Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::swa::StepWiseScreener Class Reference

#include <StepWiseScreener.hh>

Inheritance diagram for protocols::swa::StepWiseScreener:
Inheritance graph
Collaboration diagram for protocols::swa::StepWiseScreener:
Collaboration graph

Public Member Functions

 StepWiseScreener (utility::vector1< Size > const &moving_residues)
 ~StepWiseScreener ()
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...
void set_silent_file (std::string const &setting)
void set_rmsd_cutoff (core::Real const &setting)
void set_n_sample (core::Size const &setting)
void set_nstruct_centroid (core::Size const &setting)
void set_filter_native_big_bins (bool const &setting)
void set_centroid_screen (bool const &setting)
void set_ghost_loops (bool const &setting)
void set_apply_vdw_cut (bool const &setting)
void set_centroid_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
void set_centroid_score_diff_cut (core::Real const &setting)
< MainChainTorsionSetList >
const & 
main_chain_torsion_set_lists () 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)
Moveroperator= (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 Stringsinfo ()
 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

Private Member Functions

void filter_main_chain_torsion_sets ()
void prepare_ghost_pose (core::pose::Pose const &pose)
void initialize_ghost_pose (core::pose::PoseOP &ghost_pose, std::string const &desired_sequence, core::pose::Pose const &template_pose, ResMap const &ghost_map, core::kinematics::FoldTree f)
void copy_coords (core::pose::Pose &pose, core::pose::Pose const &template_pose, ResMap const &ghost_map) const
core::kinematics::FoldTree figure_out_fold_tree (ResMap const &ghost_map) const
void sample_residues_recursively (Size const which_res, Size &count, core::pose::Pose &pose)
void filter_and_output (core::pose::Pose &pose, std::string const &tag)
void get_main_chain_torsion_set_list (core::Size const &n, core::pose::Pose const &pose, MainChainTorsionSetList &main_chain_torsion_set_list)
void get_main_chain_torsion_set_list_coarse (core::Size const &n, core::pose::Pose const &pose, MainChainTorsionSetList &main_chain_torsion_set_list)
void get_main_chain_torsion_set_list_full (core::Size const &n, core::pose::Pose const &pose, core::Real const &best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
void get_main_chain_torsion_set_list_n_terminus (core::Size const &n, core::pose::Pose const &pose, core::Real const &best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
void get_main_chain_torsion_set_list_c_terminus (core::Size const &n, core::pose::Pose const &pose, core::Real const &best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
void get_main_chain_torsion_set_list_sample_phi_only (core::Size const &n, core::pose::Pose const &pose, core::Real const &best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
void get_main_chain_torsion_set_list_sample_psi_only (core::Size const &n, core::pose::Pose const &pose, core::Real const &best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
void filter_native_BIG_BINS (core::Size const &n, MainChainTorsionSetList &main_chain_torsion_set_list)
core::Size get_big_bin (core::Real const phi, core::Real const psi) const
void output_centroid_silent_struct (core::pose::Pose const &pose, core::pose::PoseCOP const &native_pose_op, std::string const silent_file, std::string const &tag)
void convert_to_centroid (core::pose::Pose &pose)

Private Attributes

utility::vector1< Sizemoving_residues_
core::Size n_sample_
core::Real rmsd_cutoff_
core::scoring::ScoreFunctionOP centroid_scorefxn_
std::string silent_file_
bool filter_native_big_bins_
bool centroid_screen_
core::Real centroid_score_ref_
core::Real centroid_score_diff_cut_
bool apply_vdw_cut_
core::Real centroid_vdw_ref_
Size nstruct_centroid_
core::scoring::Ramachandran ramachandran_
MainChainTorsionSetList main_chain_torsion_set_for_moving_residues_
< MainChainTorsionSetList
utility::vector1< core::Realcentroid_scores_
bool ghost_loops_
ResMap ghost_map_
core::pose::PoseOP ghost_pose_
core::pose::PoseOP ghost_native_pose_

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings
- 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 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...

Constructor & Destructor Documentation

protocols::swa::StepWiseScreener::StepWiseScreener ( utility::vector1< Size > const &  moving_residues)
protocols::swa::StepWiseScreener::~StepWiseScreener ( )

Member Function Documentation

void protocols::swa::StepWiseScreener::apply ( core::pose::Pose pose_to_visualize)
void protocols::swa::StepWiseScreener::convert_to_centroid ( core::pose::Pose pose)
void protocols::swa::StepWiseScreener::copy_coords ( core::pose::Pose pose,
core::pose::Pose const &  template_pose,
ResMap const &  ghost_map 
) const
core::kinematics::FoldTree protocols::swa::StepWiseScreener::figure_out_fold_tree ( ResMap const &  ghost_map) const
void protocols::swa::StepWiseScreener::filter_and_output ( core::pose::Pose pose,
std::string const &  tag 
void protocols::swa::StepWiseScreener::filter_main_chain_torsion_sets ( )
void protocols::swa::StepWiseScreener::filter_native_BIG_BINS ( core::Size const &  n,
MainChainTorsionSetList main_chain_torsion_set_list 
Size protocols::swa::StepWiseScreener::get_big_bin ( core::Real const  phi,
core::Real const  psi 
) const

