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Rosetta 3.5
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Rosetta 3.5
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#include <BackboneSampler.hh>
Public Types | |
| typedef core::scoring::ScoreFunctionCOP | ScoreFunctionCOP |
| typedef core::scoring::ScoreFunctionOP | ScoreFunctionOP |
| typedef core::pose::Pose | Pose |
Public Member Functions | |
| BackboneSampler () | |
| BackboneSampler (ScoreFunctionCOP scorefxn, core::Size const bb_moves, core::Real const mc_kt) | |
| void | apply (Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| 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... | |
| virtual | ~BackboneSampler () |
 Public Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol | |
| LigandBaseProtocol () | |
| virtual | ~LigandBaseProtocol () |
| core::scoring::ScoreFunctionOP | get_scorefxn () |
| core::scoring::ScoreFunctionCOP | get_scorefxn () const |
| core::Size | get_ligand_jump_id (core::pose::Pose const &pose) const |
| core::Size | get_ligand_id (core::pose::Pose const &pose) const |
| Return the residue sequence number for our ligand. More... | |
| core::Size | get_ligand_id (core::pose::Pose const &pose, core::Size jump_id) const |
| Return the residue sequence number for our ligand. More... | |
| void | restrain_protein_Calphas (core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::constraints::FuncOP restr_func) const |
| void | reorder_foldtree_around_mobile_regions (core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const |
| reorders a fold tree such that movement in the mobile regions will More... | |
| void | get_non_bb_clashing_rotamers (core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const |
| 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 |
Protected Member Functions | |
| void | parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, Pose const &) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| Protected Member Functions inherited from protocols::ligand_docking::LigandBaseProtocol | |
| core::scoring::ScoreFunctionOP | make_tweaked_scorefxn (std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight) |
| core::Vector | choose_desired_centroid (core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >) |
| void | move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts) |
| void | move_ligand_to_desired_centroid (core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid) |
| core::kinematics::MoveMapOP | make_movemap (core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const |
| core::pack::task::PackerTaskOP | make_packer_task (core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const |
| Shared machinery for the next two. More... | |
| core::pack::task::PackerTaskOP | make_packer_task (core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const |
| Receptor (interface?) plus ligand. More... | |
| core::pack::task::PackerTaskOP | make_packer_task_ligand_only (core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const |
| Just ligand, not the receptor. More... | |
| void | find_interface_rsds (core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const |
| void | find_interface_backbone (core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const |
| core::scoring::constraints::ConstraintOP | restrain_ligand_nbr_atom (core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const |
| void | setup_bbmin_foldtree (core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms) |
| 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 Attributes | |
| core::Size | bb_moves_ |
| core::Real | mc_kt_ |
| core::scoring::ScoreFunctionOP | scorefxn_repack_ |
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 Attributes inherited from protocols::ligand_docking::LigandBaseProtocol | |
| bool | use_soft_rep_ |
| core::scoring::ScoreFunctionOP | scorefxn_ |
| core::scoring::ScoreFunctionOP | hard_scorefxn_ |
| core::scoring::ScoreFunctionOP | soft_scorefxn_ |
| core::Real | sc_interface_padding_ |
| core::Real | bb_interface_cutoff_ |
| core::pack::rotamer_set::UnboundRotamersOperationOP | unboundrot_ |
Definition at line 29 of file BackboneSampler.hh.
Definition at line 34 of file BackboneSampler.hh.
Definition at line 32 of file BackboneSampler.hh.
Definition at line 33 of file BackboneSampler.hh.
| protocols::enzdes::BackboneSampler::BackboneSampler | ( | ) |
Definition at line 84 of file BackboneSampler.cc.
| protocols::enzdes::BackboneSampler::BackboneSampler | ( | ScoreFunctionCOP | scorefxn, |
| core::Size const | bb_moves, | ||
| core::Real const | mc_kt | ||
| ) |
Definition at line 97 of file BackboneSampler.cc.
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virtual |
Definition at line 108 of file BackboneSampler.cc.
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virtual |
Reimplemented from protocols::ligand_docking::LigandBaseProtocol.
Definition at line 116 of file BackboneSampler.cc.
References protocols::loops::add_cutpoint_variants(), protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segments_to_set(), protocols::simple_moves::BBG8T3AMover::apply(), protocols::moves::MonteCarlo::boltzmann(), protocols::simple_moves::BBG8T3AMover::factorA(), protocols::simple_moves::BBG8T3AMover::factorB(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_protein(), protocols::moves::MonteCarlo::lowest_score_pose(), protocols::simple_moves::BBGaussianMover::movemap(), core::pose::Pose::n_residue(), protocols::loops::remove_cutpoint_variants(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::residue(), protocols::moves::MonteCarlo::show_counters(), protocols::enzdes::TR(), and protocols::moves::Mover::type().
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virtual |
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 111 of file BackboneSampler.cc.
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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 53 of file BackboneSampler.hh.
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virtual |
Each derived class must specify its name. The class name.
Reimplemented from protocols::ligand_docking::LigandBaseProtocol.
Definition at line 196 of file BackboneSampler.cc.
References protocols::enzdes::BackboneSamplerCreator::mover_name().
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protectedvirtual |
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 200 of file BackboneSampler.cc.
References protocols::moves::DataMap::get().
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private |
Definition at line 71 of file BackboneSampler.hh.
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private |
Definition at line 72 of file BackboneSampler.hh.
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private |
Definition at line 73 of file BackboneSampler.hh.
1.8.4