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Rosetta
3.8
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#include <PlaceOnLoop.hh>
Public Member Functions | |
PlaceOnLoop () | |
void | apply (Pose &pose) override |
protocols::moves::MoverOP | clone () const override |
Return a clone of the Mover object. More... | |
protocols::moves::MoverOP | fresh_instance () const override |
Generates a new Mover object freshly created with the default ctor. More... | |
void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
void | set_kinematic_defaults () |
bool | minimize_toward_stub (core::pose::Pose &pose) const |
void | add_bb_csts_to_loop (core::pose::Pose &pose) const |
bool | position_stub (core::pose::Pose &pose) const |
void | ala_pose_loop (core::pose::Pose &pose) const |
bool | loop_length (core::pose::Pose &pose) |
virtual | ~PlaceOnLoop () |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
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DesignRepackMover () | |
DesignRepackMover (std::string const &name) | |
void | setup_packer_and_movemap (core::pose::Pose const &pose) |
void | parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
void | min_rb (utility::vector1< bool > const &min_rb) |
void | min_rb (bool const min_rb) |
in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More... | |
utility::vector1< bool > const & | min_rb () const |
bool | min_rb_set () const |
void | min_sc (utility::vector1< bool > const &min_sc) |
utility::vector1< bool > const & | min_sc () const |
bool | min_sc_set () const |
void | min_bb (utility::vector1< bool > const &min_bb) |
utility::vector1< bool > const & | min_bb () const |
bool | min_bb_set () const |
bool | optimize_foldtree () const |
void | optimize_foldtree (bool const opt) |
void | apply (core::pose::Pose &) override |
a dummy apply so that instantiation of this baseclass would be possible. More... | |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
void | prevent_repacking (utility::vector1< core::Size > const &p) |
utility::vector1< core::Size > const & | prevent_repacking () const |
void | restrict_to_repacking (utility::vector1< core::Size > const &p) |
utility::vector1< core::Size > const & | restrict_to_repacking () const |
void | design (bool const des) |
bool | design () const |
void | set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn) |
void | set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn) |
core::scoring::ScoreFunctionOP | scorefxn_repack () const |
core::scoring::ScoreFunctionOP | scorefxn_minimize () const |
core::pack::task::PackerTaskCOP | task () const |
core::pack::task::PackerTaskOP & | task () |
void | clear_task () |
after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More... | |
void | clear_task_factory () |
void | use_preset_task (bool const bt) |
bool | use_preset_task () const |
void | task_factory (core::pack::task::TaskFactoryOP p) |
core::pack::task::TaskFactoryOP & | task_factory () |
core::pack::task::TaskFactoryOP | task_factory () const |
~DesignRepackMover () override | |
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Mover () | |
~Mover () override | |
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 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 |
void | set_type (std::string const &setting) |
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 | 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 |
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... | |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
virtual void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. More... | |
Static Public Member Functions | |
static std::string | mover_name () |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
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static utility::tag::XMLSchemaComplexTypeGeneratorOP | get_xsd_complex_type () |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
protocols::protein_interface_design::movers::PlaceOnLoop::PlaceOnLoop | ( | ) |
References delta_length_, kinematic_mover_, and set_kinematic_defaults().
Referenced by clone().
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void protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop | ( | core::pose::Pose & | pose | ) | const |
bb_csts only affect loop. Transforms loop to poly-ala
References core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::aa_pro, core::conformation::Residue::atom_index(), core::pack::task::TaskFactory::create_packer_task(), curr_loop_end_, host_chain_, core::pose::Pose::residue(), core::pose::Pose::size(), and stub_set_.
Referenced by loop_length().
void protocols::protein_interface_design::movers::PlaceOnLoop::ala_pose_loop | ( | core::pose::Pose & | pose | ) | const |
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overridevirtual |
Implements protocols::moves::Mover.
References protocols::moves::FAIL_RETRY, loop_length(), protocols::moves::MS_SUCCESS, and protocols::moves::Mover::set_last_move_status().
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overridevirtual |
Return a clone of the Mover object.
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.
References PlaceOnLoop().
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overridevirtual |
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.
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
bool protocols::protein_interface_design::movers::PlaceOnLoop::loop_length | ( | core::pose::Pose & | pose | ) |
Chooses one user-defined loop length at random, changes the loop accordingly, and tries to close the loop with that change.
References core::chemical::aa_from_oneletter_code(), add_bb_csts_to_loop(), ala_pose_loop(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), curr_loop_end_, core::pose::Pose::delete_polymer_residue(), delta_length_, core::pose::get_restype_for_pose(), loop_begin_, loop_end_, minimize_toward_stub(), minimize_toward_stub_, core::chemical::name_from_aa(), position_stub(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::scoring::rg, core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().
Referenced by apply(), and parse_my_tag().
bool protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub | ( | core::pose::Pose & | pose | ) | const |
References protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), chain_closing_attempts_, protocols::loops::Loop::choose_cutpoint(), curr_loop_end_, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::moves::Mover::get_last_move_status(), hires_scorefxn_, kinematic_mover_, loop_begin_, protocols::moves::MS_SUCCESS, protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_task_factory(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().
Referenced by loop_length().
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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 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.
References core::conformation::Conformation::chain_begin(), chain_closing_attempts_, core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), delta_length_, hires_scorefxn_, host_chain_, loop_begin_, loop_end_, loop_length(), lores_scorefxn_, minimize_toward_stub_, protocols::rosetta_scripts::parse_score_function(), stub_set_, and protocols::protein_interface_design::movers::TR().
bool protocols::protein_interface_design::movers::PlaceOnLoop::position_stub | ( | core::pose::Pose & | pose | ) | const |
Referenced by loop_length().
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void protocols::protein_interface_design::movers::PlaceOnLoop::set_kinematic_defaults | ( | ) |
set the defaults for the kinmover. Taken from Jacob's LoopRemodel
References hires_scorefxn_, and kinematic_mover_.
Referenced by PlaceOnLoop().
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private |
Referenced by minimize_toward_stub(), and parse_my_tag().
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Referenced by add_bb_csts_to_loop(), ala_pose_loop(), loop_length(), and minimize_toward_stub().
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Referenced by loop_length(), parse_my_tag(), and PlaceOnLoop().
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Referenced by ala_pose_loop(), minimize_toward_stub(), parse_my_tag(), and set_kinematic_defaults().
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Referenced by add_bb_csts_to_loop(), and parse_my_tag().
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Referenced by minimize_toward_stub(), PlaceOnLoop(), and set_kinematic_defaults().
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Referenced by ala_pose_loop(), loop_length(), minimize_toward_stub(), and parse_my_tag().
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Referenced by loop_length(), and parse_my_tag().
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Referenced by parse_my_tag().
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Referenced by loop_length(), and parse_my_tag().
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Referenced by add_bb_csts_to_loop(), and parse_my_tag().