Create functional spec that does entire step in memory instead of using various file steps

[TJGorrie]

General workflow should be:

list_of_inputs = getInputList()# or a single input in a list
# Determine reference if needed!
for input in list_of_inputs:
    list_of_ligands = getLigandList(input)
    for ligand in list_of_ligands:
        readStructureFile
        Split out structure + ligand only
        readReferenceFile
        readMapFiles
        cutMapFilesPerLigand
        alignAllFiles
        Save!

Then the iteration over list_of_inputs can be run in parallel and the maps will be pre-cut to ligand box....