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 191 void setDefaultOptions();
198 bool supportsNamingScheme(
const String& scheme_name)
const;
205 bool supportsPseudoAtomNamingScheme(
const String& scheme_name)
const;
215 const String& old_naming_scheme,
const String& new_naming_scheme)
const;
226 bool matches(
const String& amino_acid,
const String& old_atom_name,
227 const String& old_naming_scheme,
const String& new_atom_name,
228 const String& new_naming_scheme)
const;
241 std::vector<String> resolvePseudoAtoms(
const String& amino_acid,
const String& atom_name,
242 const String& old_naming_scheme,
const String& new_naming_scheme)
const;
255 void readConversionTable_()
260 void readPseudoAtomsConversionTable_()
276 #endif // BALL_STRUCTURE_PEPTIDES_H_ std::vector< String > pseudo_conventions_
static const String PSEUDO_ATOMS_INIFile
BALL_EXPORT bool IsOneLetterCode(char aa)
std::list< String > ThreeLetterAASequence
An amino acid sequence in three-letter code.
BALL_EXPORT char OneLetterCode(const String &aa)
BALL_EXPORT ThreeLetterAASequence OneLetterToThreeLetter(const OneLetterAASequence &sequence)
std::vector< String > conventions_
BALL_EXPORT bool IsThreeLetterCode(const String &aa)
static const String INIFile
#define BALL_EMBEDDABLE(TYPE, BASE)
Default values for options.
This class provides conversion of atom names between naming schemata.
virtual ~NameConverter()
Destructor.
-*- Mode: C++; tab-width: 2; -*-
std::vector< std::vector< String > > conversion_table_
static const char * INIFile
BALL_EXPORT OneLetterAASequence ThreeLetterToOneLetter(const ThreeLetterAASequence &sequence)
String OneLetterAASequence
An amino acid sequence in one-letter code.
static const char * PSEUDO_ATOMS_INIFile
BALL_EXPORT String ThreeLetterCode(char aa)
BALL_EXPORT OneLetterAASequence GetSequence(const Protein &protein)
std::vector< std::vector< std::vector< String > > > pseudo_conversion_table_