saturator script, release 1.2.0

Tests with pytest have been reorganized to allow using them in a virtual environment e.g., within a GitHub action.

saturator script, release 1.1.0

The revised approach of this release relies more on regular expressions, than the previous release. One of the consequences is that each SMILES string now may contain one, or multiple pairs of square brackets.

saturator script, release 1.0

The revision of the script providing "saturation" of a SMILES strings offered multiple small improvements this release bundles. Backed by automatic testing (pytest), it is anticipated that the script is in a significantly better position to work on SMILES describing saturated and non-saturated (organic) compounds. This includes homo- and heteroaromatic cycles of carbon, nitrogen, oxygen, phosphorous, and sulphur (C, N, O, P, S). The SMILES string submitted may describe multiple molecules per SMILES string usually concatenated by . (period), like solvates and co-crystals.

Taking a conservative approach, the script relays CIP's (R)/(S) indicators as well as atom assigned charges identified as such in the input file to the permanent output file. Depending on the substrate, this may be sensible (e.g., tetraalkylated ammonium), or not (e.g., saturation of pyridine N-oxide). It is in the the user's responsibility to sanitize these processed strings, or to complement the description of now present stereogenic centers (e.g., saturation of methyl ethylketone) if necessary.

To prevent additional ambiguity in the permanent records written, the script automatically blocks any SMILES potentially describing tin (expressed as [Sn]) which otherwise would be «saturated» to [SN]. Thus, the script is not of use to process e.g., Stille reagents.