modernization of the syntax necessary

[nbehrnd]

At present, aRMSD deploys an old syntax of numpy, and relies on old vtk 6. Probably only "time capsules" like Linux Ubuntu 18.04 and alike are capable to successfully resolve these dependencies. Though known to work in the environment of Windows 7 (in part because libraries saved here, much prior to Gohlke's index of Python .whl shut-down) it might not smoothly work in current Windows 10/11.

[nbehrnd]

@regueiala I just see you starring this repository and thought it might be better to inform you early about issues in syntax, design, and dependencies possibly require some precautions while using this tool.

[regueiala]

@nbehrnd Thanks for the message! I'll keep that in mind.

[nbehrnd]

@regueiala I would like to come back to the issue. Below the sequential approach to use the aRMSD on a contemporary instance of Windows 10 (well, October is close...):

• fetch the content of this aRMSD repository (about 45MB)

• fetch the content of aRMSD-minimalWindowsSupport which will allow to resolve dependencies outside the old Python 2.7 (32bit) standard library (about 292MB)

• fetch the installer of Python 2.7.15 for Windows 32bit published in May 2018 (https://www.python.org/ftp/python/2.7.15/python-2.7.15.msi) still available on https://www.python.org/downloads/windows/ (about 18MO)

• during the installation be careful this one does not added to Windows' PATH variable. For one, this allows to retain a Python 3.13.x as default. For the other, this allows to write a file of name python27.bat to launch the more senior Python interpreter -- for me, a content of

  @echo off
  C:\Python27\python.exe %*
  

  is enough to then launch Python 2.7 by the command of python27.bat from either cmd.exe,
  or (by .\python27.bat) from Windows' Powershell. It might be possible to add this "link file" to Windows' PATH variable for a then systemwide access and launch of Python 2.7; I didn't investigate this further.

• the archive of aRMSD-minimalWindowsSupport doesn't contain a .whl which would allow to create virtual environment. Thus, one .whl after the other has to be installed in lines of

  python27.bat -m install "openbabel-2.4.1-cp27-cp27m-win32.whl"

  The use of quotes seems to be important here. Somewhat unexpected, during the installation of matplotlib, pip briefly collected an external dependency (and did so successfully!) from the internet (pypi.org?).

  After all, the installation proceeded without difficulties here (including openbabel which, if using pypi.org as repository, is better replaced by pip install openbabel-wheel)

• I then copy-pasted files M1.xyz, M2.xyz about two conformers of benzamide and an additional copy of python27.bat into the folder of aRMSD/armsd, i.e. the same which hosts the moderating aRMSD.py main script.

  Launch of the program, loading the structure data, alignment, the Kabsch test, display of the superposition, creation and export of the structure images and synoptic diagram by matplotlib worked well while following the pdf. The representation as anaglyph did not work; I'm told this depends both on adjustable software (for instance the version of the VTK library), as well as chip (set) and/or presence of true (dedicated) graphics card (compatibility with OpenGL software, too) on the computer used.

I thought the share of results of this "code archeology" might be equally interesting for you. To me, the "recipe" of a Windows .bat file to launch a non-default Python interpreter definitively is a detail worth to retain as a more general lesson learned (outside Python, virtual environments and tox/nox).