Allow alphafold dimers command to restrict to nearby sequences

[Tom Goddard]

It is sometimes useful to restrict predictions of dimers to sequences that are near each other on a genome. If the input fasta sequences are for an organism such as Mycoplasma genitalium in genome order, then it can be useful to do predictions of sequences within N genes of each other because nearby genes more often have direct interactions when they are co-expressed within an operon.

Would like a maxSpacing option with integer value that specifies how far apart two sequences can be in the input list and still produce dimer output. A value of 1 would mean only adjacent sequence and homo-dimers would be output.

I used this capability in the following demonstration

https://www.rbvi.ucsf.edu/chimerax/data/local-msa-sep2025/pp_screening.html

[Tom Goddard]

Done.

Added maxSpacing option. It applies to all output formats (fasta, json, yaml). The default is that there is no restriction on spacing.