Bond guessing for (water?) molecule detection
Some topolpgies (e.g. LAMMPS data files) do not include sufficient and robust information on molecules/bonds to rigorously detect e.g. water molecules.
We could use the bond-guessing feature of MDAnalysis to detect such molecules, use correct PBC information etc. by passing an appropriate flag to MAICoS.
I attach a sample SPC/E LAMMPS data file of 516 waters.