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Rosetta 3.5
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Rosetta 3.5
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Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points. More...
#include <IdealizeMover.hh>
Public Types | |
| typedef core::Real | Real |
| typedef core::pose::Pose | Pose |
 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 |
Public Member Functions | |
| IdealizeMover () | |
| virtual moves::MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| virtual 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... | |
| IdealizeMover & | atom_pair_constraint_weight (core::Real const setting) |
| IdealizeMover & | coordinate_constraint_weight (core::Real const setting) |
| IdealizeMover & | fast (bool const setting) |
| IdealizeMover & | chainbreaks (bool const setting) |
| IdealizeMover & | report_CA_rmsd (bool const setting) |
| void | apply (Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| void | set_pos_list (utility::vector1< Size > pos_list) |
| Sets the list of residue positions to idealize. More... | |
| 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... | |
| utility::vector1< core::Size > | ignore_residues_in_csts () const |
| void | ignore_residues_in_csts (utility::vector1< core::Size > const i) |
| void | impose_constraints (bool const i) |
| bool | impose_constraints () const |
| bool | constraints_only () const |
| void | constraints_only (bool const c) |
| 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 | setup_idealize_constraints (Pose &pose) |
| Add the idealize constraints to the pose's constraint set. More... | |
Additional Inherited Members | |
| 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... | |
Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points.
Definition at line 35 of file IdealizeMover.hh.
Definition at line 39 of file IdealizeMover.hh.
Definition at line 38 of file IdealizeMover.hh.
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Definition at line 42 of file IdealizeMover.hh.
References ignore_residues_in_csts_.
Referenced by clone(), and fresh_instance().
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Implements protocols::moves::Mover.
Definition at line 190 of file IdealizeMover.cc.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::all_atom_rmsd(), core::pose::Pose::append_residue_by_jump(), core::scoring::atom_pair_constraint, protocols::idealize::basic_idealize(), core::scoring::CA_rmsd(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dst, core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueTypeSet::name_map(), core::scoring::pro_close, core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and protocols::idealize::TR().
Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::abinitio::AbrelaxApplication::fold(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), and protocols::jobdist::universal_main().
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Definition at line 65 of file IdealizeMover.hh.
References atom_pair_constraint_weight_.
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Definition at line 87 of file IdealizeMover.hh.
References chainbreaks_.
Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply().
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clone has to be overridden only if clone invocation is expected.
Reimplemented from protocols::moves::Mover.
Definition at line 56 of file IdealizeMover.hh.
References IdealizeMover().
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Definition at line 114 of file IdealizeMover.hh.
References constraints_only_.
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Definition at line 115 of file IdealizeMover.hh.
References core::pack::dunbrack::c, and constraints_only_.
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Definition at line 73 of file IdealizeMover.hh.
References coordinate_constraint_weight_.
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Definition at line 80 of file IdealizeMover.hh.
References fast_.
Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::rna::create_rna_vall_torsions(), protocols::abinitio::AbrelaxApplication::fold(), protocols::antibody2::GraftOneCDRLoop::init(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), and protocols::jobdist::universal_main().
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inlinevirtual |
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 60 of file IdealizeMover.hh.
References IdealizeMover().
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virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 301 of file IdealizeMover.cc.
| utility::vector1< core::Size > protocols::idealize::IdealizeMover::ignore_residues_in_csts | ( | ) | const |
Definition at line 326 of file IdealizeMover.cc.
| void protocols::idealize::IdealizeMover::ignore_residues_in_csts | ( | utility::vector1< core::Size > const | i) |
Definition at line 321 of file IdealizeMover.cc.
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Definition at line 112 of file IdealizeMover.hh.
References impose_constraints_.
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Definition at line 113 of file IdealizeMover.hh.
References impose_constraints_.
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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 306 of file IdealizeMover.cc.
References core::pose::get_resnum_list(), and protocols::idealize::TR().
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Definition at line 93 of file IdealizeMover.hh.
References report_CA_rmsd_.
Referenced by protocols::match::downstream::LigandConformerBuilder::initialize_conformers().
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Sets the list of residue positions to idealize.
Definition at line 105 of file IdealizeMover.hh.
References pos_list_.
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Add the idealize constraints to the pose's constraint set.
Definition at line 102 of file IdealizeMover.cc.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::add_constraint(), core::pose::Pose::conformation(), core::sequence::end, core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and protocols::idealize::TR().
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Definition at line 126 of file IdealizeMover.hh.
Referenced by atom_pair_constraint_weight().
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Definition at line 130 of file IdealizeMover.hh.
Referenced by chainbreaks().
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Definition at line 133 of file IdealizeMover.hh.
Referenced by constraints_only().
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Definition at line 127 of file IdealizeMover.hh.
Referenced by coordinate_constraint_weight().
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Definition at line 129 of file IdealizeMover.hh.
Referenced by fast().
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Definition at line 128 of file IdealizeMover.hh.
Referenced by IdealizeMover().
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Definition at line 132 of file IdealizeMover.hh.
Referenced by impose_constraints().
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Definition at line 124 of file IdealizeMover.hh.
Referenced by set_pos_list().
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Definition at line 131 of file IdealizeMover.hh.
Referenced by report_CA_rmsd().
1.8.4