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protocols::forge::remodel::RemodelLoopMover Class Reference

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

#include <RemodelLoopMover.hh>

Inheritance diagram for protocols::forge::remodel::RemodelLoopMover:
Inheritance graph
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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::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 RemodelLoopMover ()
 default constructor More...
 
 RemodelLoopMover (loops::LoopsOP const loops)
 loops constructor More...
 
 RemodelLoopMover (RemodelLoopMover const &rval)
 copy constructor More...
 
 ~RemodelLoopMover () override
 default destructor More...
 
void set_param_from_options ()
 set parameters from options More...
 
MoverOP clone () const override
 clone this object More...
 
MoverOP fresh_instance () const override
 create this type of object More...
 
ScoreFunction const & scorefunction () const
 the ScoreFunction to use during modeling; More...
 
MoveMap const & false_movemap () const
 get the false movemap More...
 
Real max_linear_chainbreak () const
 if linear chainbreak is <= this value, loop is considered closed (default 0.07) More...
 
bool randomize_loops () const
 randomize loops prior to running main protocol? (default true) More...
 
core::Size allowed_closure_attempts () const
 the allowed number of overall closure attempts before apply() exits (default 3) More...
 
core::Size loophash_cycles () const
 the number of loophash closure cycles to perform (default 8) More...
 
core::Size simultaneous_cycles () const
 the number of simultaneous closure cycles to perform (default 2) More...
 
core::Size independent_cycles () const
 the number of independent closure cycles to perform (default 8) More...
 
core::Size boost_closure_cycles () const
 the maximum number of possible lockdown closure cycles to perform (default 30) More...
 
core::Size total_standard_cycles () const
 the total number of "standard" (equal to simul + independent) to perform More...
 
Real temperature () const
 temperature for mc ( default 2.0 ) More...
 
void repeat_generation_with_additional_residue (Pose &pose, Pose &repeat_pose)
 
void repeat_sync (core::pose::Pose &repeat_pose, core::Size repeat_number)
 
void repeat_propagation (Pose &pose, Pose &repeat_pose, core::Size repeat_number)
 
void scorefunction (ScoreFunction const &sfx)
 the ScoreFunction to use during modeling More...
 
void remodelData (protocols::forge::remodel::RemodelData const remodel_data)
 adds the remodel data to thei remodelLoopMover object More...
 
void false_movemap (MoveMap const &movemap)
 set the false movemap to use More...
 
void max_linear_chainbreak (Real const val)
 if linear chainbreak is <= this value, loop is considered closed More...
 
void randomize_loops (bool const flag)
 randomize loops prior to running main protocol? More...
 
void allowed_closure_attempts (core::Size const attempts)
 the allowed number of overall closure attempts before apply() exits More...
 
void loophash_cycles (core::Size const cycles)
 the number of loophash closure cycles to perform More...
 
void simultaneous_cycles (core::Size const cycles)
 the number of simultaneous closure cycles to perform More...
 
void independent_cycles (core::Size const cycles)
 the number of independent closure cycles to perform More...
 
void set_user_provided_movers (utility::vector1< moves::MoverOP > const &movers)
 
void user_provided_movers_apply_cycle (core::Size const cycle)
 
void boost_closure_cycles (core::Size const cycles)
 the maximum number of possible lockdown closure cycles to perform More...
 
void temperature (Real const temp)
 temperature for mc More...
 
void set_repeat_tail_length (core::Size const length)
 
void set_keep_input_foldtree (bool const setting)
 
void set_seal_foldtree (bool const setting)
 
loops::LoopsOP const loops () const
 the loops to model More...
 
void loops (loops::LoopsOP const loops)
 set the loops to model More...
 
void add_loop (Loop const loop)
 add a loop to model More...
 
void add_fragments (FragSetCOP fragset)
 add a fragment set More...
 
void clear_fragments ()
 clear all fragment sets More...
 
