ProFormaData.h File Reference

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/OpenMSConfig.h>
#include <optional>
#include <utility>
#include <variant>
#include <vector>

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Classes
struct	ConversionIssue
	Description of a conversion issue from Peptidoform to AASequence. More...
struct	CvAccession
	Controlled vocabulary accession for a modification. More...
struct	NamedMod
	Named modification with optional CV prefix hint. More...
struct	MassDelta
	Mass delta modification with optional source hint. More...
struct	FormulaTag
	Chemical formula with optional charge. More...
struct	GlycanComposition
	Glycan composition specification. More...
struct	InfoTag
	Info tag for arbitrary text annotations. More...
struct	PositionConstraint
	Position constraint specifying allowed residues for a modification. More...
struct	Label
	Label for cross-links, branches, or ambiguous grouping. More...
struct	Modification
	A modification with one or more alternative tags. More...
struct	SequenceElement
	A single amino acid with its modifications. More...
struct	AmbiguousRegion
	Ambiguous amino acid region. More...
struct	ModifiedRange
	Modified sequence range with shared modifications. More...
struct	UnlocalisedMod
	Unlocalised modification with optional occurrence count. More...
struct	LabileModification
	Labile modification that may be lost during fragmentation. More...
struct	GlobalModification
	Global modification applied to specific locations. More...
struct	IsotopeReplacement
	Isotope replacement for stable isotope labeling. More...
struct	AdductIon
	Adduct ion specification for charge state. More...
struct	Peptidoform
	A single peptidoform (one peptide chain) More...
struct	PeptidoformIon
	A peptidoform ion (one or more chains with optional charge) More...
struct	CrossLinkGroup
	Cross-link group connecting sites across chains. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

Typedefs
using	ModificationTag = std::variant< CvAccession, NamedMod, MassDelta, FormulaTag, GlycanComposition, InfoTag, PositionConstraint >
	Variant type representing any modification tag content.
using	SequenceSection = std::variant< SequenceElement, AmbiguousRegion, ModifiedRange >
	Variant type representing a section of the sequence.
using	GlobalModEntry = std::variant< IsotopeReplacement, GlobalModification >
	Variant type for global modification entries.
using	ChargeState = std::variant< int, std::vector< AdductIon > >
	Charge state specification.

Enumerations
enum class	AASequenceConversionPolicy { FAIL_ON_LOSS , DROP_UNLOCALISED , BEST_EFFORT }
	Conversion policy for transforming Peptidoform to AASequence. More...
enum class	ConversionIssueType {   UNRESOLVED_MOD , UNLOCALISED_MOD , LABILE_MOD , GLOBAL_MOD ,   AMBIGUOUS_MOD , AMBIGUOUS_REGION , MODIFIED_RANGE , CROSS_LINK ,   MULTIPLE_CHAINS , ALTERNATIVE_MODS , UNSUPPORTED_FEATURE }
	Issue type for AASequence conversion problems. More...
enum class	ProFormaWriteMode { LOSSLESS , CANONICAL }
	Write mode for ProForma string serialization. More...
enum class	CvDatabase {   UNIMOD , MOD , RESID , XLMOD ,   GNO }
	Controlled vocabulary database prefix for modification accessions. More...

Functions
JSON serialization
String	toJSON (const Peptidoform &pf)
	Convert a Peptidoform to JSON string representation.
Peptidoform	peptidoformFromJSON (const String &json_str)
	Construct a Peptidoform from JSON string.
String	toJSON (const PeptidoformIon &pfi)
	Convert a PeptidoformIon to JSON string representation.
PeptidoformIon	peptidoformIonFromJSON (const String &json_str)
	Construct a PeptidoformIon from JSON string.