BALL::Peptides Namespace Reference

Classes
class	AminoAcidDescriptor
class	PeptideBuilder
class	NameConverter
	This class provides conversion of atom names between naming schemata. More...

Typedefs
Type definitions
typedef std::list< String >	ThreeLetterAASequence
	An amino acid sequence in three-letter code. More...
typedef String	OneLetterAASequence
	An amino acid sequence in one-letter code. More...

Functions
Amino acid sequence conversion
BALL_EXPORT char	OneLetterCode (const String &aa)
BALL_EXPORT String	ThreeLetterCode (char aa)
BALL_EXPORT bool	IsOneLetterCode (char aa)
BALL_EXPORT bool	IsThreeLetterCode (const String &aa)
BALL_EXPORT OneLetterAASequence	ThreeLetterToOneLetter (const ThreeLetterAASequence &sequence)
BALL_EXPORT ThreeLetterAASequence	OneLetterToThreeLetter (const OneLetterAASequence &sequence)
BALL_EXPORT OneLetterAASequence	GetSequence (const Protein &protein)
BALL_EXPORT OneLetterAASequence	GetSequence (const Chain &chain)
BALL_EXPORT OneLetterAASequence	GetSequence (ResidueConstIterator it)

Typedef Documentation

typedef String BALL::Peptides::OneLetterAASequence

An amino acid sequence in one-letter code.

Definition at line 38 of file peptides.h.

typedef std::list<String> BALL::Peptides::ThreeLetterAASequence

An amino acid sequence in three-letter code.

Definition at line 35 of file peptides.h.

Function Documentation

BALL_EXPORT OneLetterAASequence BALL::Peptides::GetSequence

(

const Protein &

protein

)

Get amino acid sequence from an protein. This method iterates over all residues of the protein, calls OneLetterCode for each of the residue names, and returns the concatenation of all results.

BALL_EXPORT OneLetterAASequence BALL::Peptides::GetSequence

(

const Chain &

chain

)

Get amino acid sequence from a chain. This method iterates over all residues of the chain, calls OneLetterCode for each of the residue names, and returns the concatenation of all results.

BALL_EXPORT OneLetterAASequence BALL::Peptides::GetSequence

(

ResidueConstIterator

it

)

Get amino acid sequence from an iterator. This method iterates over all residues starting with it, calls OneLetterCode for each of the residue names, and returns the concatenation of all results.

BALL_EXPORT bool BALL::Peptides::IsOneLetterCode

(

char

aa

)

Determine whether the given character is a valid amino acid abbreviation.

Parameters

aa	amino acid abbreviation in question

Returns

bool - true if aa is a valid amino acid abbreviation, false otherwise

BALL_EXPORT bool BALL::Peptides::IsThreeLetterCode

(

const String &

aa

)

Determine whether the given string is a valid amino acid three-letter code.

Parameters

aa	amino acid string in question

Returns

bool - true if aa is a valid amino acid three-letter code, false otherwise

BALL_EXPORT char BALL::Peptides::OneLetterCode

(

const String &

aa

)

Convert a three-letter amino acid name to the one-letter abbreviation. If the string given is not the three-letter code of one of the twenty amino acids, '?' is returned. This method is not case sensitive.

BALL_EXPORT ThreeLetterAASequence BALL::Peptides::OneLetterToThreeLetter

(

const OneLetterAASequence &

sequence

)

Convert an amino acid sequence from one-letter code to three-letter code. Call ThreeLetterCode for each of the characters in the string.

BALL_EXPORT String BALL::Peptides::ThreeLetterCode

(

char

aa

)

Convert a one-letter amino acid abbreviation to its three-letter code. If the character given is not the code for one of the twenty amino acids, 'UNK' is returned. This method is not case sensitive. The strings returned are all upper cases.

BALL_EXPORT OneLetterAASequence BALL::Peptides::ThreeLetterToOneLetter

(

const ThreeLetterAASequence &

sequence

)

Convert an amino acid sequence from three-letter code to one-letter code. Call OneLetterCode for each of the amino acids in the sequence.