Rosetta 3.4
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core::coarse::Translator Class Reference

#include <Translator.hh>

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List of all members.

Classes

struct  BeadAtom

Public Types

typedef std::vector< BeadAtomAtomList
typedef std::vector< AtomListBeadList
typedef std::vector< std::string > BeadNames

Public Member Functions

 Translator (RuleSet const &rules, chemical::ResidueTypeCAP fine_res, chemical::ResidueTypeAP coarse_res)
 constructor
void pretty_print (std::ostream &os) const
int map_atom_to_bead (std::string const atom) const
 returns bead index for 'atom' in the fine-grained residue, e.g. 1 for CB, HB1, HB2, ...
int coarse_nchi () const
 number of chi-angles in coarse residue
std::string const & name () const
 residue_type ID (they are the same for coarse and fine, return either)
conformation::ResidueOP coarsify (const conformation::Residue &fine) const
 return a coarse residue with coordinates computed from the fine residue
pack::dunbrack::SingleResidueRotamerLibraryCOP get_RotamerLibrary () const
 return a DunbrackRotamerLibrary, Rotamer's and their statistics are computed from the fine residues
pack::dunbrack::CoarseRotamerSetOP coarsify (utility::vector1< pack::dunbrack::DunbrackRotamer< pack::dunbrack::FOUR > > const &fine_rotamers) const
 compute a coarse DunbrackLibrary from a fine RotamerLibrary (not inlined, to avoid circular includes)

Protected Member Functions

void add_atom (AtomList &list, const chemical::ResidueType &res, Rule::AtomToken const &atom)
 add BeadAtom to AtomList
void add_atom (AtomList &list, const chemical::ResidueType &res, int pos)
void add_remaining_sidechain (AtomList &list, const chemical::ResidueType &res)
 add all non-assigned sidechain atoms to AtomList
void add_all_remaining (AtomList &list, const chemical::ResidueType &res)
 add all non-assigned atoms to AtomList
void fix_coarsetype_geometry (chemical::ResidueTypeAP coarse_res_type)
 the PARAM files contain random geometries. fix them by coarsifying the fine-grained geometries automatically -- called by constructor

Member Typedef Documentation

typedef std::vector<std::string> core::coarse::Translator::BeadNames

Constructor & Destructor Documentation

Translator::Translator ( RuleSet const &  rules,
chemical::ResidueTypeCAP  fine_res,
chemical::ResidueTypeAP  coarse_res 
)

Member Function Documentation

void Translator::add_all_remaining ( AtomList list,
const chemical::ResidueType res 
) [protected]

add all non-assigned atoms to AtomList

References core::kinematics::add_atom(), and core::chemical::ResidueType::nheavyatoms().

void Translator::add_atom ( AtomList list,
const chemical::ResidueType res,
Rule::AtomToken const &  atom 
) [protected]
void Translator::add_atom ( AtomList list,
const chemical::ResidueType res,
int  pos 
) [protected]
void Translator::add_remaining_sidechain ( AtomList list,
const chemical::ResidueType res 
) [protected]
int Translator::coarse_nchi ( ) const

number of chi-angles in coarse residue

conformation::ResidueOP core::coarse::Translator::coarsify ( const conformation::Residue fine) const

return a coarse residue with coordinates computed from the fine residue

Referenced by create_rotamer().

pack::dunbrack::CoarseRotamerSetOP core::coarse::Translator::coarsify ( utility::vector1< pack::dunbrack::DunbrackRotamer< pack::dunbrack::FOUR > > const &  fine_rotamers) const

compute a coarse DunbrackLibrary from a fine RotamerLibrary (not inlined, to avoid circular includes)

void Translator::fix_coarsetype_geometry ( chemical::ResidueTypeAP  coarse_res_type) [protected]

the PARAM files contain random geometries. fix them by coarsifying the fine-grained geometries automatically -- called by constructor

References core::conformation::ResidueFactory::create_residue().

SingleResidueRotamerLibraryCOP Translator::get_RotamerLibrary ( ) const

return a DunbrackRotamerLibrary, Rotamer's and their statistics are computed from the fine residues

References make_table_of_pilot_apps::name.

int Translator::map_atom_to_bead ( std::string const  atom) const

returns bead index for 'atom' in the fine-grained residue, e.g. 1 for CB, HB1, HB2, ...

References strip_whitespace().

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

residue_type ID (they are the same for coarse and fine, return either)

void Translator::pretty_print ( std::ostream &  os) const

The documentation for this class was generated from the following files:
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