, Size const largest_frag_size=0)
 append fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set
FragmentMoverOPs create_per_loop_fragment_movers (loops::LoopsOP const loops, Size const largest_frag_size=0)
 create per-loop fragment movers: 1 fragment mover for each loop (uses movemaps to lock down non-loop residues)
void enforce_false_movemap (MoveMap &movemap)
 enforce settings in the false movemap
void mark_loops_moveable (loops::LoopsOP const loops, MoveMap &movemap, bool const allow_omega)
 mark bb/chi torsions of multiple loops moveable in a movemap
void mark_loop_moveable (Loop const &loop, MoveMap &movemap, bool const allow_omega)
 mark bb/chi torsion of a single loop moveable in movemap
Size count_moveable_residues (MoveMap const &movemap, Size const left, Size const right)
 count number of residues with moveable backbone torsions in the given range [left, right]

Detailed Description

Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++.


Member Typedef Documentation

Reimplemented from protocols::moves::Mover.

Reimplemented from protocols::moves::Mover.

Reimplemented from protocols::moves::Mover.


Constructor & Destructor Documentation

protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover ( )

default constructor

References set_param_from_options().

Referenced by clone(), and fresh_instance().

protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover ( loops::LoopsOP const  loops)

loops constructor

References set_param_from_options().

protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover ( RemodelLoopMover const &  rval)

copy constructor

protocols::forge::remodel::RemodelLoopMover::~RemodelLoopMover ( ) [virtual]

default destructor


Member Function Documentation

void protocols::forge::remodel::RemodelLoopMover::add_fragments ( FragSetCOP  fragset)
void protocols::forge::remodel::RemodelLoopMover::add_loop ( Loop const  loop) [inline]

add a loop to model

void protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts ( Size const  attempts) [inline]

the allowed number of overall closure attempts before apply() exits

Size protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts ( ) const [inline]

the allowed number of overall closure attempts before apply() exits (default 3)

Referenced by set_param_from_options().

void protocols::forge::remodel::RemodelLoopMover::apply ( Pose pose) [virtual]
void protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles ( Size const  cycles) [inline]

the maximum number of possible lockdown closure cycles to perform

Size protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles ( ) const [inline]

the maximum number of possible lockdown closure cycles to perform (default 30)

Referenced by apply(), boost_closure_stage(), and set_param_from_options().

void protocols::forge::remodel::RemodelLoopMover::boost_closure_stage ( Pose pose,
MonteCarlo mc,
Real const  cbreak_increment 
) [protected]

lockdown stage: close loops within some threshold w/ smallest-mer (typically 1-mer) + ccd_move only

lock down stage: close loops within some threshold w/ smallest-mer (typically 1-mer) + ccd_move only

This stage differs from simultaneous_stage() and independent_stage() in that once a loop is closed, it breaks out of the closure cycle and goes to the next one. The rationale is that once we hit the boost_closure_stage() we are desperate to close the loop, so we sacrifice diversity and instead just seek a closed solution.

References core::util::add_cutpoint_variants(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), boost_closure_cycles(), protocols::loops::loop_closure::ccd::ccd_moves(), check_closure_criteria(), count_moveable_residues(), create_fragment_movers(), protocols::loops::Loop::cut(), determine_loops_to_model(), enforce_false_movemap(), make_table_of_pilot_apps::f, core::pose::Pose::fold_tree(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), repeat_propagation(), protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), protocols::forge::remodel::RG(), protocols::moves::MonteCarlo::score_function(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::show_state(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and protocols::forge::remodel::TR().

Referenced by apply().

bool protocols::forge::remodel::RemodelLoopMover::check_closure_criteria ( Pose pose,
bool const  show_in_tracer = false 
) [protected]

check all loops for closure criteria

Parameters:
[in]poseThe pose being checked.
[in]show_in_tracerOutput state of each loop to tracer?
Returns:
true if all criteria pass, false otherwise

References core::scoring::linear_chainbreak, and protocols::forge::remodel::TR().

Referenced by apply(), boost_closure_stage(), independent_stage(), randomize_stage(), and simultaneous_stage().

void protocols::forge::remodel::RemodelLoopMover::clear_fragments ( )

clear all fragment sets

RemodelLoopMover::MoverOP protocols::forge::remodel::RemodelLoopMover::clone ( ) const [virtual]

clone this object

Reimplemented from protocols::moves::Mover.

