Disconnected Lomap networks

[hannahbaumann]

Lomap networks can sometimes be disconnected.
For one system from the PLB(pde2), there's a morpholine ring that slightly is shifted and lead to kartograf not mapping it and therefore the lomap score being very low. This results in two ligands from being disconnected from the rest of the network. I slightly increased the atom_max_distance and now got a connected network, mapping the ring.
Should the generate_lomap_network warn the user if the network is not connected?
Our network visualization (plot_atommapping_network(ligand_network)) overlays ligand names, therefore making it very difficult to visually see when networks are not connected.

[richardjgowers]

This might be more of an issue for the Lomap repo. I'll have to double check what the original Lomap CLI interface would have done in this case. It probably should be producing a connected network, and being very noisy when this doesn't happen.

[hannahbaumann]

I'm actually having trouble reproducing it right now, so it could be that it was some weird Lomap version that I was using 4 months ago when I generated all these networks for the PLB
.

[richardjgowers]

hmm, even so I'm curious what happens if you put in a scaffold hop (or something that can't map)

[IAlibay]

@atravitz this might be a good one to stick in the next release - in the gufe layer at least, it's a simple "is it connected? no? throw a warning"