Mol-116

[arp6695]

Description

Atom replacement story for PDB, CIF, and SDF files.

Checklist

• [x] Code compiles correctly
• [x] Created tests which fail without the change (if possible)
• [x] All tests passing
• [x] Extended the README / documentation, if necessary

[mag8224]

Any added tests for this?

[arp6695]

@mag8224 No unit tests. I don't believe we're writing unit tests for Docking yet, but I can pick those up when the time comes.