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Rosetta 3.5
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Rosetta 3.5
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#include <LoopRelaxMover.hh>
Public Member Functions | |
| LoopRelaxMover () | |
| LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::Loops const &loops) | |
| Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More... | |
| LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::LoopsFileData const &loops_from_file) | |
| Unresolved-loop-index constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More... | |
| LoopRelaxMover (std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, loops::GuardedLoopsFromFileOP guarded_loops) | |
| GuardedLoopsOP constructor. This constructor copies the pointer to a GuardedLoops object; Loop indices must be resolved by the time that the guarded_loops_ object is accessed, but, they need not have been resolved at the time of this object's construction. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED. More... | |
| LoopRelaxMover (LoopRelaxMover const &src) | |
| Copy-ctor; Shallow copy of all data. More... | |
| LoopRelaxMover const & | operator= (LoopRelaxMover const &rhs) |
| assignment operator; Shallow copy of all data. More... | |
| virtual | ~LoopRelaxMover () |
| virtual void | apply (core::pose::Pose &pose) |
| Apply the loop-relax protocol to a Pose. At the call to this function, the loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used. More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| void | scorefxns (core::scoring::ScoreFunctionOP cen_scorefxn, core::scoring::ScoreFunctionOP fa_scorefxn) |
| void | fa_scorefxn (core::scoring::ScoreFunctionOP fa_scorefxn) |
| void | cen_scorefxn (core::scoring::ScoreFunctionOP cen_scorefxn) |
| void | cmd_line_csts (bool setting) |
| void | copy_sidechains (bool setting) |
| void | rebuild_filter (core::Real setting) |
| void | n_rebuild_tries (core::Size setting) |
| void | remodel (std::string val) |
| void | intermedrelax (std::string val) |
| void | refine (std::string val) |
| void | relax (std::string val) |
| void | resolve_loopfile_indices (core::pose::Pose const &pose) |
| Must be called before the Loops data can be read from. More... | |
| void | loops (protocols::loops::LoopsOP const val) |
| set the Loops object (with resolved indices) directly. This would override the unresolved-indices held in the LoopsFileData if that data were set in the constructor More... | |
| void | loops_file_data (loops::LoopsFileData const &loopfiledata) |
| Set the loop file data. This will require that a Pose be presented to the LoopRelax object before get_loops() can be called. More... | |
| void | frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs) |
| bool | cmd_line_csts () const |
| bool | copy_sidechains () const |
| core::Size | n_rebuild_tries () const |
| core::Real | rebuild_filter () const |
| protocols::loops::LoopsOP | get_loops () |
| Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply. More... | |
| protocols::loops::LoopsCOP | get_loops () const |
| Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply. More... | |
| std::string | remodel () const |
| std::string | relax () const |
| std::string | intermedrelax () const |
| std::string | refine () const |
| utility::vector1 < core::fragment::FragSetOP > | frag_libs () const |
| protocols::moves::MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| protocols::moves::MoverOP | fresh_instance () const |
| this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More... | |
| void | compute_rmsd (bool const c) |
| bool | compute_rmsd () const |
| void | parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual | ~Mover () |
| virtual MoverSP | create () |
| virtual void | apply (core::io::serialization::PipeMap &pmap) |
| virtual void | parse_state (SerializableState const &state) |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
| virtual void | save_state (SerializableState &state) |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| Mover (Mover const &other) | |
| Mover & | operator= (Mover const &other) |
| assignment operator More... | |
| virtual core::Real | last_proposal_density_ratio () |
| std::string const & | type () const |
| 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... | |
| void | set_current_tag (std::string const &new_tag) |
| 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 | 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... | |
| void | type (const std::string &type_in) |
| std::string | get_type () const |
| 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... | |
| 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 bool | reinitialize_for_each_job () const |
| this function informs 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 |
| this function informs 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... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Private Member Functions | |
| void | set_defaults_ () |
Private Attributes | |
| bool | cmd_line_csts_ |
| bool | copy_sidechains_ |
| core::Size | n_rebuild_tries_ |
| core::Real | rebuild_filter_ |
| std::string | remodel_ |
| std::string | intermedrelax_ |
| std::string | refine_ |
| std::string | relax_ |
| loops::GuardedLoopsFromFileOP | guarded_loops_ |
| core::scoring::ScoreFunctionOP | cen_scorefxn_ |
| core::scoring::ScoreFunctionOP | fa_scorefxn_ |
| utility::vector1 < core::fragment::FragSetOP > | frag_libs_ |
| bool | compute_rmsd_ |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagPtr | TagPtr |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
| 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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... | |
Definition at line 39 of file LoopRelaxMover.hh.
| protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover | ( | ) |
Definition at line 139 of file LoopRelaxMover.cc.
References set_defaults_().
Referenced by clone(), protocols::comparative_modeling::LoopRelaxMoverCreator::create_mover(), and fresh_instance().
| protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover | ( | std::string const & | remodel, |
| std::string const & | intermedrelax, | ||
| std::string const & | refine, | ||
| std::string const & | relax, | ||
| loops::Loops const & | loops | ||
| ) |
Alternative constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.
Definition at line 148 of file LoopRelaxMover.cc.
| protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover | ( | std::string const & | remodel, |
| std::string const & | intermedrelax, | ||
| std::string const & | refine, | ||
| std::string const & | relax, | ||
| loops::LoopsFileData const & | loops_from_file | ||
| ) |
Unresolved-loop-index constructor. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.
Definition at line 169 of file LoopRelaxMover.cc.
| protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover | ( | std::string const & | remodel, |
| std::string const & | intermedrelax, | ||
| std::string const & | refine, | ||
| std::string const & | relax, | ||
| loops::GuardedLoopsFromFileOP | guarded_loops | ||
| ) |
GuardedLoopsOP constructor. This constructor copies the pointer to a GuardedLoops object; Loop indices must be resolved by the time that the guarded_loops_ object is accessed, but, they need not have been resolved at the time of this object's construction. BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS(). AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL NOT BE INITIALIZED.
Definition at line 187 of file LoopRelaxMover.cc.
| protocols::comparative_modeling::LoopRelaxMover::LoopRelaxMover | ( | LoopRelaxMover const & | src) |
Copy-ctor; Shallow copy of all data.
Copy-ctor; shallow copy of all data object.
Definition at line 206 of file LoopRelaxMover.cc.
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Definition at line 246 of file LoopRelaxMover.cc.
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Apply the loop-relax protocol to a Pose. At the call to this function, the loop indices originating from the loop file (which may list indices with PDB identifiers i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object in the LoopRelaxMover cannot be used.
Implements protocols::moves::Mover.
