james_util.hh File Reference

#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/id/NamedAtomID.hh>
#include <basic/database/open.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/MatrixScoringScheme.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <protocols/jumping/util.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <cmath>
#include <core/id/AtomID.hh>

Classes
class	DistancePrediction
class	DistanceMatrix
class	TorsionList

Functions
utility::vector1< utility::vector1< core::Real > >	get_ca_distances (core::pose::Pose pose, std::string const &atom_name)
utility::vector1< int >	calculate_burial (core::pose::Pose &mypose, core::Real const dist_cutoff)
utility::vector1< int >	calculate_burial (core::pose::Pose &mypose)
utility::vector1< core::Real >	calc_blosum_scores (core::sequence::SequenceAlignment const &aln)
utility::vector1< char >	get_ss (core::pose::Pose &pose)
core::Real	mean (utility::vector1< core::Real > const values)
core::Real	sd (utility::vector1< core::Real > const values)
core::pose::PoseOP	get_pose_by_id (std::string const &id)
utility::vector1< core::Real >	calc_dgaps (core::sequence::SequenceAlignment const &aln)

Detailed Description

Author

James Thompson

Function Documentation

calc_blosum_scores()

utility::vector1< core::Real > calc_blosum_scores

(

core::sequence::SequenceAlignment const &

aln

)

References aln, create_a3b_hbs::ii, basic::database::open(), create_a3b_hbs::score, legacy_score_vs_rmsd::scores, and basic::options::OptionKeys::relax::sequence.

Referenced by main().

calc_dgaps()

utility::vector1< core::Real > calc_dgaps

(

core::sequence::SequenceAlignment const &

aln

)

References ObjexxFCL::abs(), aln, end, and create_a3b_hbs::ii.

Referenced by main().

calculate_burial() [1/2]

utility::vector1< int > calculate_burial

(

core::pose::Pose &

mypose

)

References calculate_burial().

calculate_burial() [2/2]

utility::vector1< int > calculate_burial	(	core::pose::Pose &	mypose,
		core::Real const	dist_cutoff
	)

References basic::options::OptionKeys::in::file::burial, dist(), dist_cutoff, create_a3b_hbs::i, create_a3b_hbs::j, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

Referenced by calculate_burial().

get_ca_distances()

utility::vector1< utility::vector1< core::Real > > get_ca_distances	(	core::pose::Pose	pose,
		std::string const &	atom_name
	)

References create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

get_pose_by_id()

core::pose::PoseOP get_pose_by_id

(

std::string const &

id

)

References basic::options::OptionKeys::chemical::chemical, utility::file::file_exists(), subloop_histogram::iterator, pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::prefix, basic::options::OptionKeys::in::file::residue_type_set, and utility_exit_with_message.

Referenced by main().

get_ss()

utility::vector1< char > get_ss

(

core::pose::Pose &

pose

)

References create_a3b_hbs::ii, beta_nonlocal::pose, and challenge::ss.

mean()

core::Real mean

(

utility::vector1< core::Real > const

values

)

References end, and test.T040_Types::values.

Referenced by sd().

sd()

core::Real sd

(

utility::vector1< core::Real > const

values

)

References erraser_analysis::diff, end, mean(), and test.T040_Types::values.

Referenced by add_agc(), add_apc(), add_dhc(), ConstraintConfig::add_sym_cst(), add_symm_sf4(), add_symm_zns(), CA_cst_generator(), calc_dist(), MatchSet::cross_homodimer(), utility::options::ScalarOption_T_< K, T >::description(), get_rmsd(), main(), ConstraintConfig::parse_config_file(), pep_rmsd_analysis(), Bola::random_close_phipsi_from_rama(), rmsd_compute(), utility::options::ScalarOption_T_< K, T >::short_description(), and utility::options::VectorOption_T_< K, T >::short_description().