Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++. More...
#include <RemodelLoopMover.hh>
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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
| static void | register_options () |
| @registere 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 | |
| RemodelLoopMover & | operator= (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::Size > | generate_residues_to_sample (bool chooseSubsetResidues, Pose &pose, core::Size fragmentSize) |
| @setup allowed positions per stage More... | |
Private Attributes | |
| ScoreFunctionOP | sfx_ |
| the score function to use More... | |
| protocols::forge::remodel::RemodelData | remodel_data_ |
| @remodelData, 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::MoverOP > | user_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
◆ ClassicFragmentMoverOP
| typedef protocols::simple_moves::ClassicFragmentMoverOP protocols::forge::remodel::RemodelLoopMover::ClassicFragmentMoverOP |
◆ DataMap
◆ FragmentMoverOP
| typedef protocols::simple_moves::FragmentMoverOP protocols::forge::remodel::RemodelLoopMover::FragmentMoverOP |
◆ FragmentMoverOPs
| typedef utility::vector1< FragmentMoverOP > protocols::forge::remodel::RemodelLoopMover::FragmentMoverOPs |
◆ FragSetCOP
◆ FragSetOP
◆ FragSetOPs
| typedef utility::vector1< FragSetOP > protocols::forge::remodel::RemodelLoopMover::FragSetOPs |
◆ Loop
◆ Loops
◆ MonteCarlo
◆ MoveMap
◆ MoverOP
◆ Pose
◆ PoseOP
◆ Real
◆ ScoreFunction
◆ ScoreFunctionOP
◆ Size
◆ String
| typedef std::string protocols::forge::remodel::RemodelLoopMover::String |
◆ Super
◆ TagCOP
| typedef utility::tag::TagCOP protocols::forge::remodel::RemodelLoopMover::TagCOP |
Constructor & Destructor Documentation
◆ RemodelLoopMover() [1/3]
| protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover | ( | ) |
default constructor
References set_param_from_options().
◆ RemodelLoopMover() [2/3]
| protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover | ( | loops::LoopsOP const | loops | ) |
loops constructor
References set_param_from_options().
◆ RemodelLoopMover() [3/3]
| protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover | ( | RemodelLoopMover const & | rval | ) |
copy constructor
◆ ~RemodelLoopMover()
|
overridedefault |
default destructor
Member Function Documentation
◆ abinitio_stage()
|
protected |
abinitioo stage: better control of fragments. No loop closure tried
abinitio_stage::Assumes no loops need to be closed.
References protocols::loops::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), protocols::moves::MonteCarlo::boltzmann(), core::pose::Pose::constraint_set(), create_fragment_movers_limit_size(), core::pose::symmetry::is_symmetric(), protocols::moves::MonteCarlo::lowest_score_pose(), core::pose::Pose::num_jump(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), 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(), core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), temperature_, core::pose::Pose::total_residue(), and protocols::forge::remodel::TR().
Referenced by apply().
◆ add_fragments()
| void protocols::forge::remodel::RemodelLoopMover::add_fragments | ( | FragSetCOP | fragset | ) |
add a fragment set
References fragsets_.
Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply().
◆ add_loop()
|
inline |
add a loop to model
References loops_.
◆ allowed_closure_attempts() [1/2]
|
inline |
the allowed number of overall closure attempts before apply() exits (default 3)
References allowed_closure_attempts_.
◆ allowed_closure_attempts() [2/2]
|
inline |
the allowed number of overall closure attempts before apply() exits
References allowed_closure_attempts_.
◆ apply()
|
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().
◆ boost_closure_cycles() [1/2]
|
inline |
the maximum number of possible lockdown closure cycles to perform (default 30)
References boost_closure_cycles_.
Referenced by apply(), and boost_closure_stage().
◆ boost_closure_cycles() [2/2]
|
inline |
the maximum number of possible lockdown closure cycles to perform
References boost_closure_cycles_.
◆ boost_closure_stage()
|
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::loops::add_cutpoint_variants(), protocols::forge::methods::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_, core::scoring::linear_chainbreak, protocols::forge::methods::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::loops::set_single_loop_fold_tree(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::show_state(), protocols::forge::remodel::TR(), and unit_length_.
Referenced by apply().
