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protocols::swa::RigidBodySampler Class Reference

#include <RigidBodySampler.hh>

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Public Member Functions

 RigidBodySampler (utility::vector1< Size > const &fixed_res, utility::vector1< Size > const &moving_res)
 
virtual ~RigidBodySampler ()
 
void do_the_sampling (pose::Pose &pose)
 
void save_silent_struct (pose::Pose &pose, std::string const tag)
 
void output_results (utility::io::ozstream &out)
 
void output_histogram (utility::io::ozstream &out)
 
void output_silent_file (std::string const silent_file, bool const write_score_only=false)
 
void set_native_pose (pose::PoseOP native_pose)
 
void set_n_sample_alpha_full_range (Size const setting)
 
void set_n_sample_cosbeta_full_range (Size const setting)
 
void set_n_sample_gamma_full_range (Size const setting)
 
void set_alpha_min (Real const setting)
 
void set_alpha_max (Real const setting)
 
void set_alpha_increment (Real const setting)
 
void set_cosbeta_min (Real const setting)
 
void set_cosbeta_max (Real const setting)
 
void set_cosbeta_increment (Real const setting)
 
void set_gamma_min (Real const setting)
 
void set_gamma_max (Real const setting)
 
void set_gamma_increment (Real const setting)
 
void set_translation_sample (Real const box_size, Real const xyz_increment)
 
void set_x_min (Real const setting)
 
void set_x_max (Real const setting)
 
void set_x_increment (Real const setting)
 
void set_y_min (Real const setting)
 
void set_y_max (Real const setting)
 
void set_y_increment (Real const setting)
 
void set_z_min (Real const setting)
 
void set_z_max (Real const setting)
 
void set_z_increment (Real const setting)
 
void set_rmsd_cutoff (Real const setting)
 
void force_coplanar ()
 
void force_antiparallel ()
 
void force_parallel ()
 
void set_score_cutoff (Real const setting)
 
void set_score_function (core::scoring::ScoreFunctionOP setting)
 
core::scoring::ScoreFunctionOP score_function ()
 
void set_silent_file_data (core::io::silent::SilentFileDataOP sfd)
 
core::io::silent::SilentFileDataOP silent_file_data ()
 
void set_contact_cutoff (Real const setting)
 
void set_min_num_contacts (Size const setting)
 
void set_steric_dist_cutoff (Real const setting)
 
void set_min_hbonds (Size const value)
 
void set_fa_rep_cutoff (Real const value)
 
void set_o2star_trials (bool const setting)
 
void set_ignore_o2star_hbonds_in_filter (bool const setting)
 
void set_assign_WC_edges (bool const setting)
 
void assign_WC_edges_to_base_pair12 (pose::Pose &pose, io::silent::SilentStruct &s)
 
void apply_input_samples (pose::Pose &pose, std::string const rigid_body_sample_file)
 
void apply_rigid_body_settings (pose::Pose &pose, pose::Pose const &pose_start, Real const alpha, Real const beta, Real const gamma, Real const x, Real const y, Real const z)
 
void initialize_reference_axes_and_centroid (conformation::Residue const &rsd)
 

Private Member Functions

void initialize_counters ()
 
void search_rotations_and_translations (pose::Pose &pose)
 
void search_translations (pose::Pose &pose, pose::Pose const &pose_to_translate)
 
void setup_heavy_atoms (pose::Pose const &pose, utility::vector1< Vector > &pose_atoms, utility::vector1< Size > const &subset_res)
 
bool check_contact (Vector const &translation, utility::vector1< Vector > const &moving_atoms, utility::vector1< Vector > const &partner_atoms)
 
bool check_steric_overlap (Vector const &translation, utility::vector1< Vector > const &moving_atoms, utility::vector1< Vector > const &partner_atoms)
 
bool check_o2star_needs_optimization (pose::Pose const &pose)
 
bool check_num_hbonds (pose::Pose &pose)
 
bool check_fa_rep (pose::Pose &pose)
 
void save_rigid_body_settings (Real const energy)
 
void figure_out_reference_energy (pose::Pose &pose)
 

