Translator.cc File Reference

Chemical manager class. More...

#include <core/coarse/Translator.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/DunbrackRotamer.hh>
#include <core/pack/dunbrack/CoarseRotamer.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/conformation/Residue.hh>
#include <core/id/DOF_ID.hh>
#include <numeric/NumericTraits.hh>

Functions
std::string	strip_whitespace (std::string const &name)
	must be a better place for this, already exists in ResidueType.cc! More...
bool	match_mask (RotVector const &mask, int nchi, DunbrackRotamer< FOUR, Real > const &rotamer)
bool	update_mask (RotVector &mask, int nchi, RotVector const &max_bins)
pose::PoseOP	create_rotamer (Translator const &map, ResidueTypeCOP fine_res_type, DunbrackRotamer< FOUR, Real > const &rotamer)
int	find_most_frequent_rotamer (utility::vector1< DunbrackRotamer< FOUR > > const &fine_rotamers, RotVector const &mask, Size nchi, Real &pnew)
void	coarse_rotamer (Translator const &map, ResidueTypeCOP fine_res_type, ResidueTypeCOP coarse_res_type, DunbrackRotamer< FOUR, Real > const &rotamer, Size nchi, ChiVector &chi, AngleVector &angle)
void	average_rotamers (Translator const &map, ResidueTypeCOP fine_res_type, ResidueTypeCOP coarse_res_type, utility::vector1< DunbrackRotamer< FOUR > > const &fine_rotamers, RotVector const &mask, Size nchi, ChiVector &chi_mean, ChiVector &chi_std, AngleVector &angle_mean, AngleVector &angle_std)
Real	sqr (Real x)
Real	sqr3 (Real x)

Detailed Description

Chemical manager class.

Author

Oliver Lange (olang.nosp@m.e@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu)

Function Documentation

void average_rotamers	(	Translator const &	map,
		ResidueTypeCOP	fine_res_type,
		ResidueTypeCOP	coarse_res_type,
		utility::vector1< DunbrackRotamer< FOUR > > const &	fine_rotamers,
		RotVector const &	mask,
		Size	nchi,
		ChiVector &	chi_mean,
		ChiVector &	chi_std,
		AngleVector &	angle_mean,
		AngleVector &	angle_std
	)

References coarse_rotamer(), core::pack::dunbrack::increase_rotamer_precision(), match_mask(), numeric::NumericTraits< class >::pi(), sqr(), and sqr3().

void coarse_rotamer	(	Translator const &	map,
		ResidueTypeCOP	fine_res_type,
		ResidueTypeCOP	coarse_res_type,
		DunbrackRotamer< FOUR, Real > const &	rotamer,
		Size	nchi,
		ChiVector &	chi,
		AngleVector &	angle
	)

References create_rotamer(), numeric::NumericTraits< class >::pi(), and core::id::THETA.

Referenced by average_rotamers().

pose::PoseOP create_rotamer	(	Translator const &	map,
		ResidueTypeCOP	fine_res_type,
		DunbrackRotamer< FOUR, Real > const &	rotamer
	)

References core::pose::Pose::clear(), and core::coarse::Translator::coarsify().

Referenced by coarse_rotamer().

int find_most_frequent_rotamer	(	utility::vector1< DunbrackRotamer< FOUR > > const &	fine_rotamers,
		RotVector const &	mask,
		Size	nchi,
		Real &	pnew
	)

References core::pack::dunbrack::increase_rotamer_precision(), and match_mask().

bool match_mask	(	RotVector const &	mask,
		int	nchi,
		DunbrackRotamer< FOUR, Real > const &	rotamer
	)

Referenced by average_rotamers(), and find_most_frequent_rotamer().

Real sqr ( Real  x )

inline

Referenced by average_rotamers().

Real sqr3 ( Real  x )

inline

Referenced by average_rotamers().

std::string strip_whitespace ( std::string const &  name )

inline

must be a better place for this, already exists in ResidueType.cc!

References trim().

Referenced by core::coarse::Translator::add_atom(), core::util::add_covalent_linkage_helper(), core::io::pdb::bonding_distance_threshold(), core::io::pdb::PDB_DReader::createFileData(), core::coarse::Translator::map_atom_to_bead(), core::io::pdb::GeometricRenameVerticiesEquivalent::operator()(), core::sequence::read_fasta_file(), core::io::rna::RDAT::read_rdat_file(), core::chemical::read_topology_file(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::io::pdb::FileData::store_heterogen_names(), and core::io::pdb::HeaderInformation::store_title().

bool update_mask	(	RotVector &	mask,
		int	nchi,
		RotVector const &	max_bins
	)