void apply (Pose &pose) override
 apply defined moves to given Pose More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void randomize_stage (Pose &pose)
 randomize loops More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void register_options ()
 options More...
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

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 More...
 
void set_segment_stage (Pose &pose, MonteCarlo &mc)
 independent stage: single loop movement prior to MC accept/reject More...
 
void loophash_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
 independent stage: single loop movement prior to MC accept/reject More...
 
void abinitio_stage (Pose &pose, core::Size const fragmentSize, MoveMap const movemap, ScoreFunctionOP sfxOP, core::Size const max_outer_cycles, core::Size const max_inner_cycles, std::set< core::Size > const &disallowedPos, bool const recover_low, std::string stage_name, bool const smoothMoves, Real const fragScoreThreshold)
 abinitioo stage: better control of fragments. No loop closure tried More...
 
void fa_relax_stage (Pose &pose)
 quick trip to FA to push parts of the molecular apart to a reasonable distance. I'm noticing an overcollapse in centroid More...
 
protocols::symmetry::SetupNCSMover generate_ncs_csts (Pose &pose)
 @ brief sets up ncs constraints More...
 
void small_move_stage (Pose &pose, MoveMap const movemap, ScoreFunctionOP sfxOP, core::Size const max_outer_cycles, core::Size const max_inner_cycles, bool const recover_low, Real const h_range, Real const e_range, Real const l_range)
 small_move stage: only small moves More...
 
void simultaneous_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
 simultaneous stage: multiple loop movement prior to MC accept/reject More...
 
void independent_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
 independent stage: single loop movement prior to MC accept/reject More...
 
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 More...
 
loops::LoopsOP determine_loops_to_model (Pose &pose)
 determine which loops need modeling wrt to given Pose More...
 
bool check_closure_criteria (Pose &pose, bool const show_in_tracer=false)
 check all loops for closure criteria More...
 
FragmentMoverOPs create_fragment_movers (MoveMap const &movemap, core::Size const largest_frag_size=0)
 return fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set More...
 
FragmentMoverOPs create_fragment_movers_limit_size (MoveMap const &movemap, core::Size const frag_size, std::set< core::Size > const &disallowedPos, bool const smoothMoves, ScoreFunctionOP const scorefxnOP, Real const fragScoreThreshold=999.0)
 same as create_fragment_movers except with set size More...
 
void create_fragment_movers (MoveMap const &movemap, FragmentMoverOPs &frag_movers, core::Size const largest_frag_size=0)
 append fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set More...
 
FragmentMoverOPs create_per_loop_fragment_movers (loops::LoopsOP const loops, core::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) More...
 
void enforce_false_movemap (MoveMap &movemap)
 enforce settings in the false movemap More...
 
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 More...
 
void mark_loop_moveable (Loop const &loop, MoveMap &movemap, bool const allow_omega)
 mark bb/chi torsion of a single loop moveable in movemap More...
 
core::Size count_moveable_residues (MoveMap const &movemap, core::Size const left, core::Size const right)
 count number of residues with moveable backbone torsions in the given range [left, right] More...
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Private Types

typedef protocols::moves::Mover Super
 

Private Member Functions

RemodelLoopMoveroperator= (RemodelLoopMover const &rval)
 copy assignment More...
 
void set_starting_pdb (Pose &pose)
 initializes pose with starting pose More...
 
void set_starting_sequence (Pose &pose)
 initializes pose with starting sequence More...
 
void set_ideal_helices (Pose &pose)
 initializes pose with ideal helices. More...
 
std::set< core::Sizegenerate_residues_to_sample (bool chooseSubsetResidues, Pose &pose, core::Size fragmentSize)
 allowed positions per stage More...
 

Private Attributes

ScoreFunctionOP sfx_
 the score function to use More...
 
protocols::forge::remodel::RemodelData remodel_data_
 , used when constraints are defined through Remodel More...
 
MoveMap false_movemap_
 the false movemap to use More...
 
loops::LoopsOP loops_
 list of loops to model More...
 
