protocols::make_rot_lib Namespace Reference

Classes
struct	CentroidRotNum
class	MakeRotLibJob
class	MakeRotLibJobInputter
class	MakeRotLibJobInputterCreator
class	MakeRotLibMover
class	MakeRotLibOptionsData
class	RotData
struct	running_average_pair
	struct that is used in calc_centroids, values init to zero More...
struct	TorsionRange

Typedefs
typedef utility::pointer::shared_ptr < MakeRotLibJob >	MakeRotLibJobOP
typedef utility::pointer::shared_ptr < MakeRotLibJob const >	MakeRotLibJobCOP
typedef utility::pointer::shared_ptr < MakeRotLibJobInputter >	MakeRotLibJobInputterOP
typedef utility::pointer::shared_ptr < MakeRotLibJobInputter const >	MakeRotLibJobInputterCOP
typedef utility::pointer::shared_ptr < MakeRotLibMover >	MakeRotLibMoverOP
typedef utility::pointer::shared_ptr < MakeRotLibMover const >	MakeRotLibMoverCOP
typedef utility::pointer::shared_ptr < MakeRotLibOptionsData >	MakeRotLibOptionsDataOP
typedef utility::pointer::shared_ptr < MakeRotLibOptionsData const >	MakeRotLibOptionsDataCOP
typedef utility::vector1 < TorsionRange >	TorsionRangeVec
typedef utility::vector1 < TorsionRangeVec >	TorsionRangeVecVec
typedef utility::vector1 < CentroidRotNum >	CentroidRotNumVec
typedef utility::vector1 < CentroidRotNumVec >	CentroidRotNumVecVec
typedef utility::vector1< RotData >	RotDataVec
typedef RotDataVec	RotVec

Enumerations
enum	MakeRotLibPolymerType { PEPTIDE, PEPTOID }

Functions
Real	angle_diff (Real a1, Real a2)
void	asp_corrections (RotVec &rotamers)
void	glu_corrections (RotVec &rotamers)
void	phe_tyr_corrections (RotVec &rotamers)
void	min_rotamers (RotVec &rotamers, core::scoring::ScoreFunctionOP scrfxn, std::string aa_name)
void	init_rotamers_centroids (RotVec &rotamers, RotVec &centroids, Size &ncluster, std::string options_filename, std::string &aa_name, bool is_peptoid, Real omg_start_val, Real eps_start_val)
bool	calc_rotamer_clusters (RotVec &rotamers)
bool	calc_centroids (RotVec &rotamers, RotVec &centroids)
Real	calc_dist (RotData &point1, RotData &point2)
Real	avg_cluster_cen_dist (RotVec &rotamers, Size &ncluster)
void	calc_all_dist (RotVec &rotamers, RotVec &centroids)
void	get_final_rots (RotVec &rotamers, RotVec &final_rotamers, Size &nclusters)
void	get_final_rot_probs (RotVec &final_rotamers)
void	calc_std_dev (RotVec &final_rotamers, core::scoring::ScoreFunctionOP scrfxn, std::string aa_name)
void	pretty_print_rd (RotData &rot)
void	dunbrack_print (RotVec &final_rotamers, RotVec &centroids, std::string aa_name_full)
static thread_local basic::Tracer	TR ("protocols.make_rot_lib.MakeRotLibJobInputter")
static thread_local basic::Tracer	TR ("protocols.make_rot_lib.MakeRotLibMover")
static thread_local basic::Tracer	TR ("protocols.make_rot_lib.MakeRotLibOptionsData")
static thread_local basic::Tracer	TR ("protocols.make_rot_lib.RotData")

Typedef Documentation

typedef utility::vector1< CentroidRotNum > protocols::make_rot_lib::CentroidRotNumVec

typedef utility::vector1< CentroidRotNumVec > protocols::make_rot_lib::CentroidRotNumVecVec

typedef utility::pointer::shared_ptr< MakeRotLibJob const > protocols::make_rot_lib::MakeRotLibJobCOP

typedef utility::pointer::shared_ptr< MakeRotLibJobInputter const > protocols::make_rot_lib::MakeRotLibJobInputterCOP

typedef utility::pointer::shared_ptr< MakeRotLibJobInputter > protocols::make_rot_lib::MakeRotLibJobInputterOP

typedef utility::pointer::shared_ptr< MakeRotLibJob > protocols::make_rot_lib::MakeRotLibJobOP

typedef utility::pointer::shared_ptr< MakeRotLibMover const > protocols::make_rot_lib::MakeRotLibMoverCOP

typedef utility::pointer::shared_ptr< MakeRotLibMover > protocols::make_rot_lib::MakeRotLibMoverOP

typedef utility::pointer::shared_ptr< MakeRotLibOptionsData const > protocols::make_rot_lib::MakeRotLibOptionsDataCOP

typedef utility::pointer::shared_ptr< MakeRotLibOptionsData > protocols::make_rot_lib::MakeRotLibOptionsDataOP

typedef utility::vector1<RotData> protocols::make_rot_lib::RotDataVec

typedef RotDataVec protocols::make_rot_lib::RotVec

typedef utility::vector1< TorsionRange > protocols::make_rot_lib::TorsionRangeVec

typedef utility::vector1< TorsionRangeVec > protocols::make_rot_lib::TorsionRangeVecVec

Enumeration Type Documentation

enum protocols::make_rot_lib::MakeRotLibPolymerType

Enumerator
PEPTIDE
PEPTOID

Function Documentation

Real protocols::make_rot_lib::angle_diff	(	Real	a1,
		Real	a2
	)

Referenced by calc_dist().

void protocols::make_rot_lib::asp_corrections

(

RotVec &

rotamers

)

core::Real protocols::make_rot_lib::avg_cluster_cen_dist	(	RotVec &	rotamers,
		Size &	ncluster
	)

void protocols::make_rot_lib::calc_all_dist	(	RotVec &	rotamers,
		RotVec &	centroids
	)

References calc_dist().

bool protocols::make_rot_lib::calc_centroids	(	RotVec &	rotamers,
		RotVec &	centroids
	)

core::Real protocols::make_rot_lib::calc_dist	(	RotData &	point1,
		RotData &	point2
	)

References angle_diff(), protocols::make_rot_lib::RotData::get_min_chi(), and protocols::make_rot_lib::RotData::get_num_chi().

