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Rosetta 3.5
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Rosetta 3.5
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#include <MiniRelax.hh>
Public Types | |
| typedef RelaxProtocolBase | parent |
 Public Types inherited from protocols::relax::RelaxProtocolBase | |
| typedef moves::Mover | parent |
| 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 | |
| MiniRelax (core::scoring::ScoreFunctionOP scorefxn_in) | |
| MiniRelax (MiniRelax const &other) | |
| virtual | ~MiniRelax () |
| virtual protocols::moves::MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| virtual void | apply (core::pose::Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| Public Member Functions inherited from protocols::relax::RelaxProtocolBase | |
| RelaxProtocolBase (core::scoring::ScoreFunctionOP) | |
| RelaxProtocolBase (std::string const &movername="RelaxProtocol") | |
| RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP) | |
| ~RelaxProtocolBase () | |
| virtual 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 | set_defaults () |
| void | set_default_minimization_settings () |
| void | set_default_coordinate_settings () |
| void | set_default_movemap () |
| void | minimize_bond_lengths (bool setting) |
| void | minimize_bond_angles (bool setting) |
| void | minimize_bondlength_subset (int setting) |
| void | minimize_bondangle_subset (int setting) |
| bool | minimize_bond_lengths () const |
| bool | minimize_bond_angles () const |
| int | minimize_bondlength_subset () const |
| int | minimize_bondangle_subset () const |
| bool | constrain_relax_to_native_coords () const |
| bool | constrain_relax_to_start_coords () const |
| bool | constrain_coords () const |
| bool | explicit_ramp_constraints () const |
| bool | ramp_down_constraints () const |
| bool | constrain_relax_segments () const |
| bool | limit_aroma_chi2 () const |
| void | constrain_relax_to_native_coords (bool constrain_relax_to_native_coords) |
| void | constrain_relax_to_start_coords (bool constrain_relax_to_start_coords) |
| void | constrain_coords (bool constrain_coords) |
| void | ramp_down_constraints (bool ramp_down_constraints) |
| void | constrain_relax_segments (bool constrain_relax_segments) |
| void | cartesian (bool newval) |
| bool | cartesian () const |
| core::kinematics::MoveMapOP | get_movemap () |
| void | set_movemap (core::kinematics::MoveMapOP movemap) |
| void | set_min_type (std::string min_type) |
| void | set_scorefxn (core::scoring::ScoreFunctionOP score) |
| const core::scoring::ScoreFunctionCOP | get_scorefxn () const |
| void | set_task_factory (core::pack::task::TaskFactoryOP taskf) |
| core::pack::task::TaskFactoryOP const & | get_task_factory () const |
| void | set_dry_run (bool setting) |
| bool | dry_run () const |
| void | apply_disulfides (core::pose::Pose &pose) |
| 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) |
| virtual void | parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| 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 Attributes | |
| core::scoring::ScoreFunctionOP | scorefxn_ |
Additional Inherited Members | |
| Static Public Member Functions inherited from protocols::relax::RelaxProtocolBase | |
| static void | register_options () |
| Protected Member Functions inherited from protocols::relax::RelaxProtocolBase | |
| void | initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap) |
| core::scoring::ScoreFunctionOP | get_scorefxn () |
| void | set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap) |
| void | output_debug_structure (core::pose::Pose &pose, std::string prefix) |
| Protected Attributes inherited from protocols::relax::RelaxProtocolBase | |
| bool | constrain_relax_to_native_coords_ |
| bool | constrain_relax_to_start_coords_ |
| bool | constrain_coords_ |
| bool | coord_constrain_sidechains_ |
| bool | explicit_ramp_constraints_ |
| bool | ramp_down_constraints_ |
| bool | constrain_relax_segments_ |
| std::string | min_type_ |
| bool | cartesian_ |
| Do cartesian-space minimization? More... | |
| bool | limit_aroma_chi2_ |
Definition at line 26 of file MiniRelax.hh.
Definition at line 29 of file MiniRelax.hh.
| protocols::relax::MiniRelax::MiniRelax | ( | core::scoring::ScoreFunctionOP | scorefxn_in) |
Definition at line 55 of file MiniRelax.cc.
Referenced by clone().
| protocols::relax::MiniRelax::MiniRelax | ( | MiniRelax const & | other) |
Definition at line 62 of file MiniRelax.cc.
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virtual |
Definition at line 68 of file MiniRelax.cc.
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virtual |
Implements protocols::moves::Mover.
Definition at line 76 of file MiniRelax.cc.
References core::sequence::alignment_from_pose(), protocols::relax::FastRelax::apply(), protocols::relax::RelaxProtocolBase::apply_disulfides(), core::pose::Pose::constraint_set(), protocols::relax::coordinate_constrain_selection(), core::scoring::coordinate_constraint, protocols::relax::delete_virtual_residues(), core::scoring::fa_rep, core::chemical::FA_STANDARD, protocols::relax::generate_bb_coordinate_constraints(), protocols::relax::get_per_residue_scores(), core::pose::Pose::is_fullatom(), scorefxn_, core::sequence::SequenceAlignment::sequence_mapping(), core::util::switch_to_residue_type_set(), and core::pose::Pose::total_residue().
Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().
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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 71 of file MiniRelax.cc.
References MiniRelax().
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virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 174 of file MiniRelax.cc.
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private |
Definition at line 41 of file MiniRelax.hh.
Referenced by apply().
1.8.4