Miscellaneous
[Molecular Structure]

Classes
class	AddHydrogenProcessor
	Saturate atoms with hydrogen atoms. More...
class	AtomTyper
	Base class for a programable Atom typer. More...
class	BuildBondsProcessor
	Bond creation processor. More...
class	ClearChargeProcessor
	Clears the charge on all atoms. More...
class	ClearRadiusProcessor
	Clears the radius of all atoms. More...
class	AssignRadiusProcessor
	Assigns the radius to each atom. More...
class	AssignChargeProcessor
	Assigns a charge to each atom. More...
class	FragmentDB
	FragmentDB - fragment database class. More...
class	TransformationProcessor
	Transformation applicator. More...
class	HBondProcessor
	This processor computes all hydrogen bonds occuring between amino acids in the composite it is applied to. More...
class	Kekuliser
	Class to transform bonds with type "aromatic" to conjugated single and double bonds. More...
class	NodeItem< Node, Edge >
	The node type in a molecular graph. More...
class	ReconstructFragmentProcessor
	ReconstructFragmentProcessor. More...
class	ResidueChecker
	Residue Consistency Checker. More...
class	SecondaryStructureProcessor
	Secondary structure extraction from 3D structure. More...
class	UCK
	Unique Chemical Key. More...
Type definitions
typedef std::list< String >	Peptides::ThreeLetterAASequence
	An amino acid sequence in three-letter code.
typedef String	Peptides::OneLetterAASequence
	An amino acid sequence in one-letter code.
Amino acid sequence conversion
BALL_EXPORT char	Peptides::OneLetterCode (const String &aa)
	Convert a three-letter amino acid name to the one-letter abbreviation.
BALL_EXPORT String	Peptides::ThreeLetterCode (char aa)
	Convert a one-letter amino acid abbreviation to its three-letter code.
BALL_EXPORT OneLetterAASequence	Peptides::ThreeLetterToOneLetter (const ThreeLetterAASequence &sequence)
	Convert an amino acid sequence from three-letter code to one-letter code.
BALL_EXPORT ThreeLetterAASequence	Peptides::OneLetterToThreeLetter (const OneLetterAASequence &sequence)
	Convert an amino acid sequence from one-letter code to three-letter code.
BALL_EXPORT OneLetterAASequence	Peptides::GetSequence (const Protein &protein)
	Get amino acid sequence from an protein.

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Detailed Description

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Function Documentation

BALL_EXPORT OneLetterAASequence 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 char 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 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 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 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.