#include <Translator.hh>

Inheritance diagram for core::coarse::Translator:

Collaboration diagram for core::coarse::Translator:

Classes
struct	BeadAtom

Public Types
typedef std::vector< BeadAtom >	AtomList

typedef std::vector< AtomList >	BeadList

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...

Translator &	operator= (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...

Detailed Description

Definition at line 68 of file Translator.hh.

Member Typedef Documentation

typedef std::vector<BeadAtom> core::coarse::Translator::AtomList

Definition at line 95 of file Translator.hh.

typedef std::vector<AtomList> core::coarse::Translator::BeadList

Definition at line 96 of file Translator.hh.

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

Definition at line 97 of file Translator.hh.

Constructor & Destructor Documentation

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

constructor

Definition at line 130 of file Translator.cc.

References core::chemical::ResidueType::aa(), core::kinematics::add_atom(), core::coarse::Rule::FULL_ATOM, core::chemical::ResidueType::has(), core::chemical::ResidueType::name(), core::coarse::Rule::REST_ALL, and core::coarse::Rule::REST_SIDECHAIN.

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

Definition at line 111 of file Translator.hh.

Member Function Documentation

void Translator::add_all_remaining	(	AtomList &	list,
		const chemical::ResidueType &	res
	)

protected

add all non-assigned atoms to AtomList

Definition at line 124 of file Translator.cc.

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

add BeadAtom to AtomList

Definition at line 83 of file Translator.cc.

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), core::chemical::ResidueType::has(), and strip_whitespace().

void Translator::add_atom	(	AtomList &	list,
		const chemical::ResidueType &	res,
		int	pos
	)

protected

Definition at line 78 of file Translator.cc.

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

void Translator::add_remaining_sidechain	(	AtomList &	list,
		const chemical::ResidueType &	res
	)

protected

add all non-assigned sidechain atoms to AtomList

Definition at line 117 of file Translator.cc.

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

int Translator::coarse_nchi ( ) const

number of chi-angles in coarse residue

Definition at line 67 of file Translator.cc.

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

Definition at line 186 of file Translator.cc.

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

Definition at line 342 of file Translator.cc.

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, ...

Definition at line 101 of file Translator.cc.

References strip_whitespace().

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

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

Definition at line 72 of file Translator.cc.

Translator& core::coarse::Translator::operator= ( const Translator & )

inlineprivate

Definition at line 112 of file Translator.hh.

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

Definition at line 52 of file Translator.cc.

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.

Definition at line 170 of file Translator.hh.

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

Definition at line 166 of file Translator.hh.

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

private

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

Definition at line 162 of file Translator.hh.

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

private

Definition at line 163 of file Translator.hh.

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

src/core/coarse/Translator.hh
src/core/coarse/Translator.cc

Classes

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation