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julie-forman-kay-lab / IDPConformerGenerator

Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space
https://idpconformergenerator.readthedocs.io/
Apache License 2.0
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Chains that don't need to be modeled throw error in multi-chain complexes #269

Closed benjbuch closed 6 months ago

benjbuch commented 6 months ago

If the sequence in the pdb and the mapped fasta sequence are identical, an index out of range error is thrown. Most likely, because a sub-routine tries to generate conformers.

Traceback (most recent call last):
  File "miniforge3/envs/idpconfgen/bin/idpconfgen", line 33, in <module>
    sys.exit(load_entry_point('idpconfgen', 'console_scripts', 'idpconfgen')())
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "IDPConformerGenerator/src/idpconfgen/cli.py", line 142, in maincli
    cmd.func(**vars(cmd))
  File "IDPConformerGenerator/src/idpconfgen/cli_ldrs.py", line 637, in main
    DISORDER_BOUNDS[chain] = consecutive_grouper(disordered_res)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "IDPConformerGenerator/src/idpconfgen/ldrs_helper.py", line 145, in consecutive_grouper
    grouped = [[seq[0]]]
                ~~~^^^
IndexError: list index out of range

The expected behavior would probably be to skip modeling the chain with a warning. (Or likewise this is an opportunity to skip some parts if there are less than X residues?)

benjbuch commented 6 months ago

A work-around is to clip the PDB file by three or four residues and have them modeled.

menoliu commented 6 months ago

Thanks @benjbuch for catching this bug, you are correct, any perfectly matching sequences-to-PDB should not be modelled and skipped.

I will see to this at my earliest convenience!

formankay commented 6 months ago

Thanks!

From: Zi Hao (Nemo) Liu @.> Sent: March 11, 2024 11:42 AM To: julie-forman-kay-lab/IDPConformerGenerator @.> Cc: Subscribed @.***> Subject: Re: [julie-forman-kay-lab/IDPConformerGenerator] Chains that don't need to be modeled throw error in multi-chain complexes (Issue #269)

Thanks @benjbuchhttps://github.com/benjbuch for catching this bug, you are correct, any perfectly matching sequences-to-PDB should not be modelled and skipped.

I will see to this at my earliest convenience!

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benjbuch commented 6 months ago

Thank you, @menoliu!