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protocols::swa::protein::StepWiseProteinScreener Class Reference

#include <StepWiseProteinScreener.hh>

Inheritance diagram for protocols::swa::protein::StepWiseProteinScreener:
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Collaboration diagram for protocols::swa::protein::StepWiseProteinScreener:
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Public Member Functions

 StepWiseProteinScreener (protocols::swa::StepWiseJobParametersOP &job_parameters)
 
 ~StepWiseProteinScreener ()
 
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)
 
utility::vector1
< MainChainTorsionSetList >
const & 
main_chain_torsion_set_lists () const
 
utility::vector1
< utility::vector1< core::Real > > 
main_chain_torsion_set_lists_real () const
 
utility::vector1
< core::id::TorsionID
which_torsions ()
 
void setup_centroid_screen (core::Real const &centroid_score_diff_cut, std::string const &centroid_weights, core::Size const nstruct_centroid, bool const ghost_loops)
 
core::Size get_big_bin (core::Real const phi, core::Real const psi) const
 
void set_moving_residues (utility::vector1< core::Size > const &moving_res)
 
void set_fixed_residues (utility::vector1< core::Size > const &fixed_res)
 
- 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 setup_torsion_sets ()
 
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)
 
void filter_based_on_desired_secstruct (char const &secstruct, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void filter_big_bin (Size const big_bin, MainChainTorsionSetList &main_chain_torsion_set_list)
 
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)
 
void sample_cis_omega (MainChainTorsionSetList &main_chain_torsion_set_list)
 
void initialize_is_fixed_res ()
 

Private Attributes

protocols::swa::StepWiseJobParametersOP job_parameters_
 
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_
 
utility::vector1
< MainChainTorsionSetList
main_chain_torsion_sets_for_moving_residues_
 
utility::vector1< core::Realcentroid_scores_
 
bool ghost_loops_
 
ResMap ghost_map_
 
core::pose::PoseOP ghost_pose_
 
core::pose::PoseOP ghost_native_pose_
 
utility::vector1< boolis_pre_proline_
 
utility::vector1< boolis_fixed_res_
 

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
protocols::filters::Filters_map 
Filters_map
 
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::protein::StepWiseProteinScreener::StepWiseProteinScreener ( protocols::swa::StepWiseJobParametersOP job_parameters)
protocols::swa::protein::StepWiseProteinScreener::~StepWiseProteinScreener ( )

Member Function Documentation

void protocols::swa::protein::StepWiseProteinScreener::apply ( core::pose::Pose pose_to_visualize)
virtual
void protocols::swa::protein::StepWiseProteinScreener::convert_to_centroid ( core::pose::Pose pose)
private
void protocols::swa::protein::StepWiseProteinScreener::copy_coords ( core::pose::Pose pose,
core::pose::Pose const &  template_pose,
ResMap const &  ghost_map 
) const
private
core::kinematics::FoldTree protocols::swa::protein::StepWiseProteinScreener::figure_out_fold_tree ( ResMap const &  ghost_map) const
private
void protocols::swa::protein::StepWiseProteinScreener::filter_and_output ( core::pose::Pose pose,
std::string const &  tag 
)
private
void protocols::swa::protein::StepWiseProteinScreener::filter_based_on_desired_secstruct ( char const &  secstruct,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::swa::protein::StepWiseProteinScreener::filter_big_bin ( Size const  big_bin,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::swa::protein::StepWiseProteinScreener::filter_main_chain_torsion_sets ( )
private
void protocols::swa::protein::StepWiseProteinScreener::filter_native_BIG_BINS ( core::Size const &  n,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
Size protocols::swa::protein::StepWiseProteinScreener::get_big_bin ( core::Real const  phi,
core::Real const  psi 
) const
void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list ( core::Size const &  n,
core::pose::Pose const &  pose,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::swa::protein::StepWiseProteinScreener::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 
)
private
void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_coarse ( core::Size const &  n,
core::pose::Pose const &  pose,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::swa::protein::StepWiseProteinScreener::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 
)
private
void protocols::swa::protein::StepWiseProteinScreener::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 
)
private
void protocols::swa::protein::StepWiseProteinScreener::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 
)
private
void protocols::swa::protein::StepWiseProteinScreener::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 
)
private
std::string protocols::swa::protein::StepWiseProteinScreener::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::swa::protein::StepWiseProteinScreener::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 
)
private
void protocols::swa::protein::StepWiseProteinScreener::initialize_is_fixed_res ( )
private

References is_fixed_res_, and job_parameters_.

Referenced by StepWiseProteinScreener().

utility::vector1< MainChainTorsionSetList > const & protocols::swa::protein::StepWiseProteinScreener::main_chain_torsion_set_lists ( ) const
utility::vector1< utility::vector1< core::Real > > protocols::swa::protein::StepWiseProteinScreener::main_chain_torsion_set_lists_real ( ) const
void protocols::swa::protein::StepWiseProteinScreener::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 
)
private
void protocols::swa::protein::StepWiseProteinScreener::prepare_ghost_pose ( core::pose::Pose const &  pose)
private
void protocols::swa::protein::StepWiseProteinScreener::sample_cis_omega ( MainChainTorsionSetList main_chain_torsion_set_list)
private
void protocols::swa::protein::StepWiseProteinScreener::sample_residues_recursively ( Size const  which_res,
Size count,
core::pose::Pose pose 
)
private
void protocols::swa::protein::StepWiseProteinScreener::set_apply_vdw_cut ( bool const &  setting)

References apply_vdw_cut_.

Referenced by setup_centroid_screen().

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

References centroid_scorefxn_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_centroid_screen ( bool const &  setting)

References centroid_screen_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_filter_native_big_bins ( bool const &  setting)
void protocols::swa::protein::StepWiseProteinScreener::set_fixed_residues ( utility::vector1< core::Size > const &  fixed_res)

References is_fixed_res_, and job_parameters_.

void protocols::swa::protein::StepWiseProteinScreener::set_ghost_loops ( bool const &  setting)

References ghost_loops_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_moving_residues ( utility::vector1< core::Size > const &  moving_res)

References moving_residues_.

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

References n_sample_.

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

References nstruct_centroid_.

Referenced by setup_centroid_screen().

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

References rmsd_cutoff_.

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

References silent_file_.

void protocols::swa::protein::StepWiseProteinScreener::setup_centroid_screen ( core::Real const &  centroid_score_diff_cut,
std::string const &  centroid_weights,
core::Size const  nstruct_centroid,
bool const  ghost_loops 
)
void protocols::swa::protein::StepWiseProteinScreener::setup_torsion_sets ( )
private
utility::vector1< id::TorsionID > protocols::swa::protein::StepWiseProteinScreener::which_torsions ( )

References core::id::BB, and moving_residues_.

Member Data Documentation

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

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