◆ check_closure_criteria()
|
protected |
check all loops for closure criteria
- Parameters
-
[in] pose The pose being checked. [in] show_in_tracer Output state of each loop to tracer?
- Returns
- true if all criteria pass, false otherwise
References core::scoring::linear_chainbreak, protocols::forge::methods::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().
◆ clear_fragments()
| void protocols::forge::remodel::RemodelLoopMover::clear_fragments | ( | ) |
clear all fragment sets
References fragsets_.
◆ clone()
|
overridevirtual |
clone this object
Reimplemented from protocols::moves::Mover.
◆ count_moveable_residues()
|
protected |
count number of residues with moveable backbone torsions in the given range [left, right]
References core::kinematics::MoveMap::get_bb(), and core::sequence::left.
Referenced by boost_closure_stage(), independent_stage(), randomize_stage(), and simultaneous_stage().
◆ create_fragment_movers() [1/2]
|
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] movemap Use this movemap when initializing fragment movers. [in] largest_frag_size Only 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().
◆ create_fragment_movers() [2/2]
|
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] movemap Use this movemap/s when initializing fragment movers. [out] frag_movers Append fragment movers to this list. [in] largest_frag_size Only use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets. [in] movemap Use this movemap when initializing fragment movers. [out] frag_movers Append fragment movers to this list. [in] largest_frag_size Only use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets.
References core::kinematics::MoveMap::clone(), and fragsets_.
◆ create_fragment_movers_limit_size()
|
protected |
same as create_fragment_movers except with set size
return fragment movers for the list of internally kept fragment sets
- Parameters
-
[in] movemap Use this movemap when initializing fragment movers. [in] limits size and position of fragments
References core::kinematics::MoveMap::clone(), and fragsets_.
Referenced by abinitio_stage().
◆ create_per_loop_fragment_movers()
|
protected |
create per-loop fragment movers: 1 fragment mover for each loop (uses movemaps to lock down non-loop residues)
- Parameters
-
[in] loops The loops to use. [in] largest_frag_size Only use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets.
References create_fragment_movers(), enforce_false_movemap(), loops(), and mark_loop_moveable().
Referenced by insert_random_smallestmer_per_loop(), and simultaneous_stage().
◆ determine_loops_to_model()
|
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, protocols::forge::methods::linear_chainbreak(), loops_, max_linear_chainbreak_, and core::scoring::rg.
Referenced by boost_closure_stage(), independent_stage(), and insert_random_smallestmer_per_loop().
◆ enforce_false_movemap()
|
protected |
enforce settings in the false movemap
References false_movemap_, and core::kinematics::MoveMap::import_false().
Referenced by boost_closure_stage(), create_per_loop_fragment_movers(), independent_stage(), loophash_stage(), randomize_stage(), set_segment_stage(), and simultaneous_stage().
◆ fa_relax_stage()
|
protected |
quick trip to FA to push parts of the molecular apart to a reasonable distance. I'm noticing an overcollapse in centroid
relax stage
References protocols::relax::FastRelax::apply(), core::chemical::CENTROID_t, core::scoring::ScoreFunctionFactory::create_score_function(), core::chemical::FULL_ATOM_t, core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), repeat_pose_, repeat_propagation(), core::pose::Pose::secstruct(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), core::scoring::TALARIS_2013, and protocols::forge::remodel::TR().
Referenced by apply().
◆ false_movemap() [1/2]
|
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_.
◆ false_movemap() [2/2]
|
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_.
◆ fresh_instance()
|
overridevirtual |
create this type of object
Reimplemented from protocols::moves::Mover.
◆ generate_ncs_csts()
|
protected |
@ brief sets up ncs constraints
References protocols::symmetry::SetupNCSMover::add_group(), core::pose::Pose::size(), and protocols::forge::remodel::TR().
◆ generate_residues_to_sample()
|
private |
@setup allowed positions per stage
References remodel_data_, core::pose::Pose::size(), and protocols::forge::remodel::RemodelData::ss.
Referenced by apply().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ independent_cycles() [1/2]
|
inline |
the number of independent closure cycles to perform (default 8)
References independent_cycles_.
Referenced by independent_stage().
◆ independent_cycles() [2/2]
|
inline |
the number of independent closure cycles to perform
References independent_cycles_.
