This PR updates the tests so that all the examples run and if an example
fails then the test results in a failure as well. Changes include:
- Reformatting design_macrocyclic_binder.sh and
design_macrocyclic_monomer.sh to be submitted correctly by
test_diffusion.py
- Reducing the total length in design_tetrahedral_oligos.sh to reduce
run time of this test
- Changes to test_diffusion.py and main.yml to be able to run the
examples in different chunks so examples can run in parallel and to make
sure that if an example errors out, that the tests does not pass.
Currently design_ppi_scaffolded, design_timbarrel, and
design_ppi_flexible_peptide_with_secondarystructure_specification are
failing which should be addressed in other, future PRs.
A number of issues (e.g., #103 , #171 ,
https://github.com/RosettaCommons/RFdiffusion/issues/312 , #315 ) have
mentioned that RFdiffusion will change the chain IDs and residue
numbering of the input structure. The designed chain ends up as chain
"A", and the fixed chain(s) end up as chain "B". The numbering is also
reset to start at 1. This can be particularly problematic in cases where
comparisons to structures are needed, as well as multi-chain situations
where all of the chains get fused.
Inspired by @GCS-ZHN 's comment and solution referenced in Issue #103 ,
I've modified the code to maintain chain and residue numbering. In
particular:
Chains that are not "designable" will retain their original chain ID
letters and residue numbers.
Chains that are partially fixed (e.g., motif re-scaffolding) will retain
their original chain ID letters. Residues will be re-numbered from 1 to
length of chain. (It was not clear to me what the "correct" behaviour of
chain residue numbering should be, given that the length of the chain
and the position of any fixed residues might change.)
Chains that are being fully generated de novo will be assigned the first
available chain ID in the alphabet not used by any other chain. Residues
will be numbered from 1 to length of chain.
Update README to point to new [documentation
resource](https://sites.google.com/omsf.io/rfdiffusion/overview).
I also added some text in the Installation section to 1) specify that
Sergey O.'s colab notebook only contains some of the features of
RFdiffusion and 2) that there is now a Rosetta Commons-maintained docker
image.
For chains that are completely fixed, retain the residue numbering from
the input rather than renumbering. For chains that are partially or
fully designed by RFdiffusion, it isn't clear to me what the 'correct'
behaviour should be, so these chains will be re-numbered starting at
residue 1.
The output was previously renumbering all of the chains, making
comparisons to the input structures and handling of multi-chain inputs
challenging. This commit maintains the input chain ids in the
output.