Private Attributes

utility::vector1< Size > const fixed_res_
 
utility::vector1< Size > const moving_res_
 
numeric::xyzMatrix< Real > reference_axes_
 
numeric::xyzVector< Real > reference_centroid_
 
core::io::silent::SilentFileDataOP sfd_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP o2star_pack_scorefxn_
 
bool o2star_trials_
 
bool ignore_o2star_hbonds_in_filter_
 
bool assign_WC_edges_
 
Real alpha_
 
Real beta_
 
Real gamma_
 
Real delx_
 
Real dely_
 
Real delz_
 
Real alpha_min_
 
Real alpha_max_
 
Real alpha_increment_
 
Real cosbeta_min_
 
Real cosbeta_max_
 
Real cosbeta_increment_
 
Real gamma_min_
 
Real gamma_max_
 
Real gamma_increment_
 
Real x_min_
 
Real x_max_
 
Real x_increment_
 
Real y_min_
 
Real y_max_
 
Real y_increment_
 
Real z_min_
 
Real z_max_
 
Real z_increment_
 
Real score_cutoff_
 
Real best_energy_
 
Real reference_energy_
 
Size count_total_
 
Size count_good_
 
Size count_no_contact_
 
Size count_clash_
 
Size min_hbonds_
 
Real fa_rep_cutoff_
 
utility::vector1
< utility::vector1< Real > > 		all_rigid_body_settings_save_
 
Real CONTACT_CUTOFF_squared_
 
Real STERIC_DIST_CUTOFF_squared_
 
Size MIN_NUM_CONTACTS_
 
Real rmsd_cutoff_
 
pose::PoseOP native_pose_
 

Detailed Description

Definition at line 43 of file RigidBodySampler.hh.

Constructor & Destructor Documentation

protocols::swa::RigidBodySampler::RigidBodySampler ( utility::vector1< Size > const &  fixed_res,
utility::vector1< Size > const &  moving_res 
)

Definition at line 82 of file RigidBodySampler.cc.

References initialize_counters().

protocols::swa::RigidBodySampler::~RigidBodySampler ( )
virtual

Definition at line 103 of file RigidBodySampler.cc.

Member Function Documentation

void protocols::swa::RigidBodySampler::apply_input_samples ( pose::Pose &  pose,
std::string const  rigid_body_sample_file 
)

Definition at line 359 of file RigidBodySampler.cc.

References apply_rigid_body_settings(), count_total_, and sfd_.

void protocols::swa::RigidBodySampler::apply_rigid_body_settings ( pose::Pose &  pose,
pose::Pose const &  pose_start,
Real const  alpha,
Real const  beta,
Real const  gamma,
Real const  x,
Real const  y,
Real const  z 
)

Definition at line 398 of file RigidBodySampler.cc.

References alpha_, beta_, protocols::swa::create_euler_rotation(), delx_, dely_, delz_, gamma_, moving_res_, reference_axes_, reference_centroid_, protocols::swa::rotate(), and protocols::swa::translate().

Referenced by apply_input_samples().

void protocols::swa::RigidBodySampler::assign_WC_edges_to_base_pair12 ( pose::Pose &  pose,
io::silent::SilentStruct &  s 
)

Definition at line 329 of file RigidBodySampler.cc.

References core::io::silent::SilentStruct::add_energy(), protocols::rna::classify_base_pairs(), core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, core::scoring::rna::Base_pair::res1, and core::scoring::rna::Base_pair::res2.

Referenced by save_silent_struct().

bool protocols::swa::RigidBodySampler::check_contact ( Vector const &  translation,
utility::vector1< Vector > const &  moving_atoms,
utility::vector1< Vector > const &  partner_atoms 
)
private

Definition at line 487 of file RigidBodySampler.cc.

References CONTACT_CUTOFF_squared_, and MIN_NUM_CONTACTS_.

Referenced by search_translations().

bool protocols::swa::RigidBodySampler::check_fa_rep ( pose::Pose &  pose)
private

Definition at line 617 of file RigidBodySampler.cc.

References core::scoring::fa_rep, fa_rep_cutoff_, and core::init().

Referenced by search_translations().

bool protocols::swa::RigidBodySampler::check_num_hbonds ( pose::Pose &  pose)
private

Definition at line 549 of file RigidBodySampler.cc.