Referenced by filter_native_BIG_BINS().

void protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list ( core::Size const &  n,
core::pose::Pose const &  pose,
MainChainTorsionSetList main_chain_torsion_set_list 
void protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_c_terminus ( core::Size const &  n,
core::pose::Pose const &  pose,
core::Real const &  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
void protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_coarse ( core::Size const &  n,
core::pose::Pose const &  pose,
MainChainTorsionSetList main_chain_torsion_set_list 
void protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_full ( core::Size const &  n,
core::pose::Pose const &  pose,
core::Real const &  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
void protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_n_terminus ( core::Size const &  n,
core::pose::Pose const &  pose,
core::Real const &  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
void protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_phi_only ( core::Size const &  n,
core::pose::Pose const &  pose,
core::Real const &  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
void protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_psi_only ( core::Size const &  n,
core::pose::Pose const &  pose,
core::Real const &  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
std::string protocols::swa::StepWiseScreener::get_name ( ) const

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

void protocols::swa::StepWiseScreener::initialize_ghost_pose ( core::pose::PoseOP ghost_pose,
std::string const &  desired_sequence,
core::pose::Pose const &  template_pose,
ResMap const &  ghost_map,
core::kinematics::FoldTree  f 
utility::vector1< MainChainTorsionSetList > const & protocols::swa::StepWiseScreener::main_chain_torsion_set_lists ( ) const
void protocols::swa::StepWiseScreener::output_centroid_silent_struct ( core::pose::Pose const &  pose,
core::pose::PoseCOP const &  native_pose_op,
std::string const  silent_file,
std::string const &  tag 
void protocols::swa::StepWiseScreener::prepare_ghost_pose ( core::pose::Pose const &  pose)
void protocols::swa::StepWiseScreener::sample_residues_recursively ( Size const  which_res,
Size count,
core::pose::Pose pose 
void protocols::swa::StepWiseScreener::set_apply_vdw_cut ( bool const &  setting)

References apply_vdw_cut_.

void protocols::swa::StepWiseScreener::set_centroid_score_diff_cut ( core::Real const &  setting)
void protocols::swa::StepWiseScreener::set_centroid_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References centroid_scorefxn_.

void protocols::swa::StepWiseScreener::set_centroid_screen ( bool const &  setting)

References centroid_screen_.

void protocols::swa::StepWiseScreener::set_filter_native_big_bins ( bool const &  setting)
void protocols::swa::StepWiseScreener::set_ghost_loops ( bool const &  setting)

References ghost_loops_.

void protocols::swa::StepWiseScreener::set_n_sample ( core::Size const &  setting)

References n_sample_.

void protocols::swa::StepWiseScreener::set_nstruct_centroid ( core::Size const &  setting)

References nstruct_centroid_.

void protocols::swa::StepWiseScreener::set_rmsd_cutoff ( core::Real const &  setting)

References rmsd_cutoff_.

void protocols::swa::StepWiseScreener::set_silent_file ( std::string const &  setting)

References silent_file_.

Member Data Documentation

bool protocols::swa::StepWiseScreener::apply_vdw_cut_
core::Real protocols::swa::StepWiseScreener::centroid_score_diff_cut_
core::Real protocols::swa::StepWiseScreener::centroid_score_ref_
core::scoring::ScoreFunctionOP protocols::swa::StepWiseScreener::centroid_scorefxn_
utility::vector1< core::Real > protocols::swa::StepWiseScreener::centroid_scores_
bool protocols::swa::StepWiseScreener::centroid_screen_
core::Real protocols::swa::StepWiseScreener::centroid_vdw_ref_
bool protocols::swa::StepWiseScreener::filter_native_big_bins_
bool protocols::swa::StepWiseScreener::ghost_loops_
ResMap protocols::swa::StepWiseScreener::ghost_map_
core::pose::PoseOP protocols::swa::StepWiseScreener::ghost_native_pose_
core::pose::PoseOP protocols::swa::StepWiseScreener::ghost_pose_
MainChainTorsionSetList protocols::swa::StepWiseScreener::main_chain_torsion_set_for_moving_residues_
utility::vector1< MainChainTorsionSetList > protocols::swa::StepWiseScreener::main_chain_torsion_sets_for_moving_residues_
utility::vector1< Size > protocols::swa::StepWiseScreener::moving_residues_
core::Size protocols::swa::StepWiseScreener::n_sample_
Size protocols::swa::StepWiseScreener::nstruct_centroid_
core::scoring::Ramachandran protocols::swa::StepWiseScreener::ramachandran_
core::Real protocols::swa::StepWiseScreener::rmsd_cutoff_
std::string protocols::swa::StepWiseScreener::silent_file_

The documentation for this class was generated from the following files: