Searching for SMILES with "abs" stereo

This question arrived in email from one of our users:

I have a question on the
getMol() function of the MSketch applet. Does it retrieve the smiles string
properly when the structure is drawn with “abs” stereo?

For e.g. : CO[C@H]1O[C@H](OC)[C@@H](OC)[C@@H](OC)[C@@H]1OC |a:2,4,7,10,13|

(ed: the structure was modified for the request ofthe user)

This str. When pasted in MSketch
applet, shows nice but when searched for it, my Jscript function (return
applet.getMol(“smiles”); returns nothing.

If I removed the “abs” flags,
but keep the stereobond, the smiles is generated and the search returns some
hits.

 

Then I copied the extended
smiles and inserted into the URL and re-tried the search. Then the search
returned with a hit.

 

One other thing I could not
locate (yet) in the docs, is the possible parameters I can pass to the getMol()
function besides “mol” ands “smiles”.

This is added to this by the same user:

I
think I kind of resolved the issue by changing the getMol(“smiles”) to getMol(“cxsmiles”)
I picked this up from the file formats link leading to extended smiles.
Althought there is no mention of it in the e.g., (only mol and smiles were
given in the e.g.) I guessed then any of these export options should be
supported and tried it.

JChem stereo search documentation related to search differences when the abs label is used:

https://www.chemaxon.com/jchem/doc/user/query_stereochemistry.html#relative_stereo

The following string

CO[C@H]1O[C@H](OC)[C@@H](OC)[C@@H](OC)[C@@H]1OC |a:2,4,7,10,13|

contains SMILES string at the beginning and the chemaxon extended part between '|' (pipe) characters.

So if it imported as SMILES the extended part is not read and the absolute stereo information is lost.

If it is imported as cxsmiles the absolute stereo information is read.

Regarding the question:

"Does it retrieve the smiles string
properly when the structure is drawn with “abs” stereo?"

Yes it does retrieve the smiles string properly BUT the smiles part doesn't have the "abs" stereo information.

I hope the picture is more clear now.

Andras