References core::chemical::ResidueType::atom_name(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::fill_hbond_set(), fixed_res_, ignore_o2star_hbonds_in_filter_, protocols::swa::in_vector(), min_hbonds_, moving_res_, and core::pose::Pose::residue_type().

Referenced by search_translations().

bool protocols::swa::RigidBodySampler::check_o2star_needs_optimization ( pose::Pose const &  pose)
private

Definition at line 591 of file RigidBodySampler.cc.

References fixed_res_, moving_res_, core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by search_translations().

bool protocols::swa::RigidBodySampler::check_steric_overlap ( Vector const &  translation,
utility::vector1< Vector > const &  moving_atoms,
utility::vector1< Vector > const &  partner_atoms 
)
private

Definition at line 521 of file RigidBodySampler.cc.

References STERIC_DIST_CUTOFF_squared_.

Referenced by search_translations().

void protocols::swa::RigidBodySampler::do_the_sampling ( pose::Pose &  pose)

Definition at line 138 of file RigidBodySampler.cc.

References figure_out_reference_energy(), and search_rotations_and_translations().

void protocols::swa::RigidBodySampler::figure_out_reference_energy ( pose::Pose &  pose)
private

Definition at line 726 of file RigidBodySampler.cc.

References moving_res_, reference_energy_, and protocols::swa::translate().

Referenced by do_the_sampling().

void protocols::swa::RigidBodySampler::force_antiparallel ( )

Definition at line 710 of file RigidBodySampler.cc.

References cosbeta_increment_, cosbeta_max_, and cosbeta_min_.

void protocols::swa::RigidBodySampler::force_coplanar ( )

Definition at line 702 of file RigidBodySampler.cc.

References z_increment_, z_max_, and z_min_.

void protocols::swa::RigidBodySampler::force_parallel ( )

Definition at line 718 of file RigidBodySampler.cc.

References cosbeta_increment_, cosbeta_max_, and cosbeta_min_.

void protocols::swa::RigidBodySampler::initialize_counters ( )
private

Definition at line 107 of file RigidBodySampler.cc.

References all_rigid_body_settings_save_, best_energy_, count_clash_, count_good_, count_no_contact_, count_total_, and reference_energy_.

Referenced by RigidBodySampler().

void protocols::swa::RigidBodySampler::initialize_reference_axes_and_centroid ( conformation::Residue const &  rsd)

Definition at line 124 of file RigidBodySampler.cc.

References reference_axes_, and reference_centroid_.

void protocols::swa::RigidBodySampler::output_histogram ( utility::io::ozstream &  out)

Definition at line 780 of file RigidBodySampler.cc.

References all_rigid_body_settings_save_, alpha_increment_, cosbeta_increment_, count_clash_, count_no_contact_, gamma_increment_, x_increment_, y_increment_, and z_increment_.

void protocols::swa::RigidBodySampler::output_results ( utility::io::ozstream &  out)

Definition at line 736 of file RigidBodySampler.cc.

References all_rigid_body_settings_save_, alpha_increment_, cosbeta_increment_, count_clash_, count_no_contact_, gamma_increment_, x_increment_, y_increment_, and z_increment_.

void protocols::swa::RigidBodySampler::output_silent_file ( std::string const  silent_file,
bool const  write_score_only = false 
)

Definition at line 756 of file RigidBodySampler.cc.

References sfd_.

void protocols::swa::RigidBodySampler::save_rigid_body_settings ( Real const  energy)
private

Definition at line 636 of file RigidBodySampler.cc.

References all_rigid_body_settings_save_, alpha_, beta_, delx_, dely_, delz_, and gamma_.

Referenced by search_translations().

void protocols::swa::RigidBodySampler::save_silent_struct ( pose::Pose &  pose,
std::string const  tag 
)

Definition at line 300 of file RigidBodySampler.cc.

References core::scoring::all_atom_rmsd(), alpha_, alpha_increment_, assign_WC_edges_, assign_WC_edges_to_base_pair12(), beta_, cosbeta_increment_, delx_, dely_, delz_, gamma_, gamma_increment_, native_pose_, rmsd_cutoff_, sfd_, x_increment_, y_increment_, and z_increment_.