◆ independent_stage()
|
protected |
independent stage: single loop movement prior to MC accept/reject
References protocols::loops::add_cutpoint_variants(), protocols::forge::methods::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_, core::scoring::linear_chainbreak, protocols::forge::methods::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::loops::set_single_loop_fold_tree(), protocols::forge::methods::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().
◆ insert_random_smallestmer_per_loop()
|
protected |
find the smallest fragment size and insert a single such smallmer into each loop; for breaking up trapped trajectories
- Parameters
-
[in,out] pose The pose to modify. [in] only_broken_loop If 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::loops::fold_tree_from_loops(), protocols::forge::methods::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().
◆ loophash_cycles() [1/2]
|
inline |
the number of loophash closure cycles to perform (default 8)
References loophash_cycles_.
Referenced by loophash_stage().
◆ loophash_cycles() [2/2]
|
inline |
the number of loophash closure cycles to perform
References loophash_cycles_.
◆ loophash_stage()
|
protected |
independent stage: single loop movement prior to MC accept/reject
References protocols::loops::add_cutpoint_variants(), protocols::forge::methods::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::LoopHashMap::get_peptide(), protocols::loophash::get_rt_over_leap_fast(), core::sequence::ABEGOManager::index2symbol(), core::chemical::ResidueType::is_ligand(), core::pose::symmetry::is_symmetric(), keep_input_foldtree_, core::scoring::linear_chainbreak, protocols::forge::methods::linear_chainbreak(), loophash_cycles(), loops_, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), core::pose::Pose::omega(), core::scoring::omega, core::pose::Pose::phi(), core::io::pose_from_pose(), core::pose::Pose::psi(), protocols::loophash::LoopHashMap::radial_lookup(), 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::loops::set_single_loop_fold_tree(), protocols::forge::methods::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() [1/2]
|
inline |
the loops to model
References loops_.
Referenced by create_per_loop_fragment_movers(), loops(), and mark_loops_moveable().
◆ loops() [2/2]
|
inline |
◆ mark_loop_moveable()
|
protected |
mark bb/chi torsion of a single loop moveable in movemap
- Parameters
-
[in] loops The loop to use. [out] movemap The movemap to modify. [in] allow_omega Allow 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().
◆ mark_loops_moveable()
|
protected |
mark bb/chi torsions of multiple loops moveable in a movemap
- Parameters
-
[in] loops The loops to use. [out] movemap The movemap to modify. [in] allow_omega Allow bb omega to move? (should be yes when doing either fragment insertion or scoring function has omega tether, otherwise should probably be no)
References loops(), and mark_loop_moveable().
Referenced by randomize_stage(), and simultaneous_stage().
◆ max_linear_chainbreak() [1/2]
|
inline |
if linear chainbreak is <= this value, loop is considered closed (default 0.07)
References max_linear_chainbreak_.
◆ max_linear_chainbreak() [2/2]
|
inline |
if linear chainbreak is <= this value, loop is considered closed
References max_linear_chainbreak_, and protocols::hybridization::val.
◆ operator=()
|
private |
copy assignment
- Remarks
- Mover base class prevents this from working properly...
◆ randomize_loops() [1/2]
|
inline |
randomize loops prior to running main protocol? (default true)
References randomize_loops_.
◆ randomize_loops() [2/2]
|
inline |
randomize loops prior to running main protocol?
References randomize_loops_.
◆ randomize_stage()
| void protocols::forge::remodel::RemodelLoopMover::randomize_stage | ( | Pose & | pose | ) |
randomize loops
References check_closure_criteria(), count_moveable_residues(), create_fragment_movers(), enforce_false_movemap(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_loops(), core::pose::symmetry::is_symmetric(), keep_input_foldtree_, loops_, mark_loops_moveable(), protocols::forge::remodel::TR(), and unit_length_.
Referenced by apply().
◆ register_options()
|
static |
@registere options
◆ remodelData()
| void protocols::forge::remodel::RemodelLoopMover::remodelData | ( | protocols::forge::remodel::RemodelData const | remodel_data | ) |
adds the remodel data to thei remodelLoopMover object
References remodel_data_.
◆ repeat_generation_with_additional_residue()
| 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 protocols::forge::components::VarLengthBuild::apply(), apply(), and protocols::forge::remodel::RemodelMover::centroid_build().
