I'm getting an error when I try to calculate a property (e.g. charge) for an sdf/mol file with bonds marked as broken or made by a reaction (i.e. the 7th column of the bond block not 0). See the attachment. If I replace the 4 by 0 it works. Is this a bug? Anyone suggests a way to get out of it?
We will fix this.
In the previous versions, we just ignored this field, but the recent major Marvin/JChem version introduced this feature as a query option in reaction tables. This is why your molecule is treated as "query" molecule now. (We overlooked the fact that reacting centers are sometimes marked on reaction databases.)
Thank you for pointing this out.