Referenced by search_translations().

core::scoring::ScoreFunctionOP protocols::swa::RigidBodySampler::score_function ( )

Definition at line 847 of file RigidBodySampler.cc.

References scorefxn_.

void protocols::swa::RigidBodySampler::search_rotations_and_translations ( pose::Pose &  pose)
private

Definition at line 154 of file RigidBodySampler.cc.

References alpha_, alpha_increment_, alpha_max_, alpha_min_, beta_, cosbeta_increment_, cosbeta_max_, cosbeta_min_, count_good_, count_total_, protocols::swa::create_euler_rotation(), gamma_, gamma_increment_, gamma_max_, gamma_min_, moving_res_, reference_axes_, reference_centroid_, protocols::swa::rotate(), and search_translations().

Referenced by do_the_sampling().

void protocols::swa::RigidBodySampler::search_translations ( pose::Pose &  pose,
pose::Pose const &  pose_to_translate 
)
private

Definition at line 221 of file RigidBodySampler.cc.

References best_energy_, check_contact(), check_fa_rep(), check_num_hbonds(), check_o2star_needs_optimization(), check_steric_overlap(), count_clash_, count_good_, count_no_contact_, count_total_, delx_, dely_, delz_, fa_rep_cutoff_, fixed_res_, ignore_o2star_hbonds_in_filter_, min_hbonds_, moving_res_, protocols::swa::rna::o2star_minimize(), o2star_pack_scorefxn_, o2star_trials_, save_rigid_body_settings(), save_silent_struct(), score_cutoff_, setup_heavy_atoms(), sfd_, protocols::swa::translate(), protocols::swa::virtualize_o2star(), x_increment_, x_max_, x_min_, y_increment_, y_max_, y_min_, z_increment_, z_max_, and z_min_.

Referenced by search_rotations_and_translations().

void protocols::swa::RigidBodySampler::set_alpha_increment ( Real const  setting)
inline

Definition at line 77 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_alpha_max ( Real const  setting)
inline

Definition at line 76 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_alpha_min ( Real const  setting)
inline

Definition at line 75 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_assign_WC_edges ( bool const  setting)
inline

Definition at line 121 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_contact_cutoff ( Real const  setting)

Definition at line 447 of file RigidBodySampler.cc.

References CONTACT_CUTOFF_squared_.

void protocols::swa::RigidBodySampler::set_cosbeta_increment ( Real const  setting)
inline

Definition at line 81 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_cosbeta_max ( Real const  setting)
inline

Definition at line 80 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_cosbeta_min ( Real const  setting)
inline

Definition at line 79 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_fa_rep_cutoff ( Real const  value)
inline

Definition at line 118 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_gamma_increment ( Real const  setting)
inline

Definition at line 85 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_gamma_max ( Real const  setting)
inline

Definition at line 84 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_gamma_min ( Real const  setting)
inline

Definition at line 83 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_ignore_o2star_hbonds_in_filter ( bool const  setting)
inline

Definition at line 120 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_min_hbonds ( Size const  value)
inline

Definition at line 117 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_min_num_contacts ( Size const  setting)

Definition at line 454 of file RigidBodySampler.cc.

References MIN_NUM_CONTACTS_.

void protocols::swa::RigidBodySampler::set_n_sample_alpha_full_range ( Size const  setting)

Definition at line 653 of file RigidBodySampler.cc.

References alpha_increment_, alpha_max_, and alpha_min_.

void protocols::swa::RigidBodySampler::set_n_sample_cosbeta_full_range ( Size const  setting)

Definition at line 669 of file RigidBodySampler.cc.

References cosbeta_increment_, cosbeta_max_, and cosbeta_min_.

void protocols::swa::RigidBodySampler::set_n_sample_gamma_full_range ( Size const  setting)

Definition at line 661 of file RigidBodySampler.cc.

References gamma_increment_, gamma_max_, and gamma_min_.

void protocols::swa::RigidBodySampler::set_native_pose ( pose::PoseOP  native_pose)
inline

Definition at line 69 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_o2star_trials ( bool const  setting)

Definition at line 466 of file RigidBodySampler.cc.

