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18:00:48
shiho
I mean (language.smarts.parser:parse "[Na]" 'list) -> (:ATOM NIL :KIND :ORGANIC :SYMBOL "N" :BOUNDS (1 . 2))(:ATOM NIL :KIND :AROMATIC :BOUNDS (2 . 3))
18:04:52
drmeister
shiho: We can probably fix that - the usual way I do it is first to check against all two character element names and then one character element names.
18:07:05
drmeister
I set up a cando jupyterlab server on the iMacPro but I wasn't able to test it. I think it needs to be shutdown anyway and a new one started up.
18:13:25
scymtym
shiho: drmeister: one of the lists in https://github.com/scymtym/language.smarts/blob/future/src/smiles/parser/grammar.lisp#L59-L73 must be incomplete. i'm surprised how this went wrong since i copied those lists
18:15:29
drmeister
scymtym: Can we just reorder the lists? Two character names first, one character names second?
18:16:41
Bike
https://github.com/drmeister/cando/blob/bfb02a4759a12d3acd47e195ef19d7c79c07757a/src/chem/msmarts_Parser.cc#L2436-L2444 not sure it's present in what you copied from
18:17:06
scymtym
but yes, if you add "Na", it has to go in before "N" (esrap will warn about the problem)
18:21:23
scymtym
drmeister: if this variant of the SMARTS language will be an important component of cando, a formal description of the language will be needed since it deviates from the existing specifications (and those aren't optimal either)
18:21:51
drmeister
Shiho: Regarding chemistry Alex's work. I can't get into the iMacPro to fix the jupyterlab server that I set up there - so we are spinning up an Amazon machine for him to try.
18:28:06
scymtym
i pushed a commit adding "Na" to INORGANIC-ATOM-SYMBOL to the "future" branch of https://github.com/scymtym/language.smarts . the tests assert that "[Na]" is parsed as (bracketed-expression … (:atom () :kind :inorganic :symbol "Na" …) …). is that correct?
19:09:40
Bike
I tried building with my lisp gf compiler, and it's a good deal slower (build took 48m instead of 22m like usual) but everything seems to work
19:14:45
drmeister
Ok - that's consistent with expectations. I guess efficient gf dispatch is really important for good performance from cleavir.