Real max_linear_chainbreak_
 if linear chainbreak is <= this value, loop is considered closed (default 0.07) More...
 
bool randomize_loops_
 randomize loops prior to running main protocol? (default true) More...
 
core::Size repeat_tail_length_
 
core::Size allowed_closure_attempts_
 the allowed number of overall closure attempts before apply() exits (default 3) More...
 
core::Size loophash_cycles_
 the number of loophash closure cycles to perform (default 8) More...
 
core::Size simultaneous_cycles_
 the number of simultaneous closure cycles to perform (default 2) More...
 
core::Size independent_cycles_
 the number of independent closure cycles to perform (default 8) More...
 
utility::vector1< moves::MoverOPuser_provided_movers_
 collection of movers that mess with the pose every n fragment/ccd steps during inneriterations of simultaneous, and independent stage, where n is determined by the variable below gives the user a chance to add their own flavor to the fragment sampling done by this protocol More...
 
core::Size user_provided_movers_apply_cycle_
 determines how often the above movers get called during fragment insertion/ccd steps (default 3 ) More...
 
core::Size boost_closure_cycles_
 the maximum number of possible boost closure cycles to perform (default 30) More...
 
Real temperature_
 temperature for mc More...
 
FragSetOPs fragsets_
 fragment sets to use More...
 
Pose repeat_pose_
 local copy of repeat pose More...
 
core::Size unit_length_
 use this for repeat construction in conjunction with symmetry More...
 
core::Size repeat_length_
 
RemodelGlobalFrame RGF_
 RemodelGlobalFrame for helical definitions. More...
 
bool keep_input_foldtree_
 whether to keep the FoldTree untouched, i.e. trust the user to supply a decent FoldTree More...
 
bool seal_foldtree_
 whether to (true) generate a sealed fold tree or (false) keep the cut fold tree (default=true) More...
 

Detailed Description

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

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::forge::remodel::RemodelLoopMover::DataMap

Constructor & Destructor Documentation

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

default constructor

References set_param_from_options().

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 ( )
overridedefault

default destructor

Member Function Documentation

void protocols::forge::remodel::RemodelLoopMover::abinitio_stage ( Pose pose,
core::Size const  fragmentSize,
MoveMap const  movemap,
ScoreFunctionOP  sfxOP,
core::Size const  max_outer_cycles,
core::Size const  max_inner_cycles,
std::set< core::Size > const &  disallowedPos,
bool const  recover_low,
std::string  stage_name,
bool const  smoothMoves,
Real const  fragScoreThreshold 
)
protected
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

References loops_.

core::Size protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts ( ) const
inline

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

References allowed_closure_attempts_.

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

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

References allowed_closure_attempts_.

void protocols::forge::remodel::RemodelLoopMover::apply ( Pose pose)
overridevirtual

apply defined moves to given Pose

Remarks
Sets protocols::moves::MS_SUCCESS upon successful closure of all loops, otherwise sets protocols::moves::FAIL_RETRY.

Implements protocols::moves::Mover.

