Rosetta Core  2014.35
Classes | Public Types | Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
core::coarse::Translator Class Reference

#include <Translator.hh>

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::ResidueTypeCOP fine_res, chemical::ResidueTypeAP coarse_res)
 constructor More...
 
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, ... More...
 
int coarse_nchi () const
 number of chi-angles in coarse residue More...
 
std::string const & name () const
 residue_type ID (they are the same for coarse and fine, return either) More...
 
conformation::ResidueOP coarsify (const conformation::Residue &fine) const
 return a coarse residue with coordinates computed from the fine residue More...
 
pack::dunbrack::SingleResidueRotamerLibraryCOP get_RotamerLibrary () const
 return a DunbrackRotamerLibrary, Rotamer's and their statistics are computed from the fine residues More...
 
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) More...
 

Protected Member Functions

void add_atom (AtomList &list, const chemical::ResidueType &res, Rule::AtomToken const &atom)
 add BeadAtom to AtomList More...
 
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 More...
 
void add_all_remaining (AtomList &list, const chemical::ResidueType &res)
 add all non-assigned atoms to AtomList More...
 
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 More...
 

Private Member Functions

 Translator (const Translator &t)
 private copy and assigment a translator is intimately connected to its coarse_res_type, (coarse_res_type points to its translator object and vice versa... better not to copy such things More...
 
Translatoroperator= (const Translator &)
 

Private Attributes

chemical::ResidueTypeCOP coarse_res_type_
 Pointers to the connected Residue Sets... CHECK these should probably be access pointers CHECK. More...
 
chemical::ResidueTypeCOP fine_res_type_
 
BeadList beads_
 list of beads, a bead is a AtomList — which atoms of fine_rsd belong to bead of coarse_rsd More...
 
BeadNames bead_names_
 store atom and bead names of the coarse-grained residue, first bead is FULL_ATOM and contains the names of all atoms that remain in full. More...
 

Member Typedef Documentation

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

Constructor & Destructor Documentation

Translator::Translator ( RuleSet const &  rules,
chemical::ResidueTypeCOP  fine_res,
chemical::ResidueTypeAP  coarse_res 
)
core::coarse::Translator::Translator ( const Translator t)
inlineprivate

private copy and assigment a translator is intimately connected to its coarse_res_type, (coarse_res_type points to its translator object and vice versa... better not to copy such things

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

SingleResidueRotamerLibraryCOP Translator::get_RotamerLibrary ( ) const

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

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)

Translator& core::coarse::Translator::operator= ( const Translator )
inlineprivate
void Translator::pretty_print ( std::ostream &  os) const

Member Data Documentation

BeadNames core::coarse::Translator::bead_names_
private

store atom and bead names of the coarse-grained residue, first bead is FULL_ATOM and contains the names of all atoms that remain in full.

BeadList core::coarse::Translator::beads_
private

list of beads, a bead is a AtomList — which atoms of fine_rsd belong to bead of coarse_rsd

chemical::ResidueTypeCOP core::coarse::Translator::coarse_res_type_
private

Pointers to the connected Residue Sets... CHECK these should probably be access pointers CHECK.

chemical::ResidueTypeCOP core::coarse::Translator::fine_res_type_
private

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