GitLab

Update Installation.md - fix pl_upgrades clone instructions

That direct clone of branch url does not work. Replaced it with a proper clone command with -b.

Remove unnecessary double-load of config_json.

Add use_custom_templates option

Fix 3-to-1 letter conversion to use extended mapping

Update Aux_seq_files.md

formatting change to file directory structure

Fix formatting in installation.md

Rename installation.md to Installation.md to fix typo in index file.

Link OpenFold repo from the docs

The intro part taken from the main README (which makes a title on GitHub) obviously did not link to itself but now the repo is hard to find when reading the (great!) docs :)

Adds Documentation and minor quality of life fixes

Fix Colab by using OF commit from pl_upgrades

Duplicate expansion support

Fixed a small typo in permutation unit test docstring