BALL::Peptides::NameConverter Class Reference

This class provides conversion of atom names between naming schemata. More...

#include <BALL/STRUCTURE/peptides.h>

Inheritance diagram for BALL::Peptides::NameConverter:

Classes
struct	Default
	Default values for options. More...
struct	Option
	Option names. More...

Public Attributes
Public Attributes
Options	options
	options More...

Protected Member Functions
void	readConversionTable_ () throw (Exception::FileNotFound())
void	readPseudoAtomsConversionTable_ () throw (Exception::FileNotFound())

Protected Attributes
std::vector< String >	conventions_
std::vector< std::vector < String > >	conversion_table_
std::vector< String >	pseudo_conventions_
std::vector< std::vector < std::vector< String > > >	pseudo_conversion_table_

Constant Definitions
static const String	VALUE_NA
	NameConverter ()
virtual	~NameConverter ()
	Destructor. More...
void	setDefaultOptions ()
bool	supportsNamingScheme (const String &scheme_name) const
bool	supportsPseudoAtomNamingScheme (const String &scheme_name) const
String	convertName (const String &amino_acid, const String &old_atom_name, const String &old_naming_scheme, const String &new_naming_scheme) const
bool	matches (const String &amino_acid, const String &old_atom_name, const String &old_naming_scheme, const String &new_atom_name, const String &new_naming_scheme) const
std::vector< String >	resolvePseudoAtoms (const String &amino_acid, const String &atom_name, const String &old_naming_scheme, const String &new_naming_scheme) const

Additional Inherited Members
Public Types inherited from BALL::Embeddable
typedef std::vector< Embeddable * >	EmbeddableVector
Public Member Functions inherited from BALL::Embeddable
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
	Embeddable (const String &identifier="<Embeddable>")
	Embeddable (const Embeddable &embeddable)
virtual	~Embeddable ()
void	setIdentifier (const String &identifier)
const String &	getIdentifier () const
void	unregisterThis ()
virtual void	registerThis ()
Static Protected Member Functions inherited from BALL::Embeddable
static void	registerInstance_ (const std::type_info &type, const Embeddable *instance)
static void	unregisterInstance_ (const Embeddable *instance)
static Size	countInstances_ (const std::type_info &type)
static Embeddable *	getInstance_ (const std::type_info &type, Position index)
static Embeddable *	getInstance_ (const std::type_info &type, const String &identifier)

Detailed Description

This class provides conversion of atom names between naming schemata.

Name Converter class.

Converts hydrogen atom names between naming systems. The original version of this table was created by Charles Hoogstraten. The default ini file allows conversion between BMRB, SC, PDB, UCSF, MSI, XPLOR, SYBYL*, MIDAS*, and DIANA.

If no new atom name can be found the old name is returned.

Example code:

NameConverter converter();
if (   converter.supportsNamingScheme("BMRB")
    && converter.supportsNamingScheme("PDB"))
{
  ...
  String atom_name = "HB2";
  String pdb_name  = converter.convertName("ALA", atom_name, "BMRB", "PDB");
  ...
} 
if (   converter.supportsPseudoAtomNamingScheme("NMRSTAR") 
    && converter.supportsPseudoAtomNamingScheme("PDB"))
{ 
  std::vector<String> result = converter.resolvePseudoAtoms("R", "HB", "NMRSTAR", "PDB"); 
  cout << "pseudo atom HB of residue R can be matched to " << result.size() << " PDB atoms." << endl;
  

  Atom* atom = ...;
  if (converter.matches(atom->getResidue()->getName(), atom->getName(), "PDB", "HG2", "NMRSTAR"))
  {
      cout << "atom " << atom->getName() << " is a HG2 pseudo atom." << endl;
  }
}

Definition at line 150 of file peptides.h.

Constructor & Destructor Documentation

BALL::Peptides::NameConverter::NameConverter

(

)

Standard constructor

virtual BALL::Peptides::NameConverter::~NameConverter ( )

inlinevirtual

Destructor.

Definition at line 187 of file peptides.h.

Member Function Documentation

String BALL::Peptides::NameConverter::convertName	(	const String &	amino_acid,
		const String &	old_atom_name,
		const String &	old_naming_scheme,
		const String &	new_naming_scheme
	)		const

Convert atom name between two naming schemes.

If one of the naming schemes is unknown, or the name was not found, the old name is returned.

Returns

String - the converted name.

bool BALL::Peptides::NameConverter::matches	(	const String &	amino_acid,
		const String &	old_atom_name,
		const String &	old_naming_scheme,
		const String &	new_atom_name,
		const String &	new_naming_scheme
	)		const

Test whether two names for an atom are equivalent in different naming schemes.

The match can either be according the the conversion as defined in the INIFile or one atom is a pseudo atom and matches the other one according the PSEUDO_ATOMS_INIFile .

Returns

bool - true if the atom names can be matched, false otherwise.

void BALL::Peptides::NameConverter::readConversionTable_ ( ) throw (Exception::FileNotFound())

protected

Read the Conversion table from file.

void BALL::Peptides::NameConverter::readPseudoAtomsConversionTable_ ( ) throw (Exception::FileNotFound())

protected

Read the pseudo atoms conversion table from file.

std::vector<String> BALL::Peptides::NameConverter::resolvePseudoAtoms	(	const String &	amino_acid,
		const String &	atom_name,
		const String &	old_naming_scheme,
		const String &	new_naming_scheme
	)		const

Resolve pseudo atoms among naming schemes.

If the input is a pseudo atom in the given naming scheme, convert it into the list of atoms in the desired naming scheme.

Parameters

amino_acid	the amino acid type of the atom
atom_name	the atom name to test
old_naming_scheme	the naming scheme of the input
new_naming_scheme	the desired naming scheme

Returns

const std::vector<String>& - the list of atoms this atom resolves to

void BALL::Peptides::NameConverter::setDefaultOptions

(

)

Reset the options to default values.

bool BALL::Peptides::NameConverter::supportsNamingScheme

(

const String &

scheme_name

)

const

Determine whether the Converter supports the naming scheme scheme_name.

Parameters

scheme_name

naming scheme in question

Returns

bool - true if the naming scheme is supported, false otherwise

bool BALL::Peptides::NameConverter::supportsPseudoAtomNamingScheme

(

const String &

scheme_name

)

const

Determine whether the Converter supports the naming scheme scheme_name for pseudo atoms.

Parameters

scheme_name

naming scheme in question

Returns

bool - true if the naming scheme is supported, false otherwise

Member Data Documentation

std::vector<String> BALL::Peptides::NameConverter::conventions_

protected

Definition at line 263 of file peptides.h.

std::vector< std::vector <String> > BALL::Peptides::NameConverter::conversion_table_

protected

Definition at line 264 of file peptides.h.

Options BALL::Peptides::NameConverter::options

options

Definition at line 248 of file peptides.h.

std::vector<String> BALL::Peptides::NameConverter::pseudo_conventions_

protected

Definition at line 266 of file peptides.h.

std::vector< std::vector <std::vector <String> > > BALL::Peptides::NameConverter::pseudo_conversion_table_

protected

Definition at line 267 of file peptides.h.

const String BALL::Peptides::NameConverter::VALUE_NA

static

Definition at line 160 of file peptides.h.