Seeking Assistance with PLIP Installation Issues on CentOS

[Nicole-DH]

Dear PLIP Developers,

I hope this message finds you well. I'm writing to seek your guidance regarding an installation issue I've encountered while setting up PLIP (v2.4.0) on my CentOS system following the official documentation. Despite multiple attempts, I haven't been able to resolve these errors and would appreciate your expertise.

System Configuration:

• OS: CentOS Linux
• Python: 3.8.19 (via conda environment)
• Open Babel: 3.1.0
• PLIP: 2.4.0

Initial Installation Error
After verifying Open Babel's successful installation, executing plip resulted in:
ImportError: cannot import name 'pybel' from 'openbabel' (unknown location)

I installed pybel via pip, but same error occurred.

Reinstallation Error
So I reinstalled OpenBabel via Conda,
conda install -c conda-forge openbabel
but executing plip resulted in:
Segmentation fault (core dumped)

Thanks for your time and assistance in advance.

[vjhaupt]

Hi Nicole, The import error is probably due to the missing reference to pybel in the `PYTHONPATH` environment variable. Locate your pybel package and append its path to `PYTHONPATH`. Best, Joachim On 19. Mar 2025, at 06:32, Nicole ***@***.***> wrote: Dear PLIP Developers, I hope this message finds you well. I'm writing to seek your guidance regarding an installation issue I've encountered while setting up PLIP (v2.4.0) on my CentOS system following the official documentation. Despite multiple attempts, I haven't been able to resolve these errors and would appreciate your expertise. System Configuration: * OS: CentOS Linux * Python: 3.8.19 (via conda environment) * Open Babel: 3.1.0 * PLIP: 2.4.0 Initial Installation Error After verifying Open Babel's successful installation, executing plip resulted in: ImportError: cannot import name 'pybel' from 'openbabel' (unknown location) image.png (view on web)<https://github.com/user-attachments/assets/2474bdc4-d6bc-4f3c-a75b-1aba3cbbb0f4> Reinstallation Error So I reinstalled openbabel use conda, conda install -c conda-forge openbabel but executing plip resulted in: Segmentation fault (core dumped) Thanks for your time and assistance in advance. — Reply to this email directly, view it on GitHub<#173>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEJLMO7XHWRXW5GGTK2T4NT2VD6O3AVCNFSM6AAAAABZJ4IDMKVHI2DSMVQWIX3LMV43ASLTON2WKOZSHEZTANJQHE4TKMQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [Nicole-DH]Nicole-DH created an issue (pharmai/plip#173)<#173> Dear PLIP Developers, I hope this message finds you well. I'm writing to seek your guidance regarding an installation issue I've encountered while setting up PLIP (v2.4.0) on my CentOS system following the official documentation. Despite multiple attempts, I haven't been able to resolve these errors and would appreciate your expertise. System Configuration: * OS: CentOS Linux * Python: 3.8.19 (via conda environment) * Open Babel: 3.1.0 * PLIP: 2.4.0 Initial Installation Error After verifying Open Babel's successful installation, executing plip resulted in: ImportError: cannot import name 'pybel' from 'openbabel' (unknown location) image.png (view on web)<https://github.com/user-attachments/assets/2474bdc4-d6bc-4f3c-a75b-1aba3cbbb0f4> Reinstallation Error So I reinstalled openbabel use conda, conda install -c conda-forge openbabel but executing plip resulted in: Segmentation fault (core dumped) Thanks for your time and assistance in advance. — Reply to this email directly, view it on GitHub<#173>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEJLMO7XHWRXW5GGTK2T4NT2VD6O3AVCNFSM6AAAAABZJ4IDMKVHI2DSMVQWIX3LMV43ASLTON2WKOZSHEZTANJQHE4TKMQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Nicole-DH]

Hi Nicole,

The import error is probably due to the missing reference to pybel in the PYTHONPATH environment variable. Locate your pybel package and append its path to PYTHONPATH.

