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

Include dependency graph for ProForma.h:

This graph shows which files directly or indirectly include this file:

Classes
class	ProForma
	ProForma v2 peptidoform notation parser and data structures. More...

struct	ProForma::ConversionIssue
	Description of a conversion issue from Peptidoform to AASequence. More...

struct	ProForma::CvAccession
	Controlled vocabulary accession for a modification. More...

struct	ProForma::NamedMod
	Named modification with optional CV prefix hint. More...

struct	ProForma::MassDelta
	Mass delta modification with optional source hint. More...

struct	ProForma::FormulaTag
	Chemical formula with optional charge. More...

struct	ProForma::GlycanComposition
	Glycan composition specification. More...

struct	ProForma::InfoTag
	Info tag for arbitrary text annotations. More...

struct	ProForma::PositionConstraint
	Position constraint specifying allowed residues for a modification. More...

struct	ProForma::Label
	Label for cross-links, branches, or ambiguous grouping. More...

struct	ProForma::Modification
	A modification with one or more alternative tags. More...

struct	ProForma::SequenceElement
	A single amino acid with its modifications. More...

struct	ProForma::AmbiguousRegion
	Ambiguous amino acid region. More...

struct	ProForma::ModifiedRange
	Modified sequence range with shared modifications. More...

struct	ProForma::UnlocalisedMod
	Unlocalised modification with optional occurrence count. More...

struct	ProForma::LabileModification
	Labile modification that may be lost during fragmentation. More...

struct	ProForma::GlobalModification
	Global modification applied to specific locations. More...

struct	ProForma::IsotopeReplacement
	Isotope replacement for stable isotope labeling. More...

struct	ProForma::AdductIon
	Adduct ion specification for charge state. More...

struct	ProForma::Peptidoform
	A single peptidoform (one peptide chain) More...

struct	ProForma::PeptidoformIon
	A peptidoform ion (one or more chains with optional charge) More...

struct	ProForma::CrossLinkGroup
	Cross-link group connecting sites across chains. More...

class	ProForma::ParseError
	Structured parse error with context for ProForma parsing. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

Class Documentation

◆ OpenMS::ProForma::ConversionIssue

struct OpenMS::ProForma::ConversionIssue

Description of a conversion issue from Peptidoform to AASequence.

Records problems encountered when attempting to convert a ProForma Peptidoform to an OpenMS AASequence representation.

Collaboration diagram for ProForma::ConversionIssue:

[legend]

Class Members
String	description	Human-readable description.
size_t	position	Position in sequence (SIZE_MAX if not position-specific)
ConversionIssueType	type	The type of issue.

◆ OpenMS::ProForma::CvAccession

struct OpenMS::ProForma::CvAccession

Controlled vocabulary accession for a modification.

Represents a modification specified by a CV accession number, e.g., UNIMOD:35 for Oxidation. The accession string contains only the identifier portion (e.g., "35" for UNIMOD:35).

Collaboration diagram for ProForma::CvAccession:

[legend]

Class Members
String	accession	The accession identifier (e.g., "35" for UNIMOD:35, full string for GNO)
CvDatabase	database	The source database (UNIMOD, MOD, RESID, XLMOD, or GNO)

◆ OpenMS::ProForma::NamedMod

struct OpenMS::ProForma::NamedMod

Named modification with optional CV prefix hint.

Represents a modification specified by name, optionally with a CV prefix hint to disambiguate which database to search (e.g., "U:Oxidation" for UniMod, "M:Oxidation" for PSI-MOD).

Collaboration diagram for ProForma::NamedMod:

[legend]

Class Members
optional< CvDatabase >	cv_hint	Optional CV prefix hint (U, M, R, X, G)
String	name	The modification name (e.g., "Oxidation", "Phospho")

◆ OpenMS::ProForma::FormulaTag

struct OpenMS::ProForma::FormulaTag

Chemical formula with optional charge.

Represents a modification specified by chemical formula. The optional charge is specified via the :z+N suffix in ProForma (e.g., Formula:C12H20O2:z+2).

Collaboration diagram for ProForma::FormulaTag:

[legend]

Class Members
optional< int >	charge	Optional charge from :z+N suffix.
String	formula_string	The chemical formula string (e.g., "C12H20O2")

◆ OpenMS::ProForma::GlycanComposition

struct OpenMS::ProForma::GlycanComposition

Glycan composition specification.

Represents a glycan modification as a composition of monosaccharides. Each component can be either a named monosaccharide (e.g., "Hex", "HexNAc") or a custom formula specification.

Example: Glycan:HexNAc1Hex2 -> [(HexNAc, 1), (Hex, 2)]

Collaboration diagram for ProForma::GlycanComposition:

[legend]

Class Members
typedef variant< String, FormulaTag >	Monosaccharide	A monosaccharide component: either a name (String) or a custom formula (FormulaTag)

Class Members
vector< pair< Monosaccharide, int > >	components	List of (monosaccharide, count) pairs.

