Rosetta 3.5
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#include <StepWiseProteinLoopBridger.hh>
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StepWiseProteinLoopBridger (protocols::swa::StepWisePoseSampleGeneratorOP sample_generator, protocols::swa::StepWiseJobParametersOP job_parameters) | |
~StepWiseProteinLoopBridger () | |
virtual void | apply (core::pose::Pose &pose_to_visualize) |
Apply the minimizer to one pose. More... | |
virtual std::string | get_name () const |
Each derived class must specify its name. The class name. More... | |
utility::vector1 < utility::vector1< core::Real > > const & | main_chain_torsion_set_lists () const |
utility::vector1 < core::id::TorsionID > const & | which_torsions () const |
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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 MoverOP | clone () const |
clone has to be overridden only if clone invocation is expected. More... | |
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... | |
virtual 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_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
Additional Inherited Members | |
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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 |
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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... | |
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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... | |
protocols::swa::protein::StepWiseProteinLoopBridger::StepWiseProteinLoopBridger | ( | protocols::swa::StepWisePoseSampleGeneratorOP | sample_generator, |
protocols::swa::StepWiseJobParametersOP | job_parameters | ||
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References initialize_is_fixed_res(), and working_bridge_res_.
protocols::swa::protein::StepWiseProteinLoopBridger::~StepWiseProteinLoopBridger | ( | ) |
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Apply the minimizer to one pose.
Implements protocols::moves::Mover.
References figure_out_loop(), grab_main_chain_torsion_set_list(), KIC_loop_close_with_perturbations(), main_chain_torsion_sets_for_moving_residues_, pose_count_, sample_generator_, and setup_torsions().
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References core::pose::Pose::annotated_sequence(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), loop_, core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and working_bridge_res_.
Referenced by apply().
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References output_chainTORS(), core::pose::Pose::residue(), verbose_, and core::conformation::Residue::xyz().
Referenced by KIC_loop_close(), and sample_omega_recursively().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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References main_chain_torsion_sets_for_moving_residues_, core::pose::Pose::torsion(), and which_torsions_.
Referenced by apply(), and sample_omega_recursively().
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References is_fixed_res_.
Referenced by StepWiseProteinLoopBridger().
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References protocols::loops::Loop::cut(), core::chemical::AtomICoor::d(), end_res_, fill_chainTORS_info(), core::chemical::ResidueConnection::icoor(), idl_C_N_, idl_C_N_CA_, idl_CA_C_N_, loop_, core::conformation::Residue::lower_connect(), middle_offset_, middle_res_, OMEGA_MEAN_, protocols::forge::methods::order(), output_chainTORS(), core::pose::Pose::residue(), sample_omega_recursively(), seg_len_, protocols::loops::Loop::start(), start_res_, protocols::loops::Loop::stop(), core::chemical::AtomICoor::theta(), core::conformation::Residue::upper_connect(), use_icoor_geometry_, and verbose_.
Referenced by KIC_loop_close_with_perturbations().
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References KIC_loop_close(), num_perturb_steps_, perturb_torsion_, core::pose::Pose::phi(), pose_count_, core::pose::Pose::psi(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and working_bridge_res_.
Referenced by apply().
utility::vector1< utility::vector1< core::Real > > const & protocols::swa::protein::StepWiseProteinLoopBridger::main_chain_torsion_set_lists | ( | ) | const |
References main_chain_torsion_sets_for_moving_residues_.
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Referenced by fill_chainTORS_info(), and KIC_loop_close().
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References core::id::BB, is_fixed_res_, core::pose::Pose::total_residue(), and which_torsions_.
Referenced by apply().
utility::vector1< core::id::TorsionID > const & protocols::swa::protein::StepWiseProteinLoopBridger::which_torsions | ( | ) | const |
References which_torsions_.
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Referenced by KIC_loop_close(), and sample_omega_recursively().
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Referenced by KIC_loop_close().
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Referenced by KIC_loop_close().
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Referenced by KIC_loop_close().
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Referenced by initialize_is_fixed_res(), and setup_torsions().
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Referenced by sample_omega_recursively().
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Referenced by figure_out_loop(), and KIC_loop_close().
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Referenced by apply(), grab_main_chain_torsion_set_list(), and main_chain_torsion_set_lists().
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Referenced by KIC_loop_close().
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Referenced by KIC_loop_close().
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Referenced by KIC_loop_close_with_perturbations().
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Referenced by KIC_loop_close(), and sample_omega_recursively().
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Referenced by KIC_loop_close_with_perturbations().
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Referenced by apply(), and KIC_loop_close_with_perturbations().
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Referenced by apply().
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Referenced by KIC_loop_close(), and sample_omega_recursively().
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Referenced by KIC_loop_close(), and sample_omega_recursively().
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Referenced by KIC_loop_close().
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Referenced by fill_chainTORS_info(), KIC_loop_close(), and sample_omega_recursively().
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Referenced by grab_main_chain_torsion_set_list(), setup_torsions(), and which_torsions().
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Referenced by figure_out_loop(), KIC_loop_close_with_perturbations(), and StepWiseProteinLoopBridger().