Immunebuilder

Added option to set number of threads for CPU users. Thanks FBoyles

Making this version 1.0.0 as [the paper](https://www.nature.com/articles/s42003-023-04927-7) has been published.

Changes from previous version are mostly bug fixes.

Add code to remove strained side chain bonds

Small bug in how errors in b factors are saved to pdb files

Added the option to use different numbering schemes on the command line version of the interface.

Made the sequence check more strict.