5#ifndef BALL_STRUCTURE_PEPTIDES_H
6#define BALL_STRUCTURE_PEPTIDES_H
12#ifndef BALL_KERNEL_PROTEIN_H
16#ifndef BALL_DATATYPE_OPTIONS_H
20#ifndef BALL_CONCEPT_EMBEDDABLE_H
215 const String& old_naming_scheme,
const String& new_naming_scheme)
const;
227 const String& old_naming_scheme,
const String& new_atom_name,
228 const String& new_naming_scheme)
const;
242 const String& old_naming_scheme,
const String& new_naming_scheme)
const;
#define BALL_EMBEDDABLE(TYPE, BASE)
ConstBidirectionalIterator< Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraits > ResidueConstIterator
BALL_EXPORT OneLetterAASequence ThreeLetterToOneLetter(const ThreeLetterAASequence &sequence)
BALL_EXPORT OneLetterAASequence GetSequence(const Protein &protein)
BALL_EXPORT char OneLetterCode(const String &aa)
BALL_EXPORT bool IsOneLetterCode(char aa)
std::list< String > ThreeLetterAASequence
An amino acid sequence in three-letter code.
BALL_EXPORT ThreeLetterAASequence OneLetterToThreeLetter(const OneLetterAASequence &sequence)
BALL_EXPORT bool IsThreeLetterCode(const String &aa)
BALL_EXPORT String ThreeLetterCode(char aa)
String OneLetterAASequence
An amino acid sequence in one-letter code.
This class provides conversion of atom names between naming schemata.
virtual ~NameConverter()
Destructor.
std::vector< std::vector< std::vector< String > > > pseudo_conversion_table_
bool supportsPseudoAtomNamingScheme(const String &scheme_name) const
void readPseudoAtomsConversionTable_()
std::vector< String > pseudo_conventions_
std::vector< std::vector< String > > conversion_table_
std::vector< String > resolvePseudoAtoms(const String &amino_acid, const String &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
bool supportsNamingScheme(const String &scheme_name) const
std::vector< String > conventions_
void readConversionTable_()
String convertName(const String &amino_acid, const String &old_atom_name, const String &old_naming_scheme, const String &new_naming_scheme) const
static const char * PSEUDO_ATOMS_INIFile
static const char * INIFile
Default values for options.
static const String PSEUDO_ATOMS_INIFile
static const String INIFile