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
[legend]
Collaboration diagram for protocols::swa::StepWiseScreener:
Collaboration graph
[legend]

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)
 
utility::vector1
< 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)
 
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
 

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< Size > moving_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::Real > centroid_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
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...
 

Detailed Description

Definition at line 42 of file StepWiseScreener.hh.

Constructor & Destructor Documentation

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

Definition at line 85 of file StepWiseScreener.cc.

References main_chain_torsion_set_for_moving_residues_, and protocols::swa::MainChainTorsionSet().

protocols::swa::StepWiseScreener::~StepWiseScreener ( )

Definition at line 110 of file StepWiseScreener.cc.

Member Function Documentation

void protocols::swa::StepWiseScreener::apply ( core::pose::Pose &  pose_to_visualize)
virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

Definition at line 116 of file StepWiseScreener.cc.

References centroid_scores_, centroid_screen_, convert_to_centroid(), filter_main_chain_torsion_sets(), ghost_loops_, main_chain_torsion_sets_for_moving_residues_, nstruct_centroid_, prepare_ghost_pose(), and sample_residues_recursively().

void protocols::swa::StepWiseScreener::convert_to_centroid ( core::pose::Pose &  pose)
private

Definition at line 284 of file StepWiseScreener.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CENTROID, core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::remove_variant_type_from_pose_residue(), core::util::switch_to_residue_type_set(), and core::pose::Pose::total_residue().

Referenced by apply(), and prepare_ghost_pose().

void protocols::swa::StepWiseScreener::copy_coords ( core::pose::Pose &  pose,
core::pose::Pose const &  template_pose,
ResMap const &  ghost_map 
) const
private

Definition at line 223 of file StepWiseScreener.cc.

References core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_name(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by filter_and_output(), and initialize_ghost_pose().

core::kinematics::FoldTree protocols::swa::StepWiseScreener::figure_out_fold_tree ( ResMap const &  ghost_map) const
private

Definition at line 253 of file StepWiseScreener.cc.

References core::kinematics::FoldTree::new_jump().

Referenced by prepare_ghost_pose().

void protocols::swa::StepWiseScreener::filter_and_output ( core::pose::Pose &  pose,
std::string const &  tag 
)
private

Definition at line 343 of file StepWiseScreener.cc.

References apply_vdw_cut_, centroid_score_diff_cut_, centroid_score_ref_, centroid_scores_, centroid_screen_, centroid_vdw_ref_, copy_coords(), protocols::moves::Mover::get_native_pose(), ghost_loops_, ghost_map_, ghost_native_pose_, ghost_pose_, core::scoring::is_protein_backbone_including_O(), main_chain_torsion_set_for_moving_residues_, main_chain_torsion_sets_for_moving_residues_, protocols::swa::protein::output_silent_struct(), rmsd_cutoff_, core::scoring::rmsd_with_super(), silent_file_, protocols::TR(), and core::scoring::vdw.

Referenced by sample_residues_recursively().

void protocols::swa::StepWiseScreener::filter_main_chain_torsion_sets ( )
private

Definition at line 653 of file StepWiseScreener.cc.

References centroid_scores_, main_chain_torsion_sets_for_moving_residues_, and nstruct_centroid_.

Referenced by apply().

void protocols::swa::StepWiseScreener::filter_native_BIG_BINS ( core::Size const &  n,
MainChainTorsionSetList &  main_chain_torsion_set_list 
)
private

Definition at line 618 of file StepWiseScreener.cc.

References get_big_bin(), protocols::moves::Mover::get_native_pose(), protocols::swa::phi(), core::pose::Pose::phi(), protocols::swa::psi(), core::pose::Pose::psi(), and core::pose::Pose::total_residue().

Referenced by get_main_chain_torsion_set_list().

Size protocols::swa::StepWiseScreener::get_big_bin ( core::Real const  phi,
core::Real const  psi 
) const
private

Definition at line 601 of file StepWiseScreener.cc.

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 
)
private

Definition at line 403 of file StepWiseScreener.cc.

References filter_native_BIG_BINS(), filter_native_big_bins_, get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_coarse(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), core::conformation::Residue::has_variant_type(), moving_residues_, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by sample_residues_recursively().