References RemodelLoopMover().

RemodelLoopMover::Size protocols::forge::remodel::RemodelLoopMover::count_moveable_residues ( MoveMap const &  movemap,
Size const  left,
Size const  right 
) [protected]

count number of residues with moveable backbone torsions in the given range [left, right]

References core::kinematics::MoveMap::get_bb().

Referenced by boost_closure_stage(), independent_stage(), randomize_stage(), and simultaneous_stage().

RemodelLoopMover::FragmentMoverOPs protocols::forge::remodel::RemodelLoopMover::create_fragment_movers ( MoveMap const &  movemap,
Size const  largest_frag_size = 0 
) [protected]

return fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set

return fragment movers for the list of internally kept fragment sets

Parameters:
[in]movemapUse this movemap when initializing fragment movers.
[in]largest_frag_sizeOnly use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets.

References core::kinematics::MoveMap::clone(), and make_table_of_pilot_apps::f.

Referenced by boost_closure_stage(), create_per_loop_fragment_movers(), independent_stage(), and randomize_stage().

void protocols::forge::remodel::RemodelLoopMover::create_fragment_movers ( MoveMap const &  movemap,
FragmentMoverOPs frag_movers,
Size const  largest_frag_size = 0 
) [protected]

append fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set

append fragment movers for the list of internally kept fragment sets

Parameters:
[in]movemapUse this movemap when initializing fragment movers.
[out]frag_moversAppend fragment movers to this list.
[in]largest_frag_sizeOnly use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets.

References core::kinematics::MoveMap::clone(), make_table_of_pilot_apps::f, and protocols::simple_moves::ClassicFragmentMover::set_check_ss().

RemodelLoopMover::FragmentMoverOPs protocols::forge::remodel::RemodelLoopMover::create_per_loop_fragment_movers ( loops::LoopsOP const  loops,
Size const  largest_frag_size = 0 
) [protected]

create per-loop fragment movers: 1 fragment mover for each loop (uses movemaps to lock down non-loop residues)

Parameters:
[in]loopsThe loops to use.
[in]largest_frag_sizeOnly use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets.

References create_fragment_movers(), enforce_false_movemap(), and mark_loop_moveable().

Referenced by insert_random_smallestmer_per_loop(), and simultaneous_stage().

loops::LoopsOP protocols::forge::remodel::RemodelLoopMover::determine_loops_to_model ( Pose pose) [protected]

determine which loops need modeling wrt to given Pose

Remarks:
Skips closed loops and shuffles the order of the remaining loops.

References core::scoring::linear_chainbreak, and protocols::forge::remodel::RG().

Referenced by boost_closure_stage(), independent_stage(), and insert_random_smallestmer_per_loop().

void protocols::forge::remodel::RemodelLoopMover::enforce_false_movemap ( MoveMap movemap) [protected]
void protocols::forge::remodel::RemodelLoopMover::false_movemap ( MoveMap const &  movemap) [inline]

set the false movemap to use

Remarks:
All movemaps are generated with respect to this movemap. Any explicit False settings within this movemap will be retained in all descendant movemaps.
MoveMap const& protocols::forge::remodel::RemodelLoopMover::false_movemap ( ) const [inline]

get the false movemap

Remarks:
All movemaps are generated with respect to this movemap. Any explicit False settings within this movemap will be retained in all descendant movemaps.
RemodelLoopMover::MoverOP protocols::forge::remodel::RemodelLoopMover::fresh_instance ( ) const [virtual]

create this type of object

Reimplemented from protocols::moves::Mover.

References RemodelLoopMover().

std::string protocols::forge::remodel::RemodelLoopMover::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

Size protocols::forge::remodel::RemodelLoopMover::independent_cycles ( ) const [inline]

the number of independent closure cycles to perform (default 8)

Referenced by independent_stage(), and set_param_from_options().

void protocols::forge::remodel::RemodelLoopMover::independent_cycles ( Size const  cycles) [inline]

the number of independent closure cycles to perform

void protocols::forge::remodel::RemodelLoopMover::independent_stage ( Pose pose,
MonteCarlo mc,
Real const  cbreak_increment 
) [protected]
void protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop ( Pose pose,
bool const  only_broken_loops = true 
) [protected]

find the smallest fragment size and insert a single such smallmer into each loop; for breaking up trapped trajectories

Parameters:
[in,out]poseThe pose to modify.
[in]only_broken_loopIf true, only insert into broken loops, otherwise insert into all. (default true)

References create_per_loop_fragment_movers(), determine_loops_to_model(), make_table_of_pilot_apps::f, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), core::pose::symmetry::is_symmetric(), and repeat_propagation().

