[Jmol-developers] [ jmol-Bugs-3463509 ] show smiles not always providing Z/E isomer information

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Bugs item #3463509, was opened at 2011-12-21 12:27
Message generated for change (Comment added) made by molusc2
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Category: Scripting
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Paul Pillot (molusc2)
Assigned to: Bob Hanson (hansonr)
Summary: show smiles not always providing Z/E isomer information

Initial Comment:
Using scribmol, I drew but-2-ene (cis-conformation) in chemdoodle. The corresponding 3D molecule is created by Jmol.
"show smiles" gives : C/C=CC
when transfered to cactus for optimization, the resulting 3D file is in trans configuration (the 2D mol file shows a crossed double bond)
Sometimes (I can't find a reproductible scenario), when I draw the same molecule directly in Jmol, the "show smiles" gives : C(/C)=C/C which leads to a correct optimization.
In trans configuration, the results are quite similar : "show smiles" gives C(/C)=CC which leads to a crossed double bond with cactus, but provides a molecule in trans configuration (I suppose it is the default) 


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>Comment By: Paul Pillot (molusc2)
Date: 2011-12-21 12:59

Message:
My bad ! The results aren't the same via the Jmol console and via the
jmolScriptWait() method : backwards slashes are stripped which explains the
loss of information.

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You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3463509&group_id=23629