#include <RigidBodySampler.hh>

Inheritance diagram for protocols::swa::RigidBodySampler:

Collaboration diagram for protocols::swa::RigidBodySampler:

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_

Constructor & Destructor Documentation

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

References initialize_counters().

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

virtual

Member Function Documentation

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

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
	)

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
	)

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

References CONTACT_CUTOFF_squared_, and MIN_NUM_CONTACTS_.

Referenced by search_translations().

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

private

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

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

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

References STERIC_DIST_CUTOFF_squared_.

Referenced by search_translations().

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

References figure_out_reference_energy(), and search_rotations_and_translations().

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

private

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

Referenced by do_the_sampling().

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

References cosbeta_increment_, cosbeta_max_, and cosbeta_min_.

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

References z_increment_, z_max_, and z_min_.

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

References cosbeta_increment_, cosbeta_max_, and cosbeta_min_.

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

private

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)

References reference_axes_, and reference_centroid_.

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

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)

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`
	)

References sfd_.

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

private

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
	)

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 ( )

References scorefxn_.

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

private

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

private

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

inline

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

inline

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

inline

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

inline

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

References CONTACT_CUTOFF_squared_.

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

References MIN_NUM_CONTACTS_.

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

References alpha_increment_, alpha_max_, and alpha_min_.

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

References cosbeta_increment_, cosbeta_max_, and cosbeta_min_.

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

References gamma_increment_, gamma_max_, and gamma_min_.

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

inline

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

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

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

inline

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

inline

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

References sfd_.

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

References STERIC_DIST_CUTOFF_squared_.

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

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

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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

inline

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