fullrmc is not a mere atomic reverse monte carlo application but molecules and rigid bodies enabled stochastic atomic reverse modelling platform. Molecules are very important in fullrmc to define bonds, angles, improper and especially inter-molecular distance constraints, etc. When a system is atomic, one should make sure to specify that in the pdb file or use the engine to do that.

Molecules can be defined in two different ways in fullrmc.

  1. The first and more natural way of defining molecules is using a correct and complete pdb file. for more information about pdb files click here.
  2. The second way to define molecules is by using Engine.set_molecules_indexes method.

Engine methods such as ‘set_groups_as_atoms’ and ‘set_groups_as_molecules’ make full use of molecules definition. They reset the engine groups list and automatically generate respectively as list of groups of single atom each or a list of groups of single molecule each.