Subset of SMILES about dialect HOT 2 CLOSED

Points of incompatibility. These are features explicitly defined in one or the other paper, but which are different in Dialect:

• new element symbols: Db; Sg; Bh; Hs; Mt; Ds; Rg; Cn; Nh; Fl; Mc; Lv; Ts; Og
• disallowed element symbols: Ha
• disallowed symbol , (JCICS)
• disallowed charges: --; ++; +++; etc.
• disallowed bonds: :
• double branching is disallowed, e.g.: *((*))*; *(((*)))*; etc.
• reactions are disallowed, e.g.: *>>*
• all stereo descriptors except @ and @@ are disallowed
  • e.g., @@@ and @@@@ (note recursion in grammar)
  • @1
  • @AL2, @AL2, @SP1, etc.
• hydrogen is just another bracket atom
  • [HH] is valid as are [HH2] and other chemically nonsensical constructs. Contradicts JCICS.
• . is NOT a "bond of formal order zero" (p 88, bottom). It is not a bond at all. . This point is contradicted elsewhere, so must be clarified.
• integer values restrictions (previously no upper bound)
  • isotope: 0 < value < 1000
  • charge: 0 < value < 10
  • hcount: 0 < value < 10
  • map: 0 <= value < 999

Points not explained by either paper, but in Dialect:

• computing implicit hydrogen
  • on a selected atom
• selection algorithm
• deselection algorithm
  • pruning
• LL(1) formal grammar

Contradictory points resolved in Dialect:

• table of default valences
  • 1988: N(3)
  • 2003: N(3,5)
• membership of organic subset
  • H is NOT in the "aromatic subset." See Hn1cccc1, JCICS p 35 bottom left, contradicts p32 top right.
• atom selectability
  • 1988: implies "aromatic cycles" only, although in a contradictory way
  • 2003: examples of acyclic selections

from dialect.

Table of differences:

from dialect.