◆ repeat_propagation()
| void protocols::forge::remodel::RemodelLoopMover::repeat_propagation | ( | Pose & | pose, |
| Pose & | repeat_pose, | ||
| core::Size | repeat_number | ||
| ) |
References protocols::symmetry::SetupForSymmetryMover::apply(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::loops::Loop::cut(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::pose::symmetry::is_symmetric(), loops_, core::conformation::Conformation::num_chains(), core::pose::Pose::omega(), core::pose::Pose::pdb_info(), core::pose::Pose::phi(), core::pose::Pose::psi(), repeat_length_, repeat_pose_, core::pose::replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::residue_type(), protocols::forge::remodel::RemodelGlobalFrame::restore_original_cst(), RGF_, 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::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().
Referenced by abinitio_stage(), apply(), boost_closure_stage(), fa_relax_stage(), independent_stage(), insert_random_smallestmer_per_loop(), loophash_stage(), set_segment_stage(), simultaneous_stage(), and small_move_stage().
◆ repeat_sync()
| void protocols::forge::remodel::RemodelLoopMover::repeat_sync | ( | core::pose::Pose & | repeat_pose, |
| core::Size | repeat_number | ||
| ) |
References loops_, core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), repeat_length_, protocols::forge::remodel::RemodelGlobalFrame::restore_original_cst(), RGF_, 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::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::forge::remodel::TR().
Referenced by abinitio_stage(), boost_closure_stage(), independent_stage(), loophash_stage(), set_segment_stage(), simultaneous_stage(), and small_move_stage().
◆ scorefunction() [1/2]
| 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().
◆ scorefunction() [2/2]
| void protocols::forge::remodel::RemodelLoopMover::scorefunction | ( | ScoreFunction const & | sfx | ) |
the ScoreFunction to use during modeling
References core::scoring::ScoreFunction::clone(), and sfx_.
◆ set_ideal_helices()
|
private |
initializes pose with ideal helices.
sets helices to there ideal value before any sampling begins.
References protocols::simple_filters::dssp(), remodel_data_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), protocols::forge::remodel::RemodelData::ss, core::pose::Pose::total_residue(), and protocols::forge::remodel::TR().
Referenced by apply().
◆ set_keep_input_foldtree()
|
inline |
References keep_input_foldtree_.
◆ set_param_from_options()
| void protocols::forge::remodel::RemodelLoopMover::set_param_from_options | ( | ) |
set parameters from options
References allowed_closure_attempts_, boost_closure_cycles_, independent_cycles_, keep_input_foldtree_, loophash_cycles_, max_linear_chainbreak_, randomize_loops_, simultaneous_cycles_, and temperature_.
Referenced by RemodelLoopMover().
◆ set_repeat_tail_length()
|
inline |
References repeat_tail_length_.
Referenced by protocols::forge::components::VarLengthBuild::apply(), and protocols::forge::remodel::RemodelMover::centroid_build().
◆ set_seal_foldtree()
|
inline |
References seal_foldtree_.
◆ set_segment_stage()
|
protected |
independent stage: single loop movement prior to MC accept/reject
References protocols::loops::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), check_closure_criteria(), create_fragment_movers(), enforce_false_movemap(), core::pose::Pose::fold_tree(), core::pose::symmetry::is_symmetric(), keep_input_foldtree_, protocols::loophash::BackboneSegment::length(), core::scoring::linear_chainbreak, protocols::forge::methods::linear_chainbreak(), loops_, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), core::pose::Pose::omega(), core::scoring::omega, protocols::loophash::BackboneSegment::omega(), protocols::loophash::BackboneSegment::phi(), core::pose::Pose::phi(), protocols::loophash::BackboneSegment::psi(), core::pose::Pose::psi(), protocols::loops::remove_cutpoint_variants(), repeat_length_, repeat_pose_, repeat_propagation(), repeat_sync(), protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), 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::loops::set_single_loop_fold_tree(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::forge::remodel::TR(), and unit_length_.
Referenced by apply().
◆ set_starting_pdb()
|
private |
initializes pose with starting pose
copies phi,psi,omega from a starting pose.
References core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), and core::pose::Pose::size().
Referenced by apply().
◆ set_starting_sequence()
|
private |
initializes pose with starting sequence
References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::chemical::CENTROID_t, core::pose::replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::residue_type_set_for_pose(), and core::pose::Pose::size().
