removed secondary structure field from Atom. Since it is expected to change from state to state, it  is better to have it as a separate slice or map.
transition commit
The interface with reduce is working correctly but it writes to disk. I have not managed to give reduce the PDB directly with a pipe
added back images
Merged antechamber
antechamber merge
merge devel
restoring hydrogens.go
restoring part_test.go