EnzymaticDigestion::SimpleCleavageRule Struct Reference

A cleavage rule of the form "(?<=[KRX])" or "(?<=[KRX])(?!P)", as most enzymes of Enzymes.xml spell theirs. More...

#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>

Public Member Functions
bool	cleavesBetween (char nterm, char cterm) const
	Whether the rule cleaves between nterm and cterm, the residues before and after the site.

Static Public Member Functions
static std::optional< SimpleCleavageRule >	parse (const std::string &regex)
	The rule of regex if it is exactly "(?<=[" + A-Z letters + "])", optionally followed by "(?!" + one A-Z letter + ")".

Public Attributes
std::array< bool, 256 >	after {}
	residues N-terminal of a cleavage site
std::array< bool, 256 >	not_before {}
	residues C-terminal of a site that prevent the cleavage

Detailed Description

A cleavage rule of the form "(?<=[KRX])" or "(?<=[KRX])(?!P)", as most enzymes of Enzymes.xml spell theirs.

Cleaves after a residue of after unless the next residue is in not_before. tokenize_() (and the digest of FragmentIndex) apply such a rule by hand instead of running the regular expression: faster, and a regex search takes a block from boost's process-wide memory cache, which the threads of a parallel caller contend for.

Member Function Documentation

cleavesBetween()

bool cleavesBetween ( char  nterm, char  cterm  ) const

inline

Whether the rule cleaves between nterm and cterm, the residues before and after the site.

parse()

static std::optional< SimpleCleavageRule > parse ( const std::string &  regex )

static

The rule of regex if it is exactly "(?<=[" + A-Z letters + "])", optionally followed by "(?!" + one A-Z letter + ")".

Every other pattern (e.g. "()", "(?<=[A-Z])", the lookahead rules of Asp-N, "(?<=[HKRX][PX])(?!P)") yields std::nullopt and is left to the regular expression.

Member Data Documentation

after

std::array<bool, 256> after {}

residues N-terminal of a cleavage site

not_before

std::array<bool, 256> not_before {}

residues C-terminal of a site that prevent the cleavage