Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::legacy::modeler::RigidBodySampler Class Reference

#include <RigidBodySampler.hh>

Public Member Functions

 RigidBodySampler (utility::vector1< Size > const &fixed_res, utility::vector1< Size > const &moving_res)
 
virtual ~RigidBodySampler ()
 
void do_the_modeler (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_o2prime_trials (bool const setting)
 
void set_ignore_o2prime_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_o2prime_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< Realreference_axes_
 
numeric::xyzVector< Realreference_centroid_
 
core::io::silent::SilentFileDataOP sfd_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP o2prime_pack_scorefxn_
 
bool o2prime_trials_
 
bool ignore_o2prime_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_
 

Constructor & Destructor Documentation

protocols::stepwise::legacy::modeler::RigidBodySampler::RigidBodySampler ( utility::vector1< Size > const &  fixed_res,
utility::vector1< Size > const &  moving_res 
)
protocols::stepwise::legacy::modeler::RigidBodySampler::~RigidBodySampler ( )
virtual

Member Function Documentation

void protocols::stepwise::legacy::modeler::RigidBodySampler::apply_input_samples ( pose::Pose pose,
std::string const  rigid_body_sample_file 
)
void protocols::stepwise::legacy::modeler::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 
)
void protocols::stepwise::legacy::modeler::RigidBodySampler::assign_WC_edges_to_base_pair12 ( pose::Pose pose,
io::silent::SilentStruct s 
)

References classify_base_pairs().

Referenced by save_silent_struct().

bool protocols::stepwise::legacy::modeler::RigidBodySampler::check_contact ( Vector const &  translation,
utility::vector1< Vector > const &  moving_atoms,
utility::vector1< Vector > const &  partner_atoms 
)
private
bool protocols::stepwise::legacy::modeler::RigidBodySampler::check_fa_rep ( pose::Pose pose)
private
bool protocols::stepwise::legacy::modeler::RigidBodySampler::check_num_hbonds ( pose::Pose pose)
private
bool protocols::stepwise::legacy::modeler::RigidBodySampler::check_o2prime_needs_optimization ( pose::Pose const &  pose)
private
bool protocols::stepwise::legacy::modeler::RigidBodySampler::check_steric_overlap ( Vector const &  translation,
utility::vector1< Vector > const &  moving_atoms,
utility::vector1< Vector > const &  partner_atoms 
)
private
void protocols::stepwise::legacy::modeler::RigidBodySampler::do_the_modeler ( pose::Pose pose)
void protocols::stepwise::legacy::modeler::RigidBodySampler::figure_out_reference_energy ( pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::RigidBodySampler::force_antiparallel ( )
void protocols::stepwise::legacy::modeler::RigidBodySampler::force_coplanar ( )

References z_increment_, z_max_, and z_min_.

void protocols::stepwise::legacy::modeler::RigidBodySampler::force_parallel ( )
void protocols::stepwise::legacy::modeler::RigidBodySampler::initialize_counters ( )
private
void protocols::stepwise::legacy::modeler::RigidBodySampler::initialize_reference_axes_and_centroid ( conformation::Residue const &  rsd)
void protocols::stepwise::legacy::modeler::RigidBodySampler::output_histogram ( utility::io::ozstream out)
void protocols::stepwise::legacy::modeler::RigidBodySampler::output_results ( utility::io::ozstream out)
void protocols::stepwise::legacy::modeler::RigidBodySampler::output_silent_file ( std::string const  silent_file,
bool const  write_score_only = false 
)
void protocols::stepwise::legacy::modeler::RigidBodySampler::save_rigid_body_settings ( Real const  energy)
private
void protocols::stepwise::legacy::modeler::RigidBodySampler::save_silent_struct ( pose::Pose pose,
std::string const  tag 
)
core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::RigidBodySampler::score_function ( )

References scorefxn_.

void protocols::stepwise::legacy::modeler::RigidBodySampler::search_rotations_and_translations ( pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::RigidBodySampler::search_translations ( pose::Pose pose,
pose::Pose const &  pose_to_translate 
)
private
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_alpha_increment ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_alpha_max ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_alpha_min ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_assign_WC_edges ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_contact_cutoff ( Real const  setting)
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_cosbeta_increment ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_cosbeta_max ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_cosbeta_min ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_fa_rep_cutoff ( Real const  value)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_gamma_increment ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_gamma_max ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_gamma_min ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_ignore_o2prime_hbonds_in_filter ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_min_hbonds ( Size const  value)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_min_num_contacts ( Size const  setting)

