Changes between Initial Version and Version 1 of Ticket #18826, comment 1


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Timestamp:
Sep 19, 2025, 6:48:31 PM (5 weeks ago)
Author:
Tom Goddard

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  • Ticket #18826, comment 1

    initial v1  
    33I 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.
    44
    5 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}_0.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.
     5If 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.
    66
    77I 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.