References core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::hbond_lr_bb_sc, core::scoring::hbond_sc, core::scoring::hbond_sr_bb_sc, core::scoring::lk_nonpolar, o2star_pack_scorefxn_, o2star_trials_, and scorefxn_.

void protocols::swa::RigidBodySampler::set_rmsd_cutoff ( Real const  setting)
inline

Definition at line 101 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_score_cutoff ( Real const  setting)
inline

Definition at line 107 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_score_function ( core::scoring::ScoreFunctionOP  setting)
inline

Definition at line 108 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_silent_file_data ( core::io::silent::SilentFileDataOP  sfd)

Definition at line 460 of file RigidBodySampler.cc.

References sfd_.

void protocols::swa::RigidBodySampler::set_steric_dist_cutoff ( Real const  setting)

Definition at line 514 of file RigidBodySampler.cc.

References STERIC_DIST_CUTOFF_squared_.

void protocols::swa::RigidBodySampler::set_translation_sample ( Real const  box_size,
Real const  xyz_increment 
)

Definition at line 683 of file RigidBodySampler.cc.

References x_increment_, x_max_, x_min_, y_increment_, y_max_, y_min_, z_increment_, z_max_, and z_min_.

void protocols::swa::RigidBodySampler::set_x_increment ( Real const  setting)
inline

Definition at line 91 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_x_max ( Real const  setting)
inline

Definition at line 90 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_x_min ( Real const  setting)
inline

Definition at line 89 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_y_increment ( Real const  setting)
inline

Definition at line 95 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_y_max ( Real const  setting)
inline

Definition at line 94 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_y_min ( Real const  setting)
inline

Definition at line 93 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_z_increment ( Real const  setting)
inline

Definition at line 99 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_z_max ( Real const  setting)
inline

Definition at line 98 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::set_z_min ( Real const  setting)
inline

Definition at line 97 of file RigidBodySampler.hh.

void protocols::swa::RigidBodySampler::setup_heavy_atoms ( pose::Pose const &  pose,
utility::vector1< Vector > &  pose_atoms,
utility::vector1< Size > const &  subset_res 
)
private

Definition at line 426 of file RigidBodySampler.cc.

References core::conformation::Residue::is_virtual(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

Referenced by search_translations().

core::io::silent::SilentFileDataOP protocols::swa::RigidBodySampler::silent_file_data ( )
inline

Definition at line 112 of file RigidBodySampler.hh.

Member Data Documentation

utility::vector1< utility::vector1< Real > > protocols::swa::RigidBodySampler::all_rigid_body_settings_save_
private

Definition at line 214 of file RigidBodySampler.hh.

Referenced by initialize_counters(), output_histogram(), output_results(), and save_rigid_body_settings().

Real protocols::swa::RigidBodySampler::alpha_
private

Definition at line 200 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), save_rigid_body_settings(), save_silent_struct(), and search_rotations_and_translations().

Real protocols::swa::RigidBodySampler::alpha_increment_
private

Definition at line 202 of file RigidBodySampler.hh.

Referenced by output_histogram(), output_results(), save_silent_struct(), search_rotations_and_translations(), and set_n_sample_alpha_full_range().

Real protocols::swa::RigidBodySampler::alpha_max_
private

Definition at line 202 of file RigidBodySampler.hh.

Referenced by search_rotations_and_translations(), and set_n_sample_alpha_full_range().

Real protocols::swa::RigidBodySampler::alpha_min_
private

Definition at line 202 of file RigidBodySampler.hh.

Referenced by search_rotations_and_translations(), and set_n_sample_alpha_full_range().

bool protocols::swa::RigidBodySampler::assign_WC_edges_
private

Definition at line 198 of file RigidBodySampler.hh.

Referenced by save_silent_struct().

Real protocols::swa::RigidBodySampler::best_energy_
private

Definition at line 208 of file RigidBodySampler.hh.

Referenced by initialize_counters(), and search_translations().

Real protocols::swa::RigidBodySampler::beta_
private

Definition at line 200 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), save_rigid_body_settings(), save_silent_struct(), and search_rotations_and_translations().

Real protocols::swa::RigidBodySampler::CONTACT_CUTOFF_squared_
private

Definition at line 216 of file RigidBodySampler.hh.

Referenced by check_contact(), and set_contact_cutoff().