Definition at line 281 of file LoopRelaxMover.cc.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::evaluation::EvaluatorFactory::add_all_evaluators(), protocols::viewer::add_conformation_viewer(), core::pose::Pose::add_constraint(), core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), protocols::loops::add_cutpoint_variants(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), protocols::loops::loop_mover::LoopMover::add_fragments(), core::scoring::angle_constraint, core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_jump(), protocols::relax::MiniRelax::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::LoopRebuild::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::idealize::IdealizeMover::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::relax::FastRelax::apply(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::scoring::big_bin_constraint, core::id::BOGUS_ATOM_ID, core::scoring::CA_rmsd(), cen_scorefxn_, core::pose::Pose::center(), core::chemical::CENTROID, core::scoring::chainbreak, protocols::checkpoint::CheckPointer::checkpoint(), cmd_line_csts(), compute_rmsd(), core::pose::Pose::conformation(), core::scoring::constant_constraint, core::scoring::coordinate_constraint, copy_sidechains(), core::conformation::ResidueFactory::create_residue(), core::pack::interaction_graph::debug, protocols::checkpoint::CheckPointer::debug(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::scoring::dihedral_constraint, core::chemical::DISULFIDE, core::io::raw_data::DisulfideFile::disulfides(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), fa_scorefxn_, core::chemical::FA_STANDARD, protocols::moves::FAIL_RETRY, protocols::idealize::IdealizeMover::fast(), core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), frag_libs(), protocols::relax::generate_relax_from_cmd(), protocols::loops::loop_mover::LoopMover::get_checkpoints(), protocols::moves::Mover::get_current_tag(), protocols::loops::LoopMoverFactory::get_instance(), protocols::evaluation::EvaluatorFactory::get_instance(), get_loops(), guarded_loops_, core::chemical::ResidueType::has(), core::conformation::Residue::has_variant_type(), core::pose::initialize_atomid_map(), intermedrelax(), core::pose::Pose::is_fullatom(), protocols::loops::Loops::is_loop_residue(), core::conformation::Residue::is_polymer(), core::chemical::ResidueType::is_protein(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, protocols::loops::loop_rmsd(), loops(), core::pose::symmetry::make_residue_mask_symmetric(), core::pose::symmetry::make_symmetric_movemap(), protocols::moves::MS_SUCCESS, n_rebuild_tries(), core::chemical::ResidueTypeSet::name_map(), core::scoring::native_CA_rmsd(), protocols::loops::native_loop_core_CA_rmsd(), core::conformation::Residue::natoms(), core::scoring::overlap_chainbreak, core::scoring::pair, protocols::comparative_modeling::pick_loops_chainbreak(), core::import_pose::pose_from_pdb(), core::pack::task::TaskFactory::push_back(), rebuild_filter(), protocols::checkpoint::CheckPointer::recover_checkpoint(), refine(), relax(), remodel(), protocols::loops::remove_cutpoint_variants(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::residue_type_set(), core::kinematics::FoldTree::root(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), protocols::loops::loop_mover::IndependentLoopMover::set_accept_aborted_loops_(), protocols::loops::loop_mover::IndependentLoopMover::set_build_all_loops_(), protocols::loops::loop_mover::IndependentLoopMover::set_build_attempts_(), protocols::moves::Mover::set_current_tag(), protocols::loops::loop_mover::IndependentLoopMover::set_grow_attempts_(), protocols::moves::Mover::set_last_move_status(), protocols::loops::loop_mover::IndependentLoopMover::set_loop_combine_rate_(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::IndependentLoopMover::set_random_order_(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), core::pose::set_ss_from_phipsi(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), core::pose::Pose::set_xyz(), core::pose::setPoseExtraScores(), core::io::serialization::size(), core::scoring::superimpose_pose(), core::util::switch_to_residue_type_set(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), protocols::TR(), and core::conformation::Atom::xyz().
Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().
| void protocols::comparative_modeling::LoopRelaxMover::cen_scorefxn | ( | core::scoring::ScoreFunctionOP | cen_scorefxn) |
Definition at line 275 of file LoopRelaxMover.cc.
References cen_scorefxn_.
Referenced by parse_my_tag(), and scorefxns().
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clone has to be overridden only if clone invocation is expected.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
Definition at line 1331 of file LoopRelaxMover.cc.
References LoopRelaxMover().
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Definition at line 107 of file LoopRelaxMover.hh.
References cmd_line_csts_.
Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply().
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Definition at line 152 of file LoopRelaxMover.hh.
References cmd_line_csts_.
Referenced by apply(), and parse_my_tag().
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Definition at line 196 of file LoopRelaxMover.hh.
References core::pack::dunbrack::c, and compute_rmsd_.
Referenced by protocols::loop_build::LoopBuildMover::apply().
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Definition at line 197 of file LoopRelaxMover.hh.
References compute_rmsd_.
Referenced by apply(), parse_my_tag(), and set_defaults_().
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Definition at line 111 of file LoopRelaxMover.hh.
References copy_sidechains_.
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Definition at line 156 of file LoopRelaxMover.hh.
References copy_sidechains_.