References MIN_NUM_CONTACTS_.

void protocols::stepwise::legacy::modeler::RigidBodySampler::set_n_sample_alpha_full_range ( Size const  setting)
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_n_sample_cosbeta_full_range ( Size const  setting)
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_n_sample_gamma_full_range ( Size const  setting)
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_native_pose ( pose::PoseOP  native_pose)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_o2prime_trials ( bool const  setting)
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_rmsd_cutoff ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_score_cutoff ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_score_function ( core::scoring::ScoreFunctionOP  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_silent_file_data ( core::io::silent::SilentFileDataOP  sfd)

References sfd_.

void protocols::stepwise::legacy::modeler::RigidBodySampler::set_steric_dist_cutoff ( Real const  setting)
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_translation_sample ( Real const  box_size,
Real const  xyz_increment 
)
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_x_increment ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_x_max ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_x_min ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_y_increment ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_y_max ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_y_min ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_z_increment ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_z_max ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::set_z_min ( Real const  setting)
inline
void protocols::stepwise::legacy::modeler::RigidBodySampler::setup_heavy_atoms ( pose::Pose const &  pose,
utility::vector1< Vector > &  pose_atoms,
utility::vector1< Size > const &  subset_res 
)
private
core::io::silent::SilentFileDataOP protocols::stepwise::legacy::modeler::RigidBodySampler::silent_file_data ( )
inline

Member Data Documentation

utility::vector1< utility::vector1< Real > > protocols::stepwise::legacy::modeler::RigidBodySampler::all_rigid_body_settings_save_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::alpha_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::alpha_increment_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::alpha_max_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::alpha_min_
private
bool protocols::stepwise::legacy::modeler::RigidBodySampler::assign_WC_edges_
private

Referenced by save_silent_struct().

Real protocols::stepwise::legacy::modeler::RigidBodySampler::best_energy_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::beta_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::CONTACT_CUTOFF_squared_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::cosbeta_increment_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::cosbeta_max_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::cosbeta_min_
private
Size protocols::stepwise::legacy::modeler::RigidBodySampler::count_clash_
private
Size protocols::stepwise::legacy::modeler::RigidBodySampler::count_good_
private
Size protocols::stepwise::legacy::modeler::RigidBodySampler::count_no_contact_
private
Size protocols::stepwise::legacy::modeler::RigidBodySampler::count_total_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::delx_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::dely_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::delz_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::fa_rep_cutoff_
private
utility::vector1< Size > const protocols::stepwise::legacy::modeler::RigidBodySampler::fixed_res_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::gamma_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::gamma_increment_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::gamma_max_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::gamma_min_
private
bool protocols::stepwise::legacy::modeler::RigidBodySampler::ignore_o2prime_hbonds_in_filter_
private
Size protocols::stepwise::legacy::modeler::RigidBodySampler::min_hbonds_
private
Size protocols::stepwise::legacy::modeler::RigidBodySampler::MIN_NUM_CONTACTS_
private
utility::vector1< Size > const protocols::stepwise::legacy::modeler::RigidBodySampler::moving_res_
private
pose::PoseOP protocols::stepwise::legacy::modeler::RigidBodySampler::native_pose_
private

Referenced by save_silent_struct().

core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::RigidBodySampler::o2prime_pack_scorefxn_
private
bool protocols::stepwise::legacy::modeler::RigidBodySampler::o2prime_trials_
private
numeric::xyzMatrix< Real > protocols::stepwise::legacy::modeler::RigidBodySampler::reference_axes_
private
numeric::xyzVector< Real > protocols::stepwise::legacy::modeler::RigidBodySampler::reference_centroid_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::reference_energy_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::rmsd_cutoff_
private

Referenced by save_silent_struct().

Real protocols::stepwise::legacy::modeler::RigidBodySampler::score_cutoff_
private

Referenced by search_translations().

core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::RigidBodySampler::scorefxn_
private
core::io::silent::SilentFileDataOP protocols::stepwise::legacy::modeler::RigidBodySampler::sfd_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::STERIC_DIST_CUTOFF_squared_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::x_increment_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::x_max_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::x_min_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::y_increment_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::y_max_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::y_min_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::z_increment_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::z_max_
private
Real protocols::stepwise::legacy::modeler::RigidBodySampler::z_min_
private

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