Molecules are a tool for duplicating and manipulating groups of atoms. Molecules are particularly useful for initializing systems.
#assigns atoms to a molecule
molec = state.createMolecule(ids=[...])
#create a complete copy of the molecule including bonds, angles, etc.
duplicate = state.duplicateMolecule(molec)
#move the molecule by x=10
duplicate.translate(Vector(10, 0, 0))
#rotate the molecule by pi radians around the axis (1, 0, 0)
duplicate.rotate(Vector(1, 0, 0), pi)
Creating a molecule groups already-existing atoms into a molecule. This molecule can then be duplicated, translated, and rotated. Molecules can be accessed through the state.molecules member, which is a python list.
state.deleteMolecule(molec)
Molecules can also be deleted. Deleting a molecule deletes the member atoms and all associated bonds, angles, etc.