Referenced by apply(), and parse_my_tag().
| void protocols::comparative_modeling::LoopRelaxMover::fa_scorefxn | ( | core::scoring::ScoreFunctionOP | fa_scorefxn) |
Definition at line 269 of file LoopRelaxMover.cc.
References fa_scorefxn_.
Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), parse_my_tag(), and scorefxns().
| void protocols::comparative_modeling::LoopRelaxMover::frag_libs | ( | utility::vector1< core::fragment::FragSetOP > | new_libs) |
Definition at line 248 of file LoopRelaxMover.cc.
References frag_libs_.
Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and protocols::loop_build::LoopBuild_main().
| utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::LoopRelaxMover::frag_libs | ( | ) | const |
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this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
Definition at line 1328 of file LoopRelaxMover.cc.
References LoopRelaxMover().
| protocols::loops::LoopsOP protocols::comparative_modeling::LoopRelaxMover::get_loops | ( | ) |
Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply.
Definition at line 1252 of file LoopRelaxMover.cc.
References guarded_loops_.
Referenced by apply().
| protocols::loops::LoopsCOP protocols::comparative_modeling::LoopRelaxMover::get_loops | ( | ) | const |
Loops accessor. May only be retrieved after the loop indices have been resolved in a call to apply.
Definition at line 1247 of file LoopRelaxMover.cc.
References guarded_loops_.
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 1258 of file LoopRelaxMover.cc.
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Definition at line 127 of file LoopRelaxMover.hh.
References intermedrelax_.
Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().
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Definition at line 184 of file LoopRelaxMover.hh.
References intermedrelax_.
Referenced by apply(), and parse_my_tag().
| void protocols::comparative_modeling::LoopRelaxMover::loops | ( | protocols::loops::LoopsOP const | val) |
set the Loops object (with resolved indices) directly. This would override the unresolved-indices held in the LoopsFileData if that data were set in the constructor
By setting the loops object directly, the requirement is relaxed that a Pose be first given to the LoopRelax object (through a call to apply() or resolve_loopfile_indices) before the get_loops() function may be called.
Definition at line 1237 of file LoopRelaxMover.cc.
References guarded_loops_.
Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), apply(), and parse_my_tag().
| void protocols::comparative_modeling::LoopRelaxMover::loops_file_data | ( | loops::LoopsFileData const & | loopfiledata) |
Set the loop file data. This will require that a Pose be presented to the LoopRelax object before get_loops() can be called.
Set the loop file data. This will require that.
Definition at line 1242 of file LoopRelaxMover.cc.
References guarded_loops_.
Referenced by protocols::loop_build::LoopBuildMover::setup_loop_definition().
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Definition at line 119 of file LoopRelaxMover.hh.
References n_rebuild_tries_.
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Definition at line 160 of file LoopRelaxMover.hh.
References n_rebuild_tries_.
Referenced by apply(), and parse_my_tag().
| LoopRelaxMover const & protocols::comparative_modeling::LoopRelaxMover::operator= | ( | LoopRelaxMover const & | rhs) |
assignment operator; Shallow copy of all data.
Definition at line 224 of file LoopRelaxMover.cc.
References cen_scorefxn_, cmd_line_csts_, compute_rmsd_, copy_sidechains_, fa_scorefxn_, frag_libs_, guarded_loops_, intermedrelax_, n_rebuild_tries_, rebuild_filter_, refine_, relax_, and remodel_.
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Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.
Reimplemented from protocols::moves::Mover.
Definition at line 1287 of file LoopRelaxMover.cc.
References cen_scorefxn(), cen_scorefxn_, cmd_line_csts(), compute_rmsd(), copy_sidechains(), fa_scorefxn(), frag_libs_, intermedrelax(), protocols::loops::loops_definers::load_loop_definitions(), loops(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), n_rebuild_tries(), protocols::rosetta_scripts::parse_score_function(), protocols::loops::read_loop_fragments(), rebuild_filter(), refine(), relax(), and remodel().