Referenced by apply().

void protocols::forge::remodel::RemodelLoopMover::loops ( loops::LoopsOP const  loops) [inline]

set the loops to model

References loops().

loops::LoopsOP const protocols::forge::remodel::RemodelLoopMover::loops ( ) const [inline]

the loops to model

Referenced by loops().

void protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable ( Loop const &  loop,
MoveMap movemap,
bool const  allow_omega 
) [protected]

mark bb/chi torsion of a single loop moveable in movemap

Parameters:
[in]loopsThe loop to use.
[out]movemapThe movemap to modify.
[in]allow_omegaAllow bb omega to move? (should be yes when doing either fragment insertion or scoring function has omega tether, otherwise should probably be no)

References core::id::BB, core::id::omega_torsion(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by boost_closure_stage(), create_per_loop_fragment_movers(), independent_stage(), and mark_loops_moveable().

void protocols::forge::remodel::RemodelLoopMover::mark_loops_moveable ( loops::LoopsOP const  loops,
MoveMap movemap,
bool const  allow_omega 
) [protected]

mark bb/chi torsions of multiple loops moveable in a movemap

Parameters:
[in]loopsThe loops to use.
[out]movemapThe movemap to modify.
[in]allow_omegaAllow bb omega to move? (should be yes when doing either fragment insertion or scoring function has omega tether, otherwise should probably be no)

References mark_loop_moveable().

Referenced by randomize_stage(), and simultaneous_stage().

void protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak ( Real const  val) [inline]

if linear chainbreak is <= this value, loop is considered closed

Real protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak ( ) const [inline]

if linear chainbreak is <= this value, loop is considered closed (default 0.07)

Referenced by set_param_from_options().

void protocols::forge::remodel::RemodelLoopMover::randomize_loops ( bool const  flag) [inline]

randomize loops prior to running main protocol?

bool protocols::forge::remodel::RemodelLoopMover::randomize_loops ( ) const [inline]

randomize loops prior to running main protocol? (default true)

Referenced by set_param_from_options().

void protocols::forge::remodel::RemodelLoopMover::randomize_stage ( Pose pose)
void protocols::forge::remodel::RemodelLoopMover::register_options ( ) [static]

options

Reimplemented from protocols::moves::Mover.

void protocols::forge::remodel::RemodelLoopMover::repeat_generation ( Pose pose,
Pose repeat_pose 
)
void protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue ( Pose pose,
Pose repeat_pose 
)
void protocols::forge::remodel::RemodelLoopMover::repeat_propagation ( Pose pose,
Pose repeat_pose,
core::Size  repeat_number 
)
RemodelLoopMover::ScoreFunction const & protocols::forge::remodel::RemodelLoopMover::scorefunction ( ) const

the ScoreFunction to use during modeling;

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply().

void protocols::forge::remodel::RemodelLoopMover::scorefunction ( ScoreFunction const &  sfx)

the ScoreFunction to use during modeling

References core::scoring::ScoreFunction::clone().

void protocols::forge::remodel::RemodelLoopMover::set_param_from_options ( )
void protocols::forge::remodel::RemodelLoopMover::set_repeat_tail_length ( Size const  length) [inline]
Size protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles ( ) const [inline]

the number of simultaneous closure cycles to perform (default 2)

Referenced by independent_stage(), set_param_from_options(), and simultaneous_stage().

void protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles ( Size const  cycles) [inline]

the number of simultaneous closure cycles to perform

void protocols::forge::remodel::RemodelLoopMover::simultaneous_stage ( Pose pose,
MonteCarlo mc,
Real const  cbreak_increment 
) [protected]
Real protocols::forge::remodel::RemodelLoopMover::temperature ( ) const [inline]

temperature for mc ( default 2.0 )

Referenced by set_param_from_options().

void protocols::forge::remodel::RemodelLoopMover::temperature ( Real const  temp) [inline]

temperature for mc

Size protocols::forge::remodel::RemodelLoopMover::total_standard_cycles ( ) const [inline]

the total number of "standard" (equal to simul + independent) to perform

Referenced by apply(), independent_stage(), and simultaneous_stage().


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