Bugs item #3463509, was opened at 2011-12-21 12:27
Message generated for change (Comment added) made by hansonr
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Category: Scripting
Group: None
>Status: Closed
>Resolution: Invalid
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: Bob Hanson (hansonr)
Date: 2011-12-21 16:17
Message:
OK. Case closed, I think. Just have to be careful with those escapes.
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Comment By: Bob Hanson (hansonr)
Date: 2011-12-21 16:16
Message:
version of Jmol? I see no problem with Jmol 12.3 or 12.2 or 12.0
$ load $cis-butene
$ show smiles
C/C=C\C
$
So that's right. I think what is happening is whatever you are doing with
that string, you are losing the "\C" -- something is converting that to
"escape C" and losing the backslash. Is this in the applet?
>From the applet you would do something like this:
var X = jmolEvaluate("{*}.find('smiles')")
and the return will be:
"C/C=C\\C"
So Jmol is properly escaping that.
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Comment By: Paul Pillot (molusc2)
Date: 2011-12-21 13:41
Message:
I solved the aforementioned problem by using the jmolScriptWaitOutput
method instead of JmolScriptWaitAsArray.
The later strips backward slashes from the script messages.
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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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