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Chrial drawn structures in dwar / sdf different [message #358] Tue, 05 June 2018 13:15 Go to next message
Dennis is currently offline  Dennis
Messages: 3
Registered: May 2018
Location: Netherlands
Junior Member
I have a question about the way a structure is presented in a dwar file compared to a sdf file. When I draw a chiral structure with unknown chirality and save this as a dwar file and open it again, I see the structure drawn as in 1.png:
index.php?t=getfile&id=39&private=0
When I save this file as sdf file and open this sdf file, the drawn structure is different, see 2.png: index.php?t=getfile&id=40&private=0

Why is the chirality presented differently for these files? You would expect the same presentation.
  • Attachment: 1.png
    (Size: 4.80KB, Downloaded 67 times)
  • Attachment: 2.png
    (Size: 4.58KB, Downloaded 64 times)
Re: Chrial drawn structures in dwar / sdf different [message #359 is a reply to message #358] Tue, 12 June 2018 23:47 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 146
Registered: June 2014
Senior Member
In principle you are right. DataWarrior and SD-Files, both distinguish unknown chirality from a racemic.
In molfiles stereo centers are usually represented by an up- or down-bond at the stereo center.
In addition the wide-spread molfile version 2 has one flag (wrongly called 'chiral' flag), which defines,
whether the molecule is racemic (flag=0) or the drawn enantiomer (flag=1). Correctly, a racemate would have
a down- or up-bond and the chiral flag would be 0. The molfile also allows an 'either' bond, which would
describe a mixture and thus supposedly also a racemic situation.

When DataWarrior writes an unknown stereo center into the molfile, it doesn't write any stereo information
making the stereo center effectively unknown.

The problem starts when the molfile is read again. If you get SD-files from chemicals' providers, they often
encode racemates of molecules with one stereo center the same way, i.e. they don't use one of the two proper
methods described above to define the racemate. They just don't write any stereo information. Therefore,
molecules with one stereo center, which have no information, are usually meant to be racemates. For this
reason DataWarrior also treats them as racemate. Another ugly example is that many software packages
read molecules as pure enantiomers if a stereo center has an up- or down-bond, even if the chiral flag is
not set. This means, encoding a racemate the right way often creating a wrong result. This may also be
the reason for many software providers to rather write no stereo information in case of racemates.

If you need to write structure files with DataWarrior to read them again from DataWarrior I strongly suggest to
use the native format, because the conversion to and from molfiles is not guaranteed to give the same result.
This is especially true for substructures, which contain query features.

Thomas
icon14.gif  Re: Chrial drawn structures in dwar / sdf different [message #361 is a reply to message #359] Wed, 20 June 2018 11:30 Go to previous message
Dennis is currently offline  Dennis
Messages: 3
Registered: May 2018
Location: Netherlands
Junior Member
Thank you for the explanation
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