fullrmc is not a reverse monte carlo fitting tool but a stochastic engine library to model all kind of homogeneous and hybrid materials such as liquids, crystals, atomic and molecular systems, biological structures or any mixture of those. fullrmc recognizes molecules and crystal structure unitcells and make use of those to enable users with helper functions to define certain constraints properties such as bonds and angles.
From the pdb structure, fullrmc recognizes molecules or a unitcell as the collection of consecutive atoms sharing the same “Residue name”, “Sequence number” and “Segment identifier” attributes. For more information about pdb file attributes click here.
Molecules can be defined in two different ways in fullrmc.
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.
The second way to define molecules is by using Engine.set_molecules_index method.
Unitcells as well can be defined in two different ways in fullrmc.
Setting the Engine pdb structure using Engine.build_crystal_set_pdb method
Using Engine.set_structure_supercell method to parse the structure into a supercell of unitcells.
Engine methods such as ‘set_groups_as_atoms’ and ‘set_groups_as_molecules’ ‘set_groups_as_unitcells’ make full use of molecules and unitcells definition. When called, list of groups will be automatically generated to respectively create groups of single atoms, molecules or unitcells.