On Sat, Jul 30, 2011 at 3:42 PM, Richard Ball <[email protected]> wrote:
> Thanks Otis. I thought I'd give this path a try just to see what happened.
> I extracted the structure ABELEZ from the CSDB and saved it as a .mol2 file.
> Fired up the Jmol application and opened that mol file and the structure
> comes up nicely. But there is no option to export this structure as SMILES.
>
>
Just not in the menu.
print {*}.find("SMILES")
or
show SMILES
what you do with that string is totally up to you.
var s = {*}.find("SMILES")
write var s "mol.smi"
The SMILES will have all stereochemistry indicated, up through octahedral.
So that should be enough for other programs. But I don't know what to do
with it after that to get the CIP R/S designation. For simple molecules, of
course, you can send it to the resolver and get the chemical names. Jmol
will do this for you:
show chemical name
For example:
$ load $caffeine
show SMILES
[n](C)1c2=O.c23=c4[n](C)c1=O.[n](C)3c=[n]4
$ show chemical name
1,3,7-trimethylpurine-2,6-dione
1,3,7-Trimethylxanthine
71701-02-5
95789-13-2
58-08-2
SDCCGMLS-0064595.P002
PDSP2_001000
KBioGR_002325
NCIOpen2_008255
AIDS-001649
AIDS001649
Tri-Aqua
IDI1_000730
C8960_SIAL
75035_FLUKA
Mettler Toledo Calibration substance ME 18872, Caffeine
1-methyltheobromine
3,7-Dihydro-1,3,7-trimethyl-1H-purin-2,6-dion
...[and about 100 more]...
1,3,7-trimethyl-3,7-dihydro-1H-purine-2,6-dione
InChI=1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H
But that doesn't necessarily get you CIP chirality designations.
Egon, what do you recommend?
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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