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 
)
private

Definition at line 537 of file StepWiseScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::MainChainTorsionSet(), n_sample_, protocols::swa::phi(), protocols::swa::psi(), and ramachandran_.

Referenced by get_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 
)
private

Definition at line 457 of file StepWiseScreener.cc.

References core::pose::Pose::aa(), core::chemical::aa_gly, core::chemical::aa_pro, and protocols::swa::MainChainTorsionSet().

Referenced by get_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 
)
private

Definition at line 491 of file StepWiseScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::MainChainTorsionSet(), n_sample_, protocols::swa::phi(), protocols::swa::psi(), and ramachandran_.

Referenced by get_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 
)
private

Definition at line 513 of file StepWiseScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::MainChainTorsionSet(), n_sample_, protocols::swa::phi(), protocols::swa::psi(), and ramachandran_.

Referenced by get_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 
)
private

Definition at line 562 of file StepWiseScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::MainChainTorsionSet(), n_sample_, protocols::swa::phi(), protocols::swa::psi(), core::pose::Pose::psi(), ramachandran_, and protocols::TR().

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 
)
private

Definition at line 580 of file StepWiseScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::MainChainTorsionSet(), n_sample_, protocols::swa::phi(), core::pose::Pose::phi(), protocols::swa::psi(), ramachandran_, and protocols::TR().

std::string protocols::swa::StepWiseScreener::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

Definition at line 144 of file StepWiseScreener.cc.

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 
)
private

Definition at line 204 of file StepWiseScreener.cc.

References core::chemical::CENTROID, copy_coords(), core::chemical::ChemicalManager::get_instance(), core::pose::make_pose_from_sequence(), and core::chemical::ChemicalManager::residue_type_set().

Referenced by prepare_ghost_pose().

utility::vector1< MainChainTorsionSetList > const & protocols::swa::StepWiseScreener::main_chain_torsion_set_lists ( ) const

Definition at line 736 of file StepWiseScreener.cc.

References main_chain_torsion_sets_for_moving_residues_.

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 
)
private
void protocols::swa::StepWiseScreener::prepare_ghost_pose ( core::pose::Pose const &  pose)
private

Definition at line 151 of file StepWiseScreener.cc.

References centroid_score_ref_, centroid_scorefxn_, centroid_vdw_ref_, convert_to_centroid(), figure_out_fold_tree(), protocols::moves::Mover::get_native_pose(), ghost_map_, ghost_native_pose_, ghost_pose_, initialize_ghost_pose(), moving_residues_, core::pose::Pose::sequence(), core::kinematics::Jump::set_translation(), and core::scoring::vdw.

Referenced by apply().

void protocols::swa::StepWiseScreener::sample_residues_recursively ( Size const  which_res,
Size &  count,
core::pose::Pose &  pose 
)
private

Definition at line 303 of file StepWiseScreener.cc.

References filter_and_output(), get_main_chain_torsion_set_list(), main_chain_torsion_set_for_moving_residues_, moving_residues_, protocols::swa::MainChainTorsionSet::omega(), protocols::swa::MainChainTorsionSet::phi(), protocols::swa::MainChainTorsionSet::psi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by apply().

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

Definition at line 724 of file StepWiseScreener.cc.

References apply_vdw_cut_.

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

Definition at line 730 of file StepWiseScreener.cc.

References centroid_score_diff_cut_.

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

Definition at line 699 of file StepWiseScreener.cc.

References centroid_scorefxn_.

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

Definition at line 712 of file StepWiseScreener.cc.

References centroid_screen_.

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

Definition at line 706 of file StepWiseScreener.cc.

References filter_native_big_bins_.

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

Definition at line 718 of file StepWiseScreener.cc.

References ghost_loops_.

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

Definition at line 687 of file StepWiseScreener.cc.

References n_sample_.

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

Definition at line 693 of file StepWiseScreener.cc.

References nstruct_centroid_.

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

Definition at line 681 of file StepWiseScreener.cc.

References rmsd_cutoff_.

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

Definition at line 675 of file StepWiseScreener.cc.

References silent_file_.