References abinitio_stage(), allowed_closure_attempts_, protocols::symmetry::SetupForSymmetryMover::apply(), core::scoring::atom_pair_constraint, boost_closure_cycles(), boost_closure_stage(), check_closure_criteria(), core::pose::Pose::clone(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::energies(), core::pose::symmetry::extract_asymmetric_unit(), fa_relax_stage(), core::chemical::FA_STANDARD, protocols::moves::FAIL_RETRY, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_pose(), generate_residues_to_sample(), independent_stage(), insert_random_smallestmer_per_loop(), core::conformation::symmetry::is_symmetric(), core::scoring::linear_chainbreak, loophash_stage(), loops_, protocols::moves::MonteCarlo::lowest_score_pose(), protocols::moves::MS_SUCCESS, core::pose::Pose::omega(), core::pose::Pose::pdb_info(), core::pose::Pose::phi(), core::pose::Pose::psi(), randomize_loops_, randomize_stage(), remodel_data_, repeat_generation_with_additional_residue(), repeat_length_, repeat_pose_, repeat_propagation(), protocols::moves::MonteCarlo::reset(), RGF_, core::kinematics::FoldTree::root(), protocols::moves::MonteCarlo::score_function(), seal_foldtree_, core::pose::symmetry::sealed_symmetric_fold_tree(), core::pose::Pose::secstruct(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), set_ideal_helices(), protocols::moves::Mover::set_last_move_status(), protocols::forge::remodel::RemodelGlobalFrame::set_native_cst_set(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), protocols::forge::remodel::RemodelGlobalFrame::set_segment_size(), set_segment_stage(), set_starting_pdb(), set_starting_sequence(), sfx_, simultaneous_stage(), core::pose::Pose::size(), protocols::forge::remodel::RemodelData::ss, core::util::switch_to_residue_type_set(), temperature_, core::scoring::Energies::total_energy(), total_standard_cycles(), protocols::forge::remodel::TR(), and unit_length_.

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

core::Size protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles ( ) const
inline

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

References boost_closure_cycles_.

Referenced by apply(), and boost_closure_stage().

void protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles ( core::Size const  cycles)
inline

the maximum number of possible lockdown closure cycles to perform

References boost_closure_cycles_.

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 protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), boost_closure_cycles(), check_closure_criteria(), count_moveable_residues(), create_fragment_movers(), determine_loops_to_model(), enforce_false_movemap(), core::pose::Pose::fold_tree(), fragsets_, core::pose::symmetry::is_symmetric(), keep_input_foldtree_, protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), protocols::mean_field::max(), max_linear_chainbreak_, protocols::mean_field::min(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), repeat_pose_, repeat_propagation(), repeat_sync(), protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), core::scoring::rg, protocols::moves::MonteCarlo::score_function(), core::pose::Pose::secstruct(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::show_state(), protocols::forge::remodel::TR(), and unit_length_.

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 protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loops_, max_linear_chainbreak_, and protocols::forge::remodel::TR().

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

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

clear all fragment sets

References fragsets_.

RemodelLoopMover::MoverOP protocols::forge::remodel::RemodelLoopMover::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

RemodelLoopMover::Size protocols::forge::remodel::RemodelLoopMover::count_moveable_residues ( MoveMap const &  movemap,
core::Size const  left,
core::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,
core::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 fragsets_.

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

void protocols::forge::remodel::RemodelLoopMover::create_fragment_movers ( MoveMap const &  movemap,
FragmentMoverOPs frag_movers,
core::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/s 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.
[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(), and fragsets_.

RemodelLoopMover::FragmentMoverOPs protocols::forge::remodel::RemodelLoopMover::create_fragment_movers_limit_size ( MoveMap const &  movemap,
core::Size const  frag_size,
std::set< core::Size > const &  allowedPos,
bool const  smoothMoves,
ScoreFunctionOP const  scorefxnOP,
Real const  fragScoreThreshold = 999.0 
)
protected

same as create_fragment_movers except with set size

return fragment movers for the list of internally kept fragment sets

Parameters
[in]movemapUse this movemap when initializing fragment movers.
[in]limitssize and position of fragments

References core::kinematics::MoveMap::clone(), and fragsets_.

Referenced by abinitio_stage().

RemodelLoopMover::FragmentMoverOPs protocols::forge::remodel::RemodelLoopMover::create_per_loop_fragment_movers ( loops::LoopsOP const  loops,
core::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 protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loops_, max_linear_chainbreak_, and core::scoring::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::fa_relax_stage ( Pose pose)
protected
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.

References false_movemap_.

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.

References false_movemap_.

