def_scratch.md

Vocabulary and conventions

prefix, suffix of a sequence always refer to a contiguous subsequence at the left or right edge of the sequence, respectively. Note that a prefix or suffix need not be proper, and hence can include the entire sequence.

precedes, follows are always synonymous with to the left of or to the right of, respectively.

Ligand operator

A ligand operator match must have balanced parentheses.

Therefore, for a substring of a glycan in linear code to match a ligand operator, the entire matching substring must be either

• have no parentheses
  • = be the empty string, or
  • = any infix of a stem
• or have some parentheses, and therefore contain a non_main_branch,
  • ...possibly with a suffix of a subexp to its left
    • = a suffix of a substem (= part of a chain), or
    • = a complete substem (= complete chain) preceded by one or more complete(!) non_main_branches themselves preceded by a (possibly empty) suffix of a subexp
  • ...possibly with zero or more complete(!) non_main_branches followed by a (possibly empty) prefix of a stem to its right

Continuation operator

A continuation operator match must have a matching right parenthesis for every left parenthesis, but not every right parenthesis needs to be matched.

Therefore, for a substring of a glycan in linear code to match a continuation operator, the entire matching substring must either

• meet the conditions to match the ligand operator, or
• almost match a non_main_branch, where the 'almost' is that the substring need not
  • contain the left parenthesis.
  • contain a complete subexp.
• = the substring must contain a suffix of a subexp followed by )
  • ...possibly with zero or more complete(!) non_main_branches followed by a (possibly empty) prefix of a stem to its right