Member Data Documentation

bool protocols::swa::StepWiseScreener::apply_vdw_cut_
private

Definition at line 210 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and set_apply_vdw_cut().

core::Real protocols::swa::StepWiseScreener::centroid_score_diff_cut_
private

Definition at line 208 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and set_centroid_score_diff_cut().

core::Real protocols::swa::StepWiseScreener::centroid_score_ref_
private

Definition at line 207 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and prepare_ghost_pose().

core::scoring::ScoreFunctionOP protocols::swa::StepWiseScreener::centroid_scorefxn_
private

Definition at line 203 of file StepWiseScreener.hh.

Referenced by prepare_ghost_pose(), and set_centroid_scorefxn().

utility::vector1< core::Real > protocols::swa::StepWiseScreener::centroid_scores_
private

Definition at line 219 of file StepWiseScreener.hh.

Referenced by apply(), filter_and_output(), and filter_main_chain_torsion_sets().

bool protocols::swa::StepWiseScreener::centroid_screen_
private

Definition at line 206 of file StepWiseScreener.hh.

Referenced by apply(), filter_and_output(), and set_centroid_screen().

core::Real protocols::swa::StepWiseScreener::centroid_vdw_ref_
private

Definition at line 211 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and prepare_ghost_pose().

bool protocols::swa::StepWiseScreener::filter_native_big_bins_
private

Definition at line 205 of file StepWiseScreener.hh.

Referenced by get_main_chain_torsion_set_list(), and set_filter_native_big_bins().

bool protocols::swa::StepWiseScreener::ghost_loops_
private

Definition at line 221 of file StepWiseScreener.hh.

Referenced by apply(), filter_and_output(), and set_ghost_loops().

ResMap protocols::swa::StepWiseScreener::ghost_map_
private

Definition at line 222 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and prepare_ghost_pose().

core::pose::PoseOP protocols::swa::StepWiseScreener::ghost_native_pose_
private

Definition at line 223 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and prepare_ghost_pose().

core::pose::PoseOP protocols::swa::StepWiseScreener::ghost_pose_
private

Definition at line 223 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and prepare_ghost_pose().

MainChainTorsionSetList protocols::swa::StepWiseScreener::main_chain_torsion_set_for_moving_residues_
private

Definition at line 217 of file StepWiseScreener.hh.

Referenced by filter_and_output(), sample_residues_recursively(), and StepWiseScreener().

utility::vector1< MainChainTorsionSetList > protocols::swa::StepWiseScreener::main_chain_torsion_sets_for_moving_residues_
private

Definition at line 218 of file StepWiseScreener.hh.

Referenced by apply(), filter_and_output(), filter_main_chain_torsion_sets(), and main_chain_torsion_set_lists().

utility::vector1< Size > protocols::swa::StepWiseScreener::moving_residues_
private

Definition at line 199 of file StepWiseScreener.hh.

Referenced by get_main_chain_torsion_set_list(), prepare_ghost_pose(), and sample_residues_recursively().

core::Size protocols::swa::StepWiseScreener::n_sample_
private

Definition at line 200 of file StepWiseScreener.hh.

Referenced by get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), get_main_chain_torsion_set_list_sample_phi_only(), get_main_chain_torsion_set_list_sample_psi_only(), and set_n_sample().

Size protocols::swa::StepWiseScreener::nstruct_centroid_
private

Definition at line 213 of file StepWiseScreener.hh.

Referenced by apply(), filter_main_chain_torsion_sets(), and set_nstruct_centroid().

core::scoring::Ramachandran protocols::swa::StepWiseScreener::ramachandran_
private

Definition at line 215 of file StepWiseScreener.hh.

Referenced by get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), get_main_chain_torsion_set_list_sample_phi_only(), and get_main_chain_torsion_set_list_sample_psi_only().

core::Real protocols::swa::StepWiseScreener::rmsd_cutoff_
private

Definition at line 201 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and set_rmsd_cutoff().

std::string protocols::swa::StepWiseScreener::silent_file_
private

Definition at line 204 of file StepWiseScreener.hh.

Referenced by filter_and_output(), and set_silent_file().

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:56:38 for Rosetta 3.5 by   doxygen 1.8.4