RemodelLoopMover::MoverOP protocols::forge::remodel::RemodelLoopMover::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

protocols::symmetry::SetupNCSMover protocols::forge::remodel::RemodelLoopMover::generate_ncs_csts ( Pose pose)
protected

@ brief sets up ncs constraints

References core::pose::Pose::size(), and protocols::forge::remodel::TR().

std::set< core::Size > protocols::forge::remodel::RemodelLoopMover::generate_residues_to_sample ( bool  chooseSubsetResidues,
Pose pose,
core::Size  fragmentSize 
)
private

allowed positions per stage

References remodel_data_, core::pose::Pose::size(), and protocols::forge::remodel::RemodelData::ss.

Referenced by apply().

std::string protocols::forge::remodel::RemodelLoopMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

core::Size protocols::forge::remodel::RemodelLoopMover::independent_cycles ( ) const
inline

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

References independent_cycles_.

Referenced by independent_stage().

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

the number of independent closure cycles to perform

References independent_cycles_.

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

independent stage: single loop movement prior to MC accept/reject

References protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), check_closure_criteria(), count_moveable_residues(), create_fragment_movers(), determine_loops_to_model(), enforce_false_movemap(), core::pose::Pose::fold_tree(), independent_cycles(), core::pose::symmetry::is_symmetric(), protocols::loops::Loop::is_terminal(), keep_input_foldtree_, protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loops_, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), protocols::mean_field::max(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), repeat_pose_, repeat_propagation(), repeat_sync(), protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), core::scoring::rg, protocols::moves::MonteCarlo::score_function(), core::pose::Pose::secstruct(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::show_state(), simultaneous_cycles(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), total_standard_cycles(), protocols::forge::remodel::TR(), unit_length_, user_provided_movers_, and user_provided_movers_apply_cycle_.

Referenced by apply().

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(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), fragsets_, core::pose::symmetry::is_symmetric(), keep_input_foldtree_, loops_, protocols::mean_field::min(), repeat_pose_, and repeat_propagation().

Referenced by apply().

core::Size protocols::forge::remodel::RemodelLoopMover::loophash_cycles ( ) const
inline

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

References loophash_cycles_.

Referenced by loophash_stage().

void protocols::forge::remodel::RemodelLoopMover::loophash_cycles ( core::Size const  cycles)
inline

the number of loophash closure cycles to perform

References loophash_cycles_.

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

independent stage: single loop movement prior to MC accept/reject

References protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), core::chemical::CENTROID_t, check_closure_criteria(), create_fragment_movers(), enforce_false_movemap(), core::pose::Pose::fold_tree(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::loophash::get_rt_over_leap_fast(), protocols::loophash::LeapIndex::index, core::sequence::ABEGOManager::index2symbol(), core::chemical::ResidueType::is_ligand(), core::pose::symmetry::is_symmetric(), keep_input_foldtree_, protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loophash_cycles(), loops_, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), protocols::loophash::LeapIndex::offset, core::scoring::omega, core::pose::Pose::omega(), core::pose::Pose::phi(), core::io::pose_from_pose(), core::pose::Pose::psi(), protocols::hotspot_hashing::reject, core::util::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), repeat_length_, repeat_pose_, repeat_propagation(), repeat_sync(), protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), protocols::moves::MonteCarlo::score_function(), core::pose::Pose::secstruct(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::show_state(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::sequence::ABEGOManager::torsion2index(), protocols::forge::remodel::TR(), and unit_length_.

Referenced by apply().

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

the loops to model

References loops_.

Referenced by loops().

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

set the loops to model

References loops(), and 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(), loophash_stage(), mark_loops_moveable(), and set_segment_stage().

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().

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

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

References max_linear_chainbreak_.

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

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

References max_linear_chainbreak_, and protocols::hybridization::val.

RemodelLoopMover& protocols::forge::remodel::RemodelLoopMover::operator= ( RemodelLoopMover const &  rval)
private

copy assignment

Remarks
Mover base class prevents this from working properly...
bool protocols::forge::remodel::RemodelLoopMover::randomize_loops ( ) const
inline

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

References randomize_loops_.

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

randomize loops prior to running main protocol?

References randomize_loops_.

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

options

void protocols::forge::remodel::RemodelLoopMover::remodelData ( protocols::forge::remodel::RemodelData const  remodel_data)

adds the remodel data to thei remodelLoopMover object

References remodel_data_.

void protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue ( Pose pose,
Pose repeat_pose 
)

References core::pose::add_variant_type_to_pose_residue(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::loops::Loop::cut(), core::conformation::Conformation::delete_residue_slow(), core::kinematics::Edge::downstream_atom(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::is_terminus(), core::pose::Pose::jump(), core::kinematics::FoldTree::jump_edge(), loops_, core::chemical::LOWER_TERMINUS_VARIANT, core::conformation::Conformation::num_chains(), core::pose::Pose::num_jump(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::kinematics::FoldTree::renumber_jumps(), core::kinematics::FoldTree::reorder(), repeat_length_, repeat_tail_length_, core::pose::Pose::residue(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::set_jump(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::kinematics::Jump::set_rotation(), core::kinematics::Jump::set_translation(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::forge::remodel::TR(), core::chemical::UPPER_TERMINUS_VARIANT, and core::kinematics::Edge::upstream_atom().

Referenced by apply(), protocols::forge::components::VarLengthBuild::apply(), and protocols::forge::remodel::RemodelMover::centroid_build().

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

the ScoreFunction to use during modeling;

References sfx_.

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(), and sfx_.

void protocols::forge::remodel::RemodelLoopMover::set_ideal_helices ( Pose pose)
private
void protocols::forge::remodel::RemodelLoopMover::set_keep_input_foldtree ( bool const  setting)
inline

References keep_input_foldtree_.

void protocols::forge::remodel::RemodelLoopMover::set_param_from_options ( )
void protocols::forge::remodel::RemodelLoopMover::set_repeat_tail_length ( core::Size const  length)
inline
void protocols::forge::remodel::RemodelLoopMover::set_seal_foldtree ( bool const  setting)
inline

References seal_foldtree_.

void protocols::forge::remodel::RemodelLoopMover::set_segment_stage ( Pose pose,
MonteCarlo mc 
)
protected
void protocols::forge::remodel::RemodelLoopMover::set_starting_pdb ( Pose pose)
private
void protocols::forge::remodel::RemodelLoopMover::set_starting_sequence ( Pose pose)
private
void protocols::forge::remodel::RemodelLoopMover::set_user_provided_movers ( utility::vector1< moves::MoverOP > const &  movers)

References user_provided_movers_.

core::Size protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles ( ) const
inline

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

References simultaneous_cycles_.

Referenced by independent_stage(), and simultaneous_stage().

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

the number of simultaneous closure cycles to perform

References simultaneous_cycles_.

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

simultaneous stage: multiple loop movement prior to MC accept/reject

References protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), check_closure_criteria(), count_moveable_residues(), create_per_loop_fragment_movers(), enforce_false_movemap(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), core::conformation::symmetry::is_symmetric(), keep_input_foldtree_, core::scoring::linear_chainbreak, loops_, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loops_moveable(), protocols::mean_field::max(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::num_jump(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), repeat_pose_, repeat_propagation(), repeat_sync(), repeat_tail_length_, protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), core::scoring::rg, protocols::moves::MonteCarlo::score_function(), core::pose::Pose::secstruct(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), protocols::moves::MonteCarlo::show_state(), simultaneous_cycles(), total_standard_cycles(), protocols::forge::remodel::TR(), unit_length_, user_provided_movers_, and user_provided_movers_apply_cycle_.

Referenced by apply().

void protocols::forge::remodel::RemodelLoopMover::small_move_stage ( Pose pose,
MoveMap const  movemap,
ScoreFunctionOP  sfxOP,
core::Size const  max_outer_cycles,
core::Size const  max_inner_cycles,
bool const  recover_low,
Real const  h_range,
Real const  e_range,
Real const  l_range 
)
protected
Real protocols::forge::remodel::RemodelLoopMover::temperature ( ) const
inline

temperature for mc ( default 2.0 )

References temperature_.

