protocols::MakeRotLib Namespace Reference

Classes
class	RotData

Typedefs
typedef utility::vector1< RotData >	RotVec

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	peptoid_trans_hack (RotVec &rotamers)
void	peptoid_cis_hack (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 omega_start_val, Real epsilon_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)

Typedef Documentation

typedef utility::vector1<RotData> protocols::MakeRotLib::RotVec

Definition at line 33 of file MakeRotLib.hh.

Function Documentation

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

Definition at line 65 of file MakeRotLib.cc.

Referenced by core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), calc_dist(), core::pack::dunbrack::DunbrackRotamerSampleData::chi_probability(), core::scoring::mm::MMBondAngleScore::dscore(), and core::scoring::mm::MMBondAngleScore::score().

void protocols::MakeRotLib::asp_corrections

(

RotVec &

rotamers)

Definition at line 74 of file MakeRotLib.cc.

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

Definition at line 535 of file MakeRotLib.cc.

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

Definition at line 569 of file MakeRotLib.cc.

References calc_dist().

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

Definition at line 474 of file MakeRotLib.cc.

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

Definition at line 522 of file MakeRotLib.cc.

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

Referenced by calc_all_dist().

bool protocols::MakeRotLib::calc_rotamer_clusters

(

RotVec &

rotamers)

Definition at line 456 of file MakeRotLib.cc.

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

Definition at line 640 of file MakeRotLib.cc.

References protocols::simple_moves::MinMover::apply(), core::id::BB, core::io::pdb::dump_pdb(), core::chemical::FA_STANDARD, and core::chemical::ChemicalManager::get_instance().

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

Definition at line 799 of file MakeRotLib.cc.

References protocols::swa::phi(), and protocols::swa::psi().

void protocols::MakeRotLib::get_final_rot_probs

(

RotVec &

final_rotamers)

Definition at line 601 of file MakeRotLib.cc.

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

Definition at line 581 of file MakeRotLib.cc.

void protocols::MakeRotLib::glu_corrections

(

RotVec &

rotamers)

Definition at line 87 of file MakeRotLib.cc.

void protocols::MakeRotLib::init_rotamers_centroids	(	RotVec &	rotamers,
		RotVec &	centroids,
		Size &	ncluster,
		std::string	options_filename,
		std::string &	aa_name,
		bool	is_peptoid,
		Real	omega_start_val,
		Real	epsilon_start_val
	)

Definition at line 262 of file MakeRotLib.cc.

References protocols::swa::rna::file_exists(), protocols::MakeRotLib::RotData::set_inp_chi(), protocols::MakeRotLib::RotData::set_lib_chi_val(), and protocols::MakeRotLib::RotData::set_min_chi().

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

Definition at line 144 of file MakeRotLib.cc.

References protocols::simple_moves::MinMover::apply(), core::id::BB, core::scoring::fa_sol, core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::scoring::mm_lj_inter_atr, core::scoring::mm_lj_inter_rep, core::scoring::mm_lj_intra_atr, core::scoring::mm_lj_intra_rep, and core::scoring::mm_twist.

void protocols::MakeRotLib::peptoid_cis_hack

(

RotVec &

rotamers)

Definition at line 130 of file MakeRotLib.cc.

References protocols::loops::start.

void protocols::MakeRotLib::peptoid_trans_hack

(

RotVec &

rotamers)

Definition at line 113 of file MakeRotLib.cc.

References protocols::loops::start.

void protocols::MakeRotLib::phe_tyr_corrections

(

RotVec &

rotamers)

Definition at line 100 of file MakeRotLib.cc.

void protocols::MakeRotLib::pretty_print_rd

(

RotData &

rot)

Definition at line 745 of file MakeRotLib.cc.

References protocols::MakeRotLib::RotData::get_cen_dist(), protocols::MakeRotLib::RotData::get_cluster_num(), protocols::MakeRotLib::RotData::get_energy(), protocols::MakeRotLib::RotData::get_inp_chi(), protocols::MakeRotLib::RotData::get_intra_atr(), protocols::MakeRotLib::RotData::get_intra_rep(), protocols::MakeRotLib::RotData::get_min_chi(), protocols::MakeRotLib::RotData::get_min_epsilon(), protocols::MakeRotLib::RotData::get_min_omega(), protocols::MakeRotLib::RotData::get_num_chi(), protocols::MakeRotLib::RotData::get_num_clusters(), protocols::MakeRotLib::RotData::get_phi(), protocols::MakeRotLib::RotData::get_probability(), protocols::MakeRotLib::RotData::get_psi(), protocols::MakeRotLib::RotData::get_std_dev(), and protocols::MakeRotLib::RotData::get_twist().