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The previous data_dir_to_fasta.py script is very slow and requires fully reparsing mmCIF files. This new script is much faster and uses the sequence information from the alignment data instead. Note that this will not include chains for which alignments could not be generated, but we can't use those during training anyways.

This adds support for duplicate chain expansion for the alignment dir format. This script can be run on the flattened non-redundant RODA alignments to add explicit directories for all of the duplicate chains in the duplicate_chains file, symlinked to their representative chain alignment directory.

This makes it more straightforward to create an alignment database directly from the flattened RODA downloads

Changes resume_model_weights_only flag in train_openfold to reload weights only, without parsing a time step.

Merge branch 'setup-improvements' of https://github.com/aqlaboratory/openfold into setup-improvements

- much faster due to the use of threading and mp
- also supports sharding

Full multimer merge

Type fixes and README changes for multimer branch

fixed a typo in the readme for soloseq params path