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MehmetAzizYirik / MAYGEN

MAYGEN is an open source chemical structure generator based on the orderly graph generation method.
MIT License
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feature suggestion: extend consideration of stereo chemistry #83

Open nbehrnd opened 3 years ago

nbehrnd commented 3 years ago

MAYGEN (release 1.7) was deployed on sum formula C5H10O and to deposit the results in a .sdf in common. Initial observation suggests the list of isomers is incomplete when it comes to stereogenic centres,* and (E)/(Z) double bonds.

Please improve MAYGEN such the generation of isomers eventually is exhaustive.

The .sdf generated was read by DataWarrior. Right on launching, DataWarrior warns about the .sdf read (cf. the attached .zip archive with the .sdf and screen photos taken). For example, entries 11 (2-methyl cyclopropanol) and 24 (2-methyl cyclobutanol), both with two stereogenic centres display only one entry each, skipping the permutation of (R)/(S) configuration. In an exhaustive generation of isomers, entry 32 (pent-2-enol) is anticipated to yield both explicit (E), as well as explicit (Z) isomer, but is depicted like "undetermined/mixture". This detail possibly does not hurt (as much) in mass spectroscopy than in the generation of substrates for synthesis.

maygen_stereochemistry.zip

*) What about chiral sulfoxides? Perhaps a similar limitation.

MehmetAzizYirik commented 3 years ago

@nbehrnd There are no functions in MAYGEN - as not mentioned in the publication - for stereochemistry. For sure, it is in the future tasks for MAYGEN but not in the current or the coming versions.