gilleain torrance

Can't reproduce this bug. If I give the command : ./SMSD -T SDF -t Data/arom.sdf -N -O MOL -o tmp.mol then I get the subgraph in tmp.mol and Data/arom.sdf is...

Ok, so there are several separate issues here: 1) The -Q/q options are not currently designed to be used with -N. 2) The NPE in the graphics was already fixed,...

Can you not just set the initial partition for refinement to be the vertex colors? Something like this : https://github.com/gilleain/moleculegen/blob/master/src/main/java/group/graph/GraphDiscretePartitionRefiner.java#L64-L85