Colab not Working !!! Error when importing datapipeline

[SauravMaheshkar]

Great work with reproducing the original code and creating a OpenSource PyTorch Implementation ☕️☕️☕️☕️

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When I try to run the attached Colab Notebook, In the "Search against genetic databases" subsection while importing datapipeline from openfold.data, I run into a ImportError, viz.

ImportError: cannot import name 'MultipleChainsError' from 'openfold.data.templates' (/opt/conda/lib/python3.7/site-packages/openfold/data/templates.py)

The full traceback is attached below :-

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-7-8051d602620b> in <module>()
     27 from openfold.data import feature_pipeline
     28 from openfold.data import parsers
---> 29 from openfold.data import data_pipeline
     30 from openfold.data.tools import jackhmmer
     31 from openfold.model import model

/opt/conda/lib/python3.7/site-packages/openfold/data/data_pipeline.py in <module>()
     20 import numpy as np
     21 
---> 22 from openfold.data import templates, parsers, mmcif_parsing
     23 from openfold.data.tools import jackhmmer, hhblits, hhsearch
     24 from openfold.data.tools.utils import to_date

/opt/conda/lib/python3.7/site-packages/openfold/data/templates.py in <module>()
     26 import numpy as np
     27 
---> 28 from openfold.data import parsers, mmcif_parsing
     29 from openfold.data.tools import kalign
     30 from openfold.data.tools.utils import to_date

/opt/conda/lib/python3.7/site-packages/openfold/data/mmcif_parsing.py in <module>()
     27 import numpy as np
     28 
---> 29 from openfold.data.templates import MultipleChainsError
     30 import openfold.np.residue_constants as residue_constants
     31 

ImportError: cannot import name 'MultipleChainsError' from 'openfold.data.templates' (/opt/conda/lib/python3.7/site-packages/openfold/data/templates.py)

Interesting enough if I add from openfold.data.templates import MultipleChainsError I run into a circular ImportError, the error trace is attached below

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-8-71256580fa0c> in <module>()
     27 from openfold.data import feature_pipeline
     28 from openfold.data import parsers
---> 29 from openfold.data.templates import MultipleChainsError
     30 from openfold.data import data_pipeline
     31 from openfold.data.tools import jackhmmer

/opt/conda/lib/python3.7/site-packages/openfold/data/templates.py in <module>()
     26 import numpy as np
     27 
---> 28 from openfold.data import parsers, mmcif_parsing
     29 from openfold.data.tools import kalign
     30 from openfold.data.tools.utils import to_date

/opt/conda/lib/python3.7/site-packages/openfold/data/mmcif_parsing.py in <module>()
     27 import numpy as np
     28 
---> 29 from openfold.data.templates import MultipleChainsError
     30 import openfold.np.residue_constants as residue_constants
     31 

ImportError: cannot import name 'MultipleChainsError' from 'openfold.data.templates' (/opt/conda/lib/python3.7/site-packages/openfold/data/templates.py)

[gahdritz]

Sorry about that! One of the bugfixes yesterday introduced a circular import. Fixed in 0567d99

[tcapelle]

that was fast, I was coming to post the same thing.