module 'martini_openmm' has no attribute 'MartiniTopFile'

[pablo-arantes]

Hi,

I performed all the installation steps as described in the tutorial. Everything was fine and I didn't have any issues. However, when I tried to run the script, I'm having the following issue:

Can you please help to address this issue?

Please, let me know if you need more information.

Thank you.

[jlmaccal]

There must be an issue with your installation.

If you look at this line, you can see where this class is defined.

https://github.com/maccallumlab/martini_openmm/blob/78abd500302d99715e96907a06771d939ef99672/martini_openmm/martini.py#L118

[pablo-arantes]

HI,

Follow my output from installation step:

running install
/usr/local/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/usr/local/lib/python3.10/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running bdist_egg
running egg_info
writing martini_openmm.egg-info/PKG-INFO
writing dependency_links to martini_openmm.egg-info/dependency_links.txt
writing top-level names to martini_openmm.egg-info/top_level.txt
reading manifest file 'martini_openmm.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'martini_openmm.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/martini_openmm
copying build/lib/martini_openmm/martini.py -> build/bdist.linux-x86_64/egg/martini_openmm
copying build/lib/martini_openmm/__init__.py -> build/bdist.linux-x86_64/egg/martini_openmm
copying build/lib/martini_openmm/vsites.py -> build/bdist.linux-x86_64/egg/martini_openmm
byte-compiling build/bdist.linux-x86_64/egg/martini_openmm/martini.py to martini.cpython-310.pyc
byte-compiling build/bdist.linux-x86_64/egg/martini_openmm/__init__.py to __init__.cpython-310.pyc
byte-compiling build/bdist.linux-x86_64/egg/martini_openmm/vsites.py to vsites.cpython-310.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying martini_openmm.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying martini_openmm.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying martini_openmm.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying martini_openmm.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/martini_openmm-0.1-py3.10.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing martini_openmm-0.1-py3.10.egg
Removing /usr/local/lib/python3.10/site-packages/martini_openmm-0.1-py3.10.egg
Copying martini_openmm-0.1-py3.10.egg to /usr/local/lib/python3.10/site-packages
martini-openmm 0.1 is already the active version in easy-install.pth

Installed /usr/local/lib/python3.10/site-packages/martini_openmm-0.1-py3.10.egg
Processing dependencies for martini-openmm==0.1
Finished processing dependencies for martini-openmm==0.1

I'm not seeing anything worng, just a warning.

Thank you.

[pablo-arantes]

I've tried with the pip install . in the folder and I got the following output:

Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/
Processing /content/martini_openmm
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: martini-openmm
  Building wheel for martini-openmm (setup.py) ... done
  Created wheel for martini-openmm: filename=martini_openmm-0.1-py3-none-any.whl size=18280 sha256=550dd22de4cfabf51b91c7880830768d1a672c7af44ea263b1a1f3faae5977da
  Stored in directory: /tmp/pip-ephem-wheel-cache-6c_yqxgc/wheels/6a/13/1a/815004b34f618553247a41b627043a30018b0133348a8975cd
Successfully built martini-openmm
Installing collected packages: martini-openmm
  Attempting uninstall: martini-openmm
    Found existing installation: martini-openmm 0.1
    Uninstalling martini-openmm-0.1:
      Successfully uninstalled martini-openmm-0.1
Successfully installed martini-openmm-0.1

Everything seems fine, however I'm still having the same issue.

AttributeError: module 'martini_openmm' has no attribute 'MartiniTopFile'

Thank you.

[pablo-arantes]

It's working now. thank you