Scanner Error

[Paulina-GM]

Hello,

I'm trying to use the Aizynthapp on the jupyter notebooks, using the documents provided in figshare. When I run the first cell I get the following error message:

ScannerError: while scanning for the next token
found character '\t' that cannot start any token
in "", line 5, column 7:
full_uspto_03_05_19_unique_temp ...

I'm running this in a Linux cluster using python 3.8. If that's of any help.

Thanks in advance for your help.

[Paulina-GM]

Hi again,

Just a follow up. I was able to solve that issue by removing the tabs in the config file. but now I get the following error:

endosome/work/radiology/s187304/aizynth/aizynthfinder/aizynthfinder/context/policy/policies.py in load_from_config(self, **config)
109 files_spec = config.get("files", config.get("template-based", {}))
110 for key, policy_spec in files_spec.items():
--> 111 modelfile, templatefile = policy_spec
112 strategy = TemplateBasedExpansionStrategy(
113 key, self._config, source=modelfile, templatefile=templatefile

ValueError: too many values to unpack (expected 2)

Thanks again in advance for your help.

[SGenheden]

Hello
Could you paste your config-file here? I don't understand how the tabs entered into your file, but the latest exceptions comes from a mal-formated config file. You should specify a policy using something like this

policy:
  files:
    my_policy:
      - path_to_model_file
      - path_to_template_file

[Paulina-GM]

Samuel, Sorry I just realized I have some mistakes in the paths location, I’m using as well the simplified version of the config file: policy: files: my_policy: - full_uspto_03_05_19_rollout_policy.hdf5 - full_uspto_03_05_19_unique_templates.hdf5 stock: files: zinc: zinc_stock.hdf5 And now my error is different: OSError: No file or directory found at full_uspto_03_05_19_rollout_policy.hdf5 I do have the file in the aizynth forlder but I’ll see if there’s something else missing Sorry for the basic questions. I’m just a chemist wanting to use machine learning but my experience is not that much. Thanks in advance for your help From: Samuel Genheden ***@***.***> Sent: Thursday, May 5, 2022 12:10 PM To: MolecularAI/aizynthfinder ***@***.***> Cc: Paulina Gonzalez ***@***.***>; Author ***@***.***> Subject: Re: [MolecularAI/aizynthfinder] Scanner Error (Issue #68) EXTERNAL MAIL Hello Could you paste your config-file here? I don't understand how the tabs entered into your file, but the latest exceptions comes from a mal-formated config file. You should specify a policy using something like this policy: files: my_policy: - path_to_model_file - path_to_template_file — Reply to this email directly, view it on GitHub<#68 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOHPP76OMFIRQYX3G45L4MDVIP6E3ANCNFSM5VFLF6JA>. You are receiving this because you authored the thread.Message ID: ***@***.***> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

…

________________________________ UT Southwestern Medical Center The future of medicine, today.

[Paulina-GM]

Samuel, Sorry for the email bombing. The program is working now! Thank you very much eitherway. Have a nice rest of the evening! Paulina From: Samuel Genheden ***@***.***> Sent: Thursday, May 5, 2022 12:10 PM To: MolecularAI/aizynthfinder ***@***.***> Cc: Paulina Gonzalez ***@***.***>; Author ***@***.***> Subject: Re: [MolecularAI/aizynthfinder] Scanner Error (Issue #68) EXTERNAL MAIL Hello Could you paste your config-file here? I don't understand how the tabs entered into your file, but the latest exceptions comes from a mal-formated config file. You should specify a policy using something like this policy: files: my_policy: - path_to_model_file - path_to_template_file — Reply to this email directly, view it on GitHub<#68 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOHPP76OMFIRQYX3G45L4MDVIP6E3ANCNFSM5VFLF6JA>. You are receiving this because you authored the thread.Message ID: ***@***.***> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

…

________________________________ UT Southwestern Medical Center The future of medicine, today.

[SGenheden]

Glad you could sort it out. I will close this ticket now.
Do not hesitate to return with more questions, even if you think they are basic.
I am glad it found its way to a chemists, and appreciate that you and other chemists are no computer specialists.

[Paulina-GM]

Samuel, Thank you for your prompt response. This is the config file I’m currently using properties: iteration_limit: 100 return_first: false time_limit: 120 C: 1.4 cutoff_cumulative: 0.995 cutoff_number: 50 max_transforms: 6 policy: files: my_policy: -/path/to/keras/model/weights.hdf5 -/path/to/hdf5/templates.hdf5 filter: files: my_policy: /path/to/keras/model/weights.hdf5 reactants_count: filter_tag: stock: files: stock1: /path/to/stock1.hdf5 stock2: /path/to/stock1.hdf5 From: Samuel Genheden ***@***.***> Sent: Thursday, May 5, 2022 12:10 PM To: MolecularAI/aizynthfinder ***@***.***> Cc: Paulina Gonzalez ***@***.***>; Author ***@***.***> Subject: Re: [MolecularAI/aizynthfinder] Scanner Error (Issue #68) EXTERNAL MAIL Hello Could you paste your config-file here? I don't understand how the tabs entered into your file, but the latest exceptions comes from a mal-formated config file. You should specify a policy using something like this policy: files: my_policy: - path_to_model_file - path_to_template_file — Reply to this email directly, view it on GitHub<#68 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOHPP76OMFIRQYX3G45L4MDVIP6E3ANCNFSM5VFLF6JA>. You are receiving this because you authored the thread.Message ID: ***@***.***> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

…

________________________________ UT Southwestern Medical Center The future of medicine, today.

[aa0929]

#I was very excited to try it and the previous error is gone, but a new one appeared