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
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.
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

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 ( ) [inline, virtual]

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