Make atom container with geometry routines

[tomnewport]

• [ ] Build container
  • [x] Residue Container
  • [x] Add atoms
  • [x] x, y, z
  • [x] Residue name
  • [x] Atom name
  • [x] Look up additional fields
    • [x] Add additional fields
  • [x] Save to PDB
  • [ ] Open as MDAnalysis
• [x] Build in simple modification routines
  • [x] Molecule align
  • [x] Direct overlay
  • [x] Fragment align
  • [x] Distortion
• [x] Build in complicated modification routines
  • [x] Simple Bridge