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

temperature for mc

References temperature_.

core::Size protocols::forge::remodel::RemodelLoopMover::total_standard_cycles ( ) const
inline

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

References independent_cycles_, loophash_cycles_, and simultaneous_cycles_.

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

void protocols::forge::remodel::RemodelLoopMover::user_provided_movers_apply_cycle ( core::Size const  cycle)
inline

Member Data Documentation

core::Size protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts_
private

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

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

core::Size protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles_
private

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

Referenced by boost_closure_cycles(), and set_param_from_options().

MoveMap protocols::forge::remodel::RemodelLoopMover::false_movemap_
private

the false movemap to use

Remarks
All movemaps are generated with respect to this movemap. Any False explicit settings within this movemap will be retained in all descendant movemaps.

Referenced by enforce_false_movemap(), and false_movemap().

FragSetOPs protocols::forge::remodel::RemodelLoopMover::fragsets_
private
core::Size protocols::forge::remodel::RemodelLoopMover::independent_cycles_
private

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

Referenced by independent_cycles(), set_param_from_options(), and total_standard_cycles().

bool protocols::forge::remodel::RemodelLoopMover::keep_input_foldtree_
private
core::Size protocols::forge::remodel::RemodelLoopMover::loophash_cycles_
private

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

Referenced by loophash_cycles(), set_param_from_options(), and total_standard_cycles().

loops::LoopsOP protocols::forge::remodel::RemodelLoopMover::loops_
private
Real protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak_
private

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

Referenced by boost_closure_stage(), check_closure_criteria(), determine_loops_to_model(), max_linear_chainbreak(), and set_param_from_options().

bool protocols::forge::remodel::RemodelLoopMover::randomize_loops_
private

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

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

protocols::forge::remodel::RemodelData protocols::forge::remodel::RemodelLoopMover::remodel_data_
private

, used when constraints are defined through Remodel

Referenced by apply(), generate_residues_to_sample(), remodelData(), and set_ideal_helices().

core::Size protocols::forge::remodel::RemodelLoopMover::repeat_length_
private
Pose protocols::forge::remodel::RemodelLoopMover::repeat_pose_
private
core::Size protocols::forge::remodel::RemodelLoopMover::repeat_tail_length_
private
RemodelGlobalFrame protocols::forge::remodel::RemodelLoopMover::RGF_
private

RemodelGlobalFrame for helical definitions.

Referenced by apply(), repeat_propagation(), and repeat_sync().

bool protocols::forge::remodel::RemodelLoopMover::seal_foldtree_
private

whether to (true) generate a sealed fold tree or (false) keep the cut fold tree (default=true)

Referenced by apply(), and set_seal_foldtree().

ScoreFunctionOP protocols::forge::remodel::RemodelLoopMover::sfx_
private

the score function to use

Referenced by apply(), and scorefunction().

core::Size protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles_
private

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

Referenced by set_param_from_options(), simultaneous_cycles(), and total_standard_cycles().

Real protocols::forge::remodel::RemodelLoopMover::temperature_
private
core::Size protocols::forge::remodel::RemodelLoopMover::unit_length_
private

use this for repeat construction in conjunction with symmetry

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

utility::vector1< moves::MoverOP > protocols::forge::remodel::RemodelLoopMover::user_provided_movers_
private

collection of movers that mess with the pose every n fragment/ccd steps during inneriterations of simultaneous, and independent stage, where n is determined by the variable below gives the user a chance to add their own flavor to the fragment sampling done by this protocol

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

core::Size protocols::forge::remodel::RemodelLoopMover::user_provided_movers_apply_cycle_
private

determines how often the above movers get called during fragment insertion/ccd steps (default 3 )

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


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