Referenced by calc_all_dist().

bool protocols::make_rot_lib::calc_rotamer_clusters

(

RotVec &

rotamers

)

void protocols::make_rot_lib::calc_std_dev	(	RotVec &	final_rotamers,
		core::scoring::ScoreFunctionOP	scrfxn,
		std::string	aa_name
	)

References protocols::simple_moves::MinMover::apply(), FA_STANDARD, and numeric::nonnegative_principal_angle_degrees().

void protocols::make_rot_lib::dunbrack_print	(	RotVec &	final_rotamers,
		RotVec &	centroids,
		std::string	aa_name_full
	)

References max(), and numeric::principal_angle_degrees().

void protocols::make_rot_lib::get_final_rot_probs

(

RotVec &

final_rotamers

)

void protocols::make_rot_lib::get_final_rots	(	RotVec &	rotamers,
		RotVec &	final_rotamers,
		Size &	nclusters
	)

void protocols::make_rot_lib::glu_corrections

(

RotVec &

rotamers

)

void protocols::make_rot_lib::init_rotamers_centroids	(	RotVec &	rotamers,
		RotVec &	centroids,
		Size &	ncluster,
		std::string	options_filename,
		std::string &	aa_name,
		bool	is_peptoid,
		Real	omg_start_val,
		Real	eps_start_val
	)

References utility::file::file_exists(), getline(), options, protocols::make_rot_lib::RotData::set_inp_chi(), protocols::make_rot_lib::RotData::set_lib_chi_val(), protocols::make_rot_lib::RotData::set_min_chi(), and utility_exit_with_message.

void protocols::make_rot_lib::min_rotamers	(	RotVec &	rotamers,
		core::scoring::ScoreFunctionOP	scrfxn,
		std::string	aa_name
	)

References core::pose::Pose::append_residue_by_jump(), protocols::simple_moves::MinMover::apply(), core::pose::Pose::chi(), core::pose::Pose::energies(), fa_sol, FA_STANDARD, mm_lj_inter_atr, mm_lj_inter_rep, mm_lj_intra_atr, mm_lj_intra_rep, mm_twist, numeric::nonnegative_principal_angle_degrees(), core::scoring::Energies::residue_total_energies(), core::pose::Pose::set_chi(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::scoring::Energies::total_energy().

void protocols::make_rot_lib::phe_tyr_corrections

(

RotVec &

rotamers

)

void protocols::make_rot_lib::pretty_print_rd

(

RotData &

rot

)

References cout, protocols::make_rot_lib::RotData::get_cen_dist(), protocols::make_rot_lib::RotData::get_cluster_num(), protocols::make_rot_lib::RotData::get_energy(), protocols::make_rot_lib::RotData::get_inp_chi(), protocols::make_rot_lib::RotData::get_intra_atr(), protocols::make_rot_lib::RotData::get_intra_rep(), protocols::make_rot_lib::RotData::get_min_chi(), protocols::make_rot_lib::RotData::get_min_eps(), protocols::make_rot_lib::RotData::get_min_omg(), protocols::make_rot_lib::RotData::get_num_chi(), protocols::make_rot_lib::RotData::get_num_clusters(), protocols::make_rot_lib::RotData::get_phi(), protocols::make_rot_lib::RotData::get_probability(), protocols::make_rot_lib::RotData::get_psi(), protocols::make_rot_lib::RotData::get_std_dev(), and protocols::make_rot_lib::RotData::get_twist().

static thread_local basic::Tracer protocols::make_rot_lib::TR ( "protocols.make_rot_lib.RotData"  )

static

static thread_local basic::Tracer protocols::make_rot_lib::TR ( "protocols.make_rot_lib.MakeRotLibOptionsData"  )

static

static thread_local basic::Tracer protocols::make_rot_lib::TR ( "protocols.make_rot_lib.MakeRotLibJobInputter"  )

static

Referenced by protocols::make_rot_lib::MakeRotLibMover::apply(), protocols::make_rot_lib::MakeRotLibMover::calc_final_rotamer_probs(), protocols::make_rot_lib::MakeRotLibMover::calc_standard_deviations(), protocols::make_rot_lib::MakeRotLibJobInputter::fill_jobs(), protocols::make_rot_lib::RotData::load(), protocols::make_rot_lib::MakeRotLibJobInputter::MakeRotLibJobInputter(), protocols::make_rot_lib::MakeRotLibMover::MakeRotLibMover(), protocols::make_rot_lib::MakeRotLibMover::minimize_all_rotamers(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), and protocols::make_rot_lib::MakeRotLibJobInputter::pose_from_job().

static thread_local basic::Tracer protocols::make_rot_lib::TR ( "protocols.make_rot_lib.MakeRotLibMover"  )

static