Best, Joachim

Hi Joachim,

Thanks for your advice. I tried to add the PYTHONPATH for pybel, but another error appears.
ImportError: cannot import name 'Iterable' from partially initialized module 'typing' (most likely due to a circular import)

[vjhaupt]

Yeah. Sorry. It is really not so trivial to get OpenBabel to work. I cannot provide support on that issue. Why don’t you try our docker image for plip? This will save you all the hassle... On 19. Mar 2025, at 07:35, Nicole ***@***.***> wrote: Hi Nicole, The import error is probably due to the missing reference to pybel in the PYTHONPATH environment variable. Locate your pybel package and append its path to PYTHONPATH. Best, Joachim Hi Joachim, Thanks for your advice. I tried to add the PYTHONPATH for pybel, but another error appears. ImportError: cannot import name 'Iterable' from partially initialized module 'typing' (most likely due to a circular import) image.png (view on web)<https://github.com/user-attachments/assets/25d299b0-b349-4c2d-9f5a-926a45183307> — Reply to this email directly, view it on GitHub<#173 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEJLMO7ELWQLUIYBOV6NUZL2VEFZTAVCNFSM6AAAAABZJ4IDMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMZVGQ4DIOJWGE>. You are receiving this because you commented.Message ID: ***@***.***> [Nicole-DH]Nicole-DH left a comment (pharmai/plip#173)<#173 (comment)> Hi Nicole, The import error is probably due to the missing reference to pybel in the PYTHONPATH environment variable. Locate your pybel package and append its path to PYTHONPATH. Best, Joachim Hi Joachim, Thanks for your advice. I tried to add the PYTHONPATH for pybel, but another error appears. ImportError: cannot import name 'Iterable' from partially initialized module 'typing' (most likely due to a circular import) image.png (view on web)<https://github.com/user-attachments/assets/25d299b0-b349-4c2d-9f5a-926a45183307> — Reply to this email directly, view it on GitHub<#173 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEJLMO7ELWQLUIYBOV6NUZL2VEFZTAVCNFSM6AAAAABZJ4IDMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMZVGQ4DIOJWGE>. You are receiving this because you commented.Message ID: ***@***.***>

[Nicole-DH]

Yeah. Sorry. It is really not so trivial to get OpenBabel to work. I cannot provide support on that issue. Why don’t you try our docker image for plip? This will save you all the hassle...

On 19. Mar 2025, at 07:35, Nicole @.***> wrote:

Hi Nicole,

The import error is probably due to the missing reference to pybel in the PYTHONPATH environment variable. Locate your pybel package and append its path to PYTHONPATH.

Best, Joachim

Hi Joachim,

Thanks for your advice. I tried to add the PYTHONPATH for pybel, but another error appears.
ImportError: cannot import name 'Iterable' from partially initialized module 'typing' (most likely due to a circular import)

image.png (view on web)https://github.com/user-attachments/assets/25d299b0-b349-4c2d-9f5a-926a45183307

—
Reply to this email directly, view it on GitHub<#173 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEJLMO7ELWQLUIYBOV6NUZL2VEFZTAVCNFSM6AAAAABZJ4IDMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMZVGQ4DIOJWGE.
You are receiving this because you commented.Message ID: @.***>

[Nicole-DH]Nicole-DH left a comment (pharmai/plip#173)<#173 (comment)>

Hi Nicole,

The import error is probably due to the missing reference to pybel in the PYTHONPATH environment variable. Locate your pybel package and append its path to PYTHONPATH.

Best, Joachim

Hi Joachim,

Thanks for your advice. I tried to add the PYTHONPATH for pybel, but another error appears.
ImportError: cannot import name 'Iterable' from partially initialized module 'typing' (most likely due to a circular import)

image.png (view on web)https://github.com/user-attachments/assets/25d299b0-b349-4c2d-9f5a-926a45183307

—
Reply to this email directly, view it on GitHub<#173 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEJLMO7ELWQLUIYBOV6NUZL2VEFZTAVCNFSM6AAAAABZJ4IDMKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMZVGQ4DIOJWGE.
You are receiving this because you commented.Message ID: @.***>

Yes, docker is a good choice, but I don't have it installed on my machine and I am not a root user. Anyway, I will try. Many thanks.