| Re: Loss of stereochemical information when importing sdf file [message #472 is a reply to message #464] |
Tue, 12 February 2019 20:39  |
thomas
Messages: 663
Registered: June 2014
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Senior Member |
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I assume that your SD-File contains racemates. SD-files version 2 contain the so-called chiral-flag (5th entry in 4th line of every molfile), which defines, whether a molecule is a racemate or pure enantiomer. If this flag is 0, then even if the molecule contains up/down stereo bonds it must be interpreted as racemic.
After reading these SD-files DataWarrior knows that the stereo centers are racemic and not unknown (DataWarrior distinguishes this). Smiles do not distinguish between racemic and absolute stereo centers. Thus, if a racemic molecule has multiple stereo centers, DataWarrior writes the stereo configuration of these (@ and @@) into the smiles in order to retain the relative configuration. In the special case where the molecule only contains one stereo center, DataWarrior might omit the stereo information, because there is no relative stereo configuration. Currently, it does not, but I should probably change that.
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