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| | MapHotspot () |
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| void | apply (core::pose::Pose &pose) override |
| | Main Method. More...
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| void | GenerateMap (core::pose::Pose const &start_pose, core::pose::Pose &curr_pose, core::Size const jump_number) |
| | this is the recursive function where the functionality takes place More...
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| void | MinimizeHotspots (core::pose::Pose &pose) |
| | minimizes rb and sc dofs for all of the hotspots More...
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| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override |
| | Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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| protocols::moves::MoverOP | clone () const override |
| | Return a clone of the Mover object. More...
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| protocols::moves::MoverOP | fresh_instance () const override |
| | Generates a new Mover object freshly created with the default ctor. More...
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| void | output_pose (core::pose::Pose const &pose) const |
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| RotamerSetOP | create_rotamer_set (core::pose::Pose const &, core::Size const hotspot_resnum, core::Size const explosion) const |
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| | ~MapHotspot () override |
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| std::string | get_name () const override |
| | Each derived class must specify its name. The class name. More...
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| | Mover () |
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| virtual MoverOP | create () |
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| MoverCOP | get_self_ptr () const |
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| MoverOP | get_self_ptr () |
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| MoverCAP | get_self_weak_ptr () const |
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| MoverAP | get_self_weak_ptr () |
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| | Mover (std::string const &type_name) |
| | sets the type for a mover; name_ has been removed (2010/05/14) More...
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| 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...
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| 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...
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| 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...
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| MoverStatus | get_last_move_status () const |
| | end parser interface, start Job Distributor interface///////////// More...
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| 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...
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| virtual core::pose::PoseOP | get_additional_output () |
| | Mechanism by which a mover may return multiple output poses from a single input pose. More...
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| void | set_type (std::string const &setting) |
| | Set the 'type' string. More...
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| std::string | get_type () const |
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| void | type (const std::string &type_in) |
| | Set the 'type' string. More...
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| std::string const & | type () const |
| | Get the set 'type' string. More...
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| virtual void | set_input_pose (PoseCOP pose) |
| | setter for poses contained for rms More...
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| 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...
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| PoseCOP | get_input_pose () const |
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| PoseCOP | get_native_pose () const |
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| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
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| jobdist::BasicJobCOP | get_current_job () const |
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| virtual void | set_current_tag (std::string const &new_tag) |
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| 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...
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| virtual void | show (std::ostream &output=std::cout) const |
| | Outputs details about the Mover, including current settings. More...
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| virtual core::Real | last_proposal_density_ratio () |
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| 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...
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| virtual Strings & | info () |
| | non-const accessor More...
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| virtual Strings const & | info () const |
| | const accessor More...
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| 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...
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Generates a new Mover object freshly created with the default ctor.
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.
this is the recursive function where the functionality takes place
A function that recursively goes over all jumps. Within each function, the residue-identities related to that jump are cycled, and for each of those, it iterates over the rotamer set. for each residue type, the best-energy (scorefxn) rotamer, that fulfills all of the user-defined filters is chosen and then we move deeper into the recursion with the next jump. Stopping condition is the final iteration over the final jump at which point a decoy is output, or if no rotamer for the particular residue identity meets all filters (exit with no decoy generation).
References core::chemical::aa_from_oneletter_code(), allowed_aas_per_jump_, core::conformation::Conformation::chain_begin(), protocols::score_filters::ScoreTypeFilter::compute(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), create_rotamer_set(), explosion_, core::pose::get_restype_for_pose(), core::scoring::get_score_function(), jump_filters_, jump_movers_, MinimizeHotspots(), core::chemical::ResidueTypeBase::mode(), core::chemical::name_from_aa(), core::pose::Pose::num_jump(), output_pose(), core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), rot(), core::scoring::total_score, and protocols::protein_interface_design::movers::TR().
Referenced by apply().
| void protocols::protein_interface_design::movers::MapHotspot::parse_my_tag |
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utility::tag::TagCOP |
tag, |
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basic::datacache::DataMap & |
data |
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) |
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overridevirtual |
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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References allowed_aas_per_jump_, clash_check_, explosion_, file_name_prefix_, core::scoring::get_score_function_name(), jump_filters_, jump_movers_, minimization_scorefxns_, mover_name(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), and protocols::protein_interface_design::movers::TR().
Public Types inherited from protocols::moves::Mover