Real protocols::swa::RigidBodySampler::cosbeta_increment_
private

Definition at line 203 of file RigidBodySampler.hh.

Referenced by force_antiparallel(), force_parallel(), output_histogram(), output_results(), save_silent_struct(), search_rotations_and_translations(), and set_n_sample_cosbeta_full_range().

Real protocols::swa::RigidBodySampler::cosbeta_max_
private

Definition at line 203 of file RigidBodySampler.hh.

Referenced by force_antiparallel(), force_parallel(), search_rotations_and_translations(), and set_n_sample_cosbeta_full_range().

Real protocols::swa::RigidBodySampler::cosbeta_min_
private

Definition at line 203 of file RigidBodySampler.hh.

Referenced by force_antiparallel(), force_parallel(), search_rotations_and_translations(), and set_n_sample_cosbeta_full_range().

Size protocols::swa::RigidBodySampler::count_clash_
private

Definition at line 210 of file RigidBodySampler.hh.

Referenced by initialize_counters(), output_histogram(), output_results(), and search_translations().

Size protocols::swa::RigidBodySampler::count_good_
private

Definition at line 210 of file RigidBodySampler.hh.

Referenced by initialize_counters(), search_rotations_and_translations(), and search_translations().

Size protocols::swa::RigidBodySampler::count_no_contact_
private

Definition at line 210 of file RigidBodySampler.hh.

Referenced by initialize_counters(), output_histogram(), output_results(), and search_translations().

Size protocols::swa::RigidBodySampler::count_total_
private

Definition at line 210 of file RigidBodySampler.hh.

Referenced by apply_input_samples(), initialize_counters(), search_rotations_and_translations(), and search_translations().

Real protocols::swa::RigidBodySampler::delx_
private

Definition at line 200 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), save_rigid_body_settings(), save_silent_struct(), and search_translations().

Real protocols::swa::RigidBodySampler::dely_
private

Definition at line 200 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), save_rigid_body_settings(), save_silent_struct(), and search_translations().

Real protocols::swa::RigidBodySampler::delz_
private

Definition at line 200 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), save_rigid_body_settings(), save_silent_struct(), and search_translations().

Real protocols::swa::RigidBodySampler::fa_rep_cutoff_
private

Definition at line 212 of file RigidBodySampler.hh.

Referenced by check_fa_rep(), and search_translations().

utility::vector1< Size > const protocols::swa::RigidBodySampler::fixed_res_
private

Definition at line 190 of file RigidBodySampler.hh.

Referenced by check_num_hbonds(), check_o2star_needs_optimization(), and search_translations().

Real protocols::swa::RigidBodySampler::gamma_
private

Definition at line 200 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), save_rigid_body_settings(), save_silent_struct(), and search_rotations_and_translations().

Real protocols::swa::RigidBodySampler::gamma_increment_
private

Definition at line 204 of file RigidBodySampler.hh.

Referenced by output_histogram(), output_results(), save_silent_struct(), search_rotations_and_translations(), and set_n_sample_gamma_full_range().

Real protocols::swa::RigidBodySampler::gamma_max_
private

Definition at line 204 of file RigidBodySampler.hh.

Referenced by search_rotations_and_translations(), and set_n_sample_gamma_full_range().

Real protocols::swa::RigidBodySampler::gamma_min_
private

Definition at line 204 of file RigidBodySampler.hh.

Referenced by search_rotations_and_translations(), and set_n_sample_gamma_full_range().

bool protocols::swa::RigidBodySampler::ignore_o2star_hbonds_in_filter_
private

Definition at line 198 of file RigidBodySampler.hh.

Referenced by check_num_hbonds(), and search_translations().

Size protocols::swa::RigidBodySampler::min_hbonds_
private

Definition at line 211 of file RigidBodySampler.hh.

Referenced by check_num_hbonds(), and search_translations().

Size protocols::swa::RigidBodySampler::MIN_NUM_CONTACTS_
private

Definition at line 217 of file RigidBodySampler.hh.

