| C=C double bonds/search by extended stereochemistry [message #1447] |
Tue, 30 November 2021 17:11  |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Hello Thomas,
my understanding of DataWarrior's manual is that the program internally stores
the molecules in a format capable to discern and (if selecting .sdf v3000)
export of double bonds including those without explicit assignment of (E)/(Z)
configuration. As anticipated, the SMILES strings
C/C=C/C
C/C=C\C
CC=CC
yield three different representations of but-2-ene.
For a small test set (cf. double_bond.dwar and the screen photos in the .zip
archive attached), I aimed to use the features of extended stereochemisty as a
criterion to retain a sub set (Chemisty -> From Chemical Structure -> Add
Substructure Count), including the unassigned double bond visualized as a
crossed double bond. So far, the attempts failed.
As anticipated, the search pattern of (cis)-butene, retained both (cis)-butene
and cyclohexene and withdrew the oxime. However -- contrasting to anticipation
-- (trans)-butene and the unassigned butene equally were retained. Does the
search for, e.g. crossed double bonds, require a particular instruction?
Version info: DataWarrior 5.5.0 for Linux in Debian 12/bookworm (branch
testing), including the update as «development version» as fetched on Sunday,
2021-11-28.
Norwid
[Updated on: Tue, 30 November 2021 17:26] Report message to a moderator |
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| Re: C=C double bonds/search by extended stereochemistry [message #1466 is a reply to message #1447] |
Tue, 11 January 2022 16:12  |
thomas
Messages: 711
Registered: June 2014
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Senior Member |
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Dear Norwid,
sorry for the long delay. I somehow missed your question. As default DataWarrior does not match the stereo configuration of atoms or bonds on the substructure search. You may, however, require for individual atoms or bonds a stereo configuration match. In the editor select the lasso tool and double click an atom or bond. In the dialog that opens, you can select 'Match Stereo Configuration'. Then DataWarrior uses the 'Enhanced Stereo Representation' rules defined by MDL many years ago, e.g. a racemic center in the query matches a racemic, OR, and pure R- or S-center. An explicit R in the query only matches a pure R. For stereo bonds you cannot select 'Match Stereo' for cross bonds, which is in-line with the atom-logic, because an unknown configuration always matches all better specified configurations in the MDL logic. This means you can directly search for E- and Z-bonds, but not for unspecified (cross). You could, however, do that with two individual inverted filters, i.e. excluding E- and excluding Z-.
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