Comments (2)
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.
- e.g.,
- 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." SeeHn1cccc1
, 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:
Feature | SMILES | Dialect |
---|---|---|
element symbol Ha | accepts | rejects |
element symbols Db; Sg; Bh; Hs; Mt; Rg; Cn; Nh; Fl; Mc; Lv; Ts; and Og | rejects | accepts |
future element symbols approved by IUPAC | rejects | accepts |
comma symbol (, ) |
may accept | rejects |
multiple branching e.g., *((*))* ) |
accepts | rejects |
reactions using greater than symbol (> ) |
accepts | rejects |
extended stereodescriptors e.g., @@@ , @@@@ , @AL1 , @1 , and @SP1 |
accepts | rejects |
use of stereodescriptors on odd cumulene centers | accepts | rejects |
virtual hydrogen count on hydrogen | probably rejects | accepts |
detachments are bonds of "formal order zero" | probably accepts | rejects |
upper and lower bounds on atomic properties | rejects | accepts |
nitrogen default valence includes 5 | partially accepts | accepts |
unbracketed hydrogen atom | partially accepts | rejects |
acyclic atom selection | partially accepts | accepts |
from dialect.
Related Issues (20)
- Standardize placement of references
- Use smart quotes HOT 2
- Selected star
- Add `isotope` to Table 2
- Add reference for LL(1) grammar.
- Drop support for "H0", "+0"/"-0" and "[0H]"
- Revert transuranium element additions
- Re-phrase Table 5 entries for clarity
- Eliminate indexes on Atom and Bond
- Add reference for PIKAChU HOT 1
- ProtoSMILES is just the Chapter
- Drop atom rank
- Under Reading Strings, "root atom" should be "head"
- Remove reference to the paper in README HOT 1
- README: remove exception to close for extension statement
- Figure: Representative Dialect Examples.
- Figure: Tree vs. Graph
- Figure: Node Order
- Figure: Nodes and Edge Associations
- Figure: Elements
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from dialect.