Mayor bug fixes¶
Fixed two bugs in kekulization of large molecules. First, some large molecules would fail kekulization when they were actually ok. Second, even when they were kekulized correctly, the method would still return false.
This tweaks the MDL mol file reader to use the test
dimension != 3instead of “dimension == 2” when deciding to honor the wedge/hash bonds or to determine the chirality from 3D coordinates. The subtle difference is that at the point this code is called, the dimension is not necessarily “2” or “3” if the (optional) header line is missing. If the header has been omitted, we treat the molfile like a 2D file (which it most probably is).
Changed SMARTS parser to allow a TAB character (
\t) to be treated as a separator following a SMARTS pattern. This reflects similar functionality in the SMILES parser and simplifies the task of writing “patty”-like applications.