◆ OpenMS::ProForma::InfoTag

struct OpenMS::ProForma::InfoTag

Info tag for arbitrary text annotations.

Represents an INFO: tag in ProForma that carries arbitrary text metadata about a modification or site. Example: INFO:provenance_data

Collaboration diagram for ProForma::InfoTag:

[legend]

Class Members
String	text	The info text content.

◆ OpenMS::ProForma::PositionConstraint

struct OpenMS::ProForma::PositionConstraint

Position constraint specifying allowed residues for a modification.

Represents a Position: tag in ProForma that constrains where a modification can be localized. This is typically used as an alternative to a modification to indicate its possible sites.

Example: [Oxidation|Position:M] means Oxidation can only occur at M residues

Collaboration diagram for ProForma::PositionConstraint:

[legend]

Class Members
bool	c_term = false	True if modification can be at C-terminus.
bool	n_term = false	True if modification can be at N-terminus.
vector< char >	residues	List of allowed amino acid residues.

◆ OpenMS::ProForma::Modification

struct OpenMS::ProForma::Modification

A modification with one or more alternative tags.

In ProForma, a modification can have multiple alternatives separated by |, representing uncertainty about the exact modification. Each alternative consists of a tag and an optional label.

Example: K[Phospho|+79.97] has two alternatives

The resolved_mod field is populated by resolveModifications() and points to the ResidueModification in ModificationsDB (for the first/primary alternative).

Collaboration diagram for ProForma::Modification:

[legend]

Class Members
vector< pair< ModificationTag, optional< Label > > >	alternatives	Each alternative is a (tag, optional_label) pair.
const ResidueModification *	resolved_mod = nullptr	Resolved modification pointer (populated by resolveModifications) Points to the ResidueModification for the first alternative, if found

◆ OpenMS::ProForma::SequenceElement

struct OpenMS::ProForma::SequenceElement

A single amino acid with its modifications.

Represents one position in the peptide sequence: the amino acid residue and zero or more modifications attached to it.

Collaboration diagram for ProForma::SequenceElement:

[legend]

Class Members
char	amino_acid	Single-letter amino acid code (A-Z)
vector< Modification >	modifications	Modifications at this position.

◆ OpenMS::ProForma::AmbiguousRegion

struct OpenMS::ProForma::AmbiguousRegion

Ambiguous amino acid region.

Represents a region where the amino acid sequence is uncertain. ProForma notation: (?DQ) means either D or Q at this position.

Collaboration diagram for ProForma::AmbiguousRegion:

[legend]

Class Members
vector< SequenceElement >	elements	The ambiguous amino acid possibilities.

◆ OpenMS::ProForma::ModifiedRange

struct OpenMS::ProForma::ModifiedRange

Modified sequence range with shared modifications.

Represents a subsequence where one or more modifications apply to the entire range, but the exact position is uncertain.

ProForma notation: (EOSFORMS)[+19.0523] means +19.0523 applies somewhere in EOSFORMS

Collaboration diagram for ProForma::ModifiedRange:

[legend]

Class Members
vector< SequenceElement >	elements	The amino acids in the range.
vector< Modification >	modifications	Modifications applying to the entire range.

◆ OpenMS::ProForma::UnlocalisedMod

struct OpenMS::ProForma::UnlocalisedMod

Unlocalised modification with optional occurrence count.

Represents a modification that is known to exist on the peptide but whose exact position is unknown. The occurrence specifies how many instances of this modification are present.

ProForma notation: [Phospho]?PEPTIDE or [Phospho]^2?PEPTIDE

Collaboration diagram for ProForma::UnlocalisedMod:

[legend]

Class Members
vector< Modification >	modifications	The unlocalised modification(s)
optional< int >	occurrence	Optional occurrence count from ^N suffix.

◆ OpenMS::ProForma::LabileModification

struct OpenMS::ProForma::LabileModification

Labile modification that may be lost during fragmentation.

Labile modifications are typically lost during ionization or fragmentation and thus may not be observed in MS/MS spectra.

ProForma notation: {Glycan:Hex}PEPTIDE

Collaboration diagram for ProForma::LabileModification:

[legend]

Class Members
Modification	modification	The labile modification.

◆ OpenMS::ProForma::GlobalModification

struct OpenMS::ProForma::GlobalModification

Global modification applied to specific locations.

A global modification applies the same modification to all occurrences of specified residues or termini throughout the peptide.