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Definition at line 115 of file LoopRelaxMover.hh.
References rebuild_filter_.
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Definition at line 164 of file LoopRelaxMover.hh.
References rebuild_filter_.
Referenced by apply(), and parse_my_tag().
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Definition at line 131 of file LoopRelaxMover.hh.
References refine_.
Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().
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Definition at line 188 of file LoopRelaxMover.hh.
References refine_.
Referenced by apply(), and parse_my_tag().
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Definition at line 135 of file LoopRelaxMover.hh.
References relax_.
Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().
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Definition at line 180 of file LoopRelaxMover.hh.
References relax_.
Referenced by apply(), and parse_my_tag().
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Definition at line 123 of file LoopRelaxMover.hh.
References remodel_.
Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), and protocols::medal::MedalMover::do_loop_closure().
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Definition at line 176 of file LoopRelaxMover.hh.
References remodel_.
Referenced by apply(), and parse_my_tag().
| void protocols::comparative_modeling::LoopRelaxMover::resolve_loopfile_indices | ( | core::pose::Pose const & | pose) |
Must be called before the Loops data can be read from.
Definition at line 1229 of file LoopRelaxMover.cc.
References guarded_loops_.
| void protocols::comparative_modeling::LoopRelaxMover::scorefxns | ( | core::scoring::ScoreFunctionOP | cen_scorefxn, |
| core::scoring::ScoreFunctionOP | fa_scorefxn | ||
| ) |
Definition at line 259 of file LoopRelaxMover.cc.
References cen_scorefxn(), and fa_scorefxn().
Referenced by protocols::loop_build::LoopBuildMover::apply(), and protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply().
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Definition at line 1262 of file LoopRelaxMover.cc.
References cen_scorefxn_, cmd_line_csts_, compute_rmsd(), copy_sidechains_, fa_scorefxn_, protocols::loops::get_cen_scorefxn(), protocols::loops::get_fa_scorefxn(), intermedrelax_, protocols::loops::loop_mover::loops_set_chainbreak_weight(), n_rebuild_tries_, rebuild_filter_, refine_, relax_, and remodel_.
Referenced by LoopRelaxMover().
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Definition at line 226 of file LoopRelaxMover.hh.
Referenced by apply(), cen_scorefxn(), operator=(), parse_my_tag(), and set_defaults_().
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Definition at line 213 of file LoopRelaxMover.hh.
Referenced by cmd_line_csts(), operator=(), and set_defaults_().
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Definition at line 230 of file LoopRelaxMover.hh.
Referenced by compute_rmsd(), and operator=().
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Definition at line 214 of file LoopRelaxMover.hh.
Referenced by copy_sidechains(), operator=(), and set_defaults_().
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Definition at line 227 of file LoopRelaxMover.hh.
Referenced by apply(), fa_scorefxn(), operator=(), and set_defaults_().
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Definition at line 229 of file LoopRelaxMover.hh.
Referenced by frag_libs(), operator=(), and parse_my_tag().
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Definition at line 224 of file LoopRelaxMover.hh.
Referenced by apply(), get_loops(), loops(), loops_file_data(), operator=(), and resolve_loopfile_indices().
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Definition at line 220 of file LoopRelaxMover.hh.
Referenced by intermedrelax(), operator=(), and set_defaults_().
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Definition at line 216 of file LoopRelaxMover.hh.
Referenced by n_rebuild_tries(), operator=(), and set_defaults_().
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Definition at line 217 of file LoopRelaxMover.hh.
Referenced by operator=(), rebuild_filter(), and set_defaults_().
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Definition at line 221 of file LoopRelaxMover.hh.
Referenced by operator=(), refine(), and set_defaults_().
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Definition at line 222 of file LoopRelaxMover.hh.
Referenced by operator=(), relax(), and set_defaults_().
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Definition at line 219 of file LoopRelaxMover.hh.
Referenced by operator=(), remodel(), and set_defaults_().
1.8.4