Referenced by apply().
◆ set_user_provided_movers()
| void protocols::forge::remodel::RemodelLoopMover::set_user_provided_movers | ( | utility::vector1< moves::MoverOP > const & | movers | ) |
References user_provided_movers_.
◆ simultaneous_cycles() [1/2]
|
inline |
the number of simultaneous closure cycles to perform (default 2)
References simultaneous_cycles_.
Referenced by independent_stage(), and simultaneous_stage().
◆ simultaneous_cycles() [2/2]
|
inline |
the number of simultaneous closure cycles to perform
References simultaneous_cycles_.
◆ simultaneous_stage()
|
protected |
simultaneous stage: multiple loop movement prior to MC accept/reject
References protocols::loops::add_cutpoint_variants(), protocols::forge::methods::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::loops::fold_tree_from_loops(), protocols::forge::methods::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().
◆ small_move_stage()
|
protected |
small_move stage: only small moves
small_move_stage::Assumes no loops need to be closed.
References protocols::loops::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), protocols::moves::MonteCarlo::boltzmann(), core::pose::Pose::constraint_set(), protocols::moves::MonteCarlo::lowest_score_pose(), core::pose::Pose::num_jump(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::loops::remove_cutpoint_variants(), repeat_pose_, repeat_propagation(), repeat_sync(), repeat_tail_length_, protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), 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(), core::pose::Pose::size(), temperature_, and protocols::forge::remodel::TR().
◆ temperature() [1/2]
|
inline |
temperature for mc ( default 2.0 )
References temperature_.
◆ temperature() [2/2]
|
inline |
temperature for mc
References temperature_.
◆ total_standard_cycles()
|
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().
◆ user_provided_movers_apply_cycle()
|
inline |
References user_provided_movers_apply_cycle_.
Member Data Documentation
◆ 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().
◆ 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().
◆ 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().
◆ fragsets_
|
private |
fragment sets to use
Referenced by add_fragments(), boost_closure_stage(), clear_fragments(), create_fragment_movers(), create_fragment_movers_limit_size(), and insert_random_smallestmer_per_loop().
◆ 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().
◆ keep_input_foldtree_
|
private |
whether to keep the FoldTree untouched, i.e. trust the user to supply a decent FoldTree
Referenced by boost_closure_stage(), independent_stage(), insert_random_smallestmer_per_loop(), loophash_stage(), randomize_stage(), set_keep_input_foldtree(), set_param_from_options(), set_segment_stage(), and simultaneous_stage().
◆ 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_
|
private |
list of loops to model
Referenced by add_loop(), apply(), check_closure_criteria(), determine_loops_to_model(), independent_stage(), insert_random_smallestmer_per_loop(), loophash_stage(), loops(), randomize_stage(), repeat_generation_with_additional_residue(), repeat_propagation(), repeat_sync(), set_segment_stage(), and simultaneous_stage().
◆ 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().
◆ randomize_loops_
|
private |
randomize loops prior to running main protocol? (default true)
Referenced by apply(), randomize_loops(), and set_param_from_options().
◆ remodel_data_
|
private |
@remodelData, used when constraints are defined through Remodel
Referenced by apply(), generate_residues_to_sample(), remodelData(), and set_ideal_helices().
◆ repeat_length_
|
private |
◆ repeat_pose_
|
private |
local copy of repeat pose
Referenced by abinitio_stage(), apply(), boost_closure_stage(), fa_relax_stage(), independent_stage(), insert_random_smallestmer_per_loop(), loophash_stage(), repeat_propagation(), set_segment_stage(), simultaneous_stage(), and small_move_stage().
◆ repeat_tail_length_
|
private |
◆ RGF_
|
private |
RemodelGlobalFrame for helical definitions.
Referenced by apply(), repeat_propagation(), and repeat_sync().
◆ 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().
◆ sfx_
|
private |
the score function to use
Referenced by apply(), and scorefunction().
◆ 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().
◆ temperature_
|
private |
temperature for mc
Referenced by abinitio_stage(), apply(), set_param_from_options(), small_move_stage(), and temperature().
◆ 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().
◆ 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().
◆ 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:
- src/protocols/forge/remodel/RemodelLoopMover.hh
- src/protocols/forge/remodel/RemodelLoopMover.cc