Referenced by check_contact(), and set_min_num_contacts().

utility::vector1< Size > const protocols::swa::RigidBodySampler::moving_res_
private

Definition at line 191 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), check_num_hbonds(), check_o2star_needs_optimization(), figure_out_reference_energy(), search_rotations_and_translations(), and search_translations().

pose::PoseOP protocols::swa::RigidBodySampler::native_pose_
private

Definition at line 221 of file RigidBodySampler.hh.

Referenced by save_silent_struct().

core::scoring::ScoreFunctionOP protocols::swa::RigidBodySampler::o2star_pack_scorefxn_
private

Definition at line 197 of file RigidBodySampler.hh.

Referenced by search_translations(), and set_o2star_trials().

bool protocols::swa::RigidBodySampler::o2star_trials_
private

Definition at line 198 of file RigidBodySampler.hh.

Referenced by search_translations(), and set_o2star_trials().

numeric::xyzMatrix< Real > protocols::swa::RigidBodySampler::reference_axes_
private

Definition at line 192 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), initialize_reference_axes_and_centroid(), and search_rotations_and_translations().

numeric::xyzVector< Real > protocols::swa::RigidBodySampler::reference_centroid_
private

Definition at line 193 of file RigidBodySampler.hh.

Referenced by apply_rigid_body_settings(), initialize_reference_axes_and_centroid(), and search_rotations_and_translations().

Real protocols::swa::RigidBodySampler::reference_energy_
private

Definition at line 208 of file RigidBodySampler.hh.

Referenced by figure_out_reference_energy(), and initialize_counters().

Real protocols::swa::RigidBodySampler::rmsd_cutoff_
private

Definition at line 219 of file RigidBodySampler.hh.

Referenced by save_silent_struct().

Real protocols::swa::RigidBodySampler::score_cutoff_
private

Definition at line 208 of file RigidBodySampler.hh.

Referenced by search_translations().

core::scoring::ScoreFunctionOP protocols::swa::RigidBodySampler::scorefxn_
private

Definition at line 197 of file RigidBodySampler.hh.

Referenced by score_function(), and set_o2star_trials().

core::io::silent::SilentFileDataOP protocols::swa::RigidBodySampler::sfd_
private

Definition at line 195 of file RigidBodySampler.hh.

Referenced by apply_input_samples(), output_silent_file(), save_silent_struct(), search_translations(), and set_silent_file_data().

Real protocols::swa::RigidBodySampler::STERIC_DIST_CUTOFF_squared_
private

Definition at line 216 of file RigidBodySampler.hh.

Referenced by check_steric_overlap(), and set_steric_dist_cutoff().

Real protocols::swa::RigidBodySampler::x_increment_
private

Definition at line 205 of file RigidBodySampler.hh.

Referenced by output_histogram(), output_results(), save_silent_struct(), search_translations(), and set_translation_sample().

Real protocols::swa::RigidBodySampler::x_max_
private

Definition at line 205 of file RigidBodySampler.hh.

Referenced by search_translations(), and set_translation_sample().

Real protocols::swa::RigidBodySampler::x_min_
private

Definition at line 205 of file RigidBodySampler.hh.

Referenced by search_translations(), and set_translation_sample().

Real protocols::swa::RigidBodySampler::y_increment_
private

Definition at line 206 of file RigidBodySampler.hh.

Referenced by output_histogram(), output_results(), save_silent_struct(), search_translations(), and set_translation_sample().

Real protocols::swa::RigidBodySampler::y_max_
private

Definition at line 206 of file RigidBodySampler.hh.

Referenced by search_translations(), and set_translation_sample().

Real protocols::swa::RigidBodySampler::y_min_
private

Definition at line 206 of file RigidBodySampler.hh.

Referenced by search_translations(), and set_translation_sample().

Real protocols::swa::RigidBodySampler::z_increment_
private

Definition at line 207 of file RigidBodySampler.hh.

Referenced by force_coplanar(), output_histogram(), output_results(), save_silent_struct(), search_translations(), and set_translation_sample().

Real protocols::swa::RigidBodySampler::z_max_
private

Definition at line 207 of file RigidBodySampler.hh.

Referenced by force_coplanar(), search_translations(), and set_translation_sample().

Real protocols::swa::RigidBodySampler::z_min_
private

Definition at line 207 of file RigidBodySampler.hh.

Referenced by force_coplanar(), search_translations(), and set_translation_sample().

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