Christian Kramer
Christian Kramer
For a rather complex multi-ring natural-product like compound, bond.IsInRing() does not correctly identify one of the bonds as ring bond. The compound has 3 non-ring bonds. RDKit identifies a fourth...
Double- and triple-cuts can produce regioisomers, where the constant parts are just swapped. Examples are these transformations: Double cut: [*:1]CC1(CC1)[*:2] >> [*:1]C1(CC1)C[*:2] Triple cut: [*:1]c1cc([*:2])c([*:3])cc1 >> [*:1]c1cc([*:3])c([*:2])cc1 It may be...
The Smallest-transformation-only appears to not reduce single-cut transformations to H>>X transformations. For example, the transformation [*:1]c1ccccc1 >> [*:1]c1ccc(F)cc1 is still in the database, although it could be reduced to [*:1][H]...
With the current implementation of smallest-transformation only, some reducible double-cut transformations are still present in the database. For example, this transformation [*:1]C(F)[*:2] >> [*:1]C(Cl)[*:2] can be reduced to that transformation...
Most of the Cut-SMARTS currently cut bonds between aliphatic carbon and Halogens. This may not be desirable, since it leads to CF3 and OCF3 groups being split up. These splits...
When mmpdb transform is called, the algorithm currently fragments the input molecule and searches for replacements for all fragments in the DB. This can then be filtered by the substructure...