MSeq(x)

molecular sequence
 
SSeq(x)

syntactic sequence
 
ASeq(x)

abstract sequence
 
Jun(x)

junction
 
PBS(x)

primitive biological symbol

x is a syntactic sequence (SSeq).

DMSeq(x)

directed molecular sequence

x is a molecular sequence (MSeq).

DSSeq(x)

directed syntactic sequence

x is a syntactic sequence (SSeq).

mPO(x, y)

molecular part of

x and y are molecular sequences (MSeq).

sPO(x, y)

syntactic part of

x and y are syntactic sequences (SSeq).

aPO(x, y)

abstract part of

x and y are abstract sequences (ASeq).

mPPO(x, y)

molecular proper part of

x and y are molecular sequences (MSeq).

sPPO(x, y)

syntactic proper part of

x and y are syntactic sequences (SSeq).

aPPO(x, y)

abstract proper part of

x and y are abstract sequences (ASeq).

moverlap(x, y)

molecular overlap

x and y are molecular sequences (MSeq).

soverlap(x, y)

syntactic overlap

x and y are syntactic sequences (SSeq).

aoverlap(x, y)

abstract overlap

x and y are abstract sequences (ASeq).

mdisjoint(x, y)

molecular disjointness

x and y are molecular sequences (MSeq).

sdisjoint(x, y)

syntactic disjointness

x and y are syntactic sequences (SSeq).

adisjoint(x, y)

abstract disjointness

x and y are abstract sequences (ASeq).

sto(x, y)

syntactic token of

x is a syntactic (SSeq), y an abstract sequence (ASeq).

mto(x, y)

molecular token of

x is a molecular (MSeq), y an abstract sequence (ASeq).

Rep(x, y)

representation

x is a syntactic (SSeq), y a molecular sequence (MSeq).

between(j, p_{1}, p_{2}, s)

between

j is a junction (Jun), p_{1} and p_{2} are primitive symbols (PBS) and s is a syntactic sequence (SSeq). j is a junction between p_{1} and p_{2} in the syntactic sequence s.

end(j, p, s)

ends

j is a junction (Jun), p a primitive symbol (PBS) and s is a syntactic sequence (SSeq). The junction j ends the syntactic sequence s and is adjacent to the primitive symbol p (which is the first or last symbol of s).

first(j, p, s)

first

j is a junction (Jun), p a primitive symbol (PBS) and s a syntactic sequence (SSeq).

last(j, p, s)

last

j is a junction (Jun), p a primitive symbol (PBS) and s a syntactic sequence (SSeq).

in(j, s)

in

j is a junction (Jun) and s a syntactic sequence (SSeq).

s_{1} ≡ s_{2}

equivalence

s_{1} and s_{2} are directed syntactic sequences (DSSeq).

conn(j_{1}, j_{2})

connection

j_{1} and j_{2} are junctions (Jun).
