producing a homodimer

[victoriapopov]

About 2 weeks ago i managed to model homodimers by providing the same sequence twice via python. Now it is not working and I'm getting the error- "raise ValueError("Duplicate entity %s found" % entity)".
Why has it changed and how can I model homodimers now?

[arogozhnikov]

You just need to give them different names, like so:

example_fasta = """
>protein|name=peptide-1
AGSHSMRYFST
>protein|name=peptide-2
AGSHSMRYFSTDM
"""

[arogozhnikov]

I don't see where/why it would come from then.

I'm not sure this error comes from our code then - we don't have Duplicate entity is the codebase, so I need your stacktrace + output of pip freeze to make any conclusion. Better yet, an example of failing input.

Side comment: new input format uses name=, this was changed more than a month ago (sep 20), not two weeks

[victoriapopov]

Thanks for the feedback,
I'm attaching both the output from pip freeze and the error log.
requirements.txt
err.txt

[arogozhnikov]

thanks, we just fixed it, please try installing fresh version with

pip install git+https://github.com/chaidiscovery/chai-lab.git

[victoriapopov]

Hi,
thanks a lot for the reply.
unfortunately even after updating the version I still encounter the same issue.
I also tried running the example fasta from #245
and still got "ValueError: Duplicate entity <ihm.Entity(peptide-2)> found".
error.txt

[arogozhnikov]

example from #245 works on main (there is no peptide-2 among names). Example from #251 also works on main. Pls check you have fresh version from the main branch.