Implement initial guess feature

[Poko18]

Hi,

This pull request implements the --initial-guess feature, inspired by the functionality available in ColabDesign.

Related issue:

• --initial_guess feature #432

Description:

• It enables the handling of protein structure inputs (.pdb and .cif) - using alphafold parser

• The introduction of the --initial-guess flag allows for the utilization of protein structure atom positions as input. This can be achieved either through the primary input or by specifying the structure input after the --initial-guess flag.

• Minor adjustments to the Alphafold code have been made to accommodate this new feature:

• Handle initial guess (ColabFold) steineggerlab/alphafold#8

[Poko18]

This update enables the handling of protein structure inputs (.pdb and .cif) using the AlphaFold parser.

• You can now use ColabFold with .pdb or .cif input
• You can use the --initial-guess flag in the following ways:
  • Provide a sequence from a .pdb or .cif file and add the flag to use coordinates for the initial guess:

    colabfold_batch test.pdb out/ --initial-guess

  • Add a .fasta file as input, utilizing the RFdiffusion polyglycine backbone as the initial guess:

    colabfold_batch test.fasta out/ --initial-guess backbone.pdb

Without and with initial guess

[ajasja]

@sokrypton a friendly bump :)