Make alphafold dimers and monomers commands write Boltz yaml input files

[Tom Goddard]

The alphafold dimers and monomers commands currently can write out fasta files suitable for Colabfold or json suitable for AlphaFold 3 predictions. I'd like them also to be able output yaml files suitable for Boltz predictions.

Also I want to be able to include specified MSA files instead of using the Colabfold MSA server in the Boltz input files.

[Tom Goddard]

Done.

I added an outputYaml option (default false) and an msaDirectory option to both alphafold dimers and alphafold monomers commands. A separate yaml input file is made for each monomer or dimer with name matching the monomer or dimer sequence names.

If the msaDirectory is specified then the yaml output will specify MSA files in that directory with file names of the form {seq1-name}_{seq2-name}_0.csv and {seq1-name}_{seq2-name}_1.csv. The msaDirectory and MSA files need not exist and can be created later by MSA computation software before the Boltz predictions are run. If no msaDirectory option is given then no MSA files are specified in the Boltz yaml input.

I also added an option listSequences default false controlling whether descriptions of all the monomers and dimers are output to the log. Formerly they were always logged but this could be a very long list that is often not needed.

[Tom Goddard]

The msaDirectory option only works with Boltz yaml output right now. I plan to make it also work with AlphaFold 3 json output in the near future.