Starting from the current release, certain classes of divalent selenium compounds can be handled by SZYBKI. Currently only some compounds in which selenium is bonded to the hydrogen or carbon atoms can be processed. Those compounds include selenols (RSeH) and selenides (RSeR1) in which Se is bonded to alkyl or aromatic carbon atoms, with the following exceptions:
In the restriction above the MMFF94 aromaticity model is adopted, so for example a pyridine derivative, pyridine-3-selenol can be processed, but a pyran derivative 2H-pyran-3-selenol cannot.
Previous SZYBKI releases attempted to assign the “closest” MMFF94 atom type to those atoms for which a unique MMFF94 type could not be found. Starting from the 1.3.5 SZYBKI Application release this feature is removed, so consequently the input molecules containing such atoms will not be processed.
Ligand RMSD which might be extracted from OESzybkiResults object, can optionally refer to heavy atoms only. A new public function:
in OESzybki class has been added for that purpose.