ProForma notation: <[TMT6plex]@K,N-term>

Collaboration diagram for ProForma::GlobalModification:

[legend]

Class Members
vector< String >	locations	Target locations ("K", "N-term", "C-term:K", etc.)
Modification	modification	The modification to apply.

◆ OpenMS::ProForma::IsotopeReplacement

struct OpenMS::ProForma::IsotopeReplacement

Isotope replacement for stable isotope labeling.

Represents global replacement of an element with a specific isotope, used for stable isotope labeling experiments.

ProForma notation: <13C> or <15N> or <D>

Collaboration diagram for ProForma::IsotopeReplacement:

[legend]

Class Members
String	isotope	The isotope specification (e.g., "13C", "15N", "D")

◆ OpenMS::ProForma::AdductIon

struct OpenMS::ProForma::AdductIon

Adduct ion specification for charge state.

Represents an adduct ion contributing to the charge state of a peptidoform ion. Multiple adducts can combine to give the total charge.

ProForma notation: Na:z+1 in /[Na:z+1,H:z+1]

Collaboration diagram for ProForma::AdductIon:

[legend]

Class Members
int	charge	The charge contribution of this adduct.
String	formula	The adduct formula (e.g., "Na", "H", "K")
optional< int >	occurrence	Optional occurrence count from ^N suffix.

◆ OpenMS::ProForma::Peptidoform

struct OpenMS::ProForma::Peptidoform

A single peptidoform (one peptide chain)

Represents a complete peptide chain including:

Optional name identifier (from v2.1 extension)
Global modifications (<13C>, <[TMT6plex]@K>)
Unlocalised modifications ([Phospho]?)
Labile modifications ({Glycan:Hex})
N-terminal modifications ([Acetyl]-)
The amino acid sequence with modifications
C-terminal modifications (-[Amidated])

Collaboration diagram for ProForma::Peptidoform:

[legend]

Class Members
vector< Modification >	c_term_mods	C-terminal modifications: -[Amidated].
optional< ChargeState >	charge	Optional per-chain charge (for chimeric spectra)
vector< GlobalModEntry >	global_mods	Global modifications: `<13C>`, `<[TMT6plex]@K>`
vector< LabileModification >	labile_mods	Labile modifications: {Glycan:Hex}.
vector< Modification >	n_term_mods	N-terminal modifications: [Acetyl]-.
optional< String >	name	Optional name from (>name) v2.1 extension.
vector< SequenceSection >	sequence	The sequence with modifications.
vector< UnlocalisedMod >	unlocalised_mods	Unlocalised modifications: [Phospho]?

◆ OpenMS::ProForma::PeptidoformIon

struct OpenMS::ProForma::PeptidoformIon

A peptidoform ion (one or more chains with optional charge)

Represents one or more peptide chains that form a single ion species. Multiple chains can be present in cross-linked or multi-chain entities.

ProForma notation: chains are separated by //

Collaboration diagram for ProForma::PeptidoformIon:

[legend]

Class Members
vector< Peptidoform >	chains	One or more peptide chains (separated by // or + in ProForma)
optional< ChargeState >	charge	Optional charge state specification.
bool	is_chimeric = false	True if chains are chimeric (+ separator), false if cross-linked (//)
optional< String >	name	Optional name from (>>name) v2.1 extension.

◆ OpenMS::ProForma::CrossLinkGroup

struct OpenMS::ProForma::CrossLinkGroup

Cross-link group connecting sites across chains.

Groups together all sites that share a cross-link label. Each site is identified by its chain index and position within that chain.

Derived during parsing from matching #XL labels.

Collaboration diagram for ProForma::CrossLinkGroup:

[legend]

Class Members
String	label	The cross-link label (e.g., `XL1`)
vector< pair< size_t, size_t > >	sites	(chain_index, site_index) pairs

Classes

Namespaces

Class Documentation

◆ OpenMS::ProForma::ConversionIssue

◆ OpenMS::ProForma::CvAccession

◆ OpenMS::ProForma::NamedMod

◆ OpenMS::ProForma::FormulaTag

◆ OpenMS::ProForma::GlycanComposition

◆ OpenMS::ProForma::InfoTag

◆ OpenMS::ProForma::PositionConstraint

◆ OpenMS::ProForma::Modification

◆ OpenMS::ProForma::SequenceElement

◆ OpenMS::ProForma::AmbiguousRegion

◆ OpenMS::ProForma::ModifiedRange

◆ OpenMS::ProForma::UnlocalisedMod

◆ OpenMS::ProForma::LabileModification

◆ OpenMS::ProForma::GlobalModification

◆ OpenMS::ProForma::IsotopeReplacement

◆ OpenMS::ProForma::AdductIon

◆ OpenMS::ProForma::Peptidoform

◆ OpenMS::ProForma::PeptidoformIon

◆ OpenMS::ProForma::CrossLinkGroup