command-line tool

[François Bérenger]

Hello,

Is there a way to have a command-line tool for this use case:

• I am in a terminal
• I want to create a 2D picture (as a grid) of all molecules in the input file
• as a .png or .pdf, or ("a la rigueur") as a .html file.

I am not under jupyter or what not.

My input files are either .sdf, .mol2 or .smi (and in a SMILES file, the SMILES string are the first field/column).

Thanks a lot,
Francois.

[Cédric Bouysset]

Hi Francois,

• There's no CLI in mols2grid but you could just make a simple script to emulate that.
• You can generate the complete grid of molecules (as opposed to the paginated document) by specifying template="table" (see below). Please refer to the documentation for more info on the other arguments that you can supply.
• You can save an HTML doc by using mols2grid.save(input, output="document.html", template="table", <your other args>) instead of mols2grid.display. The HTML document will have a special attribute inside (page-break-inside: avoid) which prevents page breaks if you decide to then convert that HTML to a PDF with multiple pages. There are some CLI utilities to do that conversion to pdf and images (wkhtmltopdf among others) or most browsers and OS have a print-to-pdf functionality.

Feel free to close the issue if it answers your question.

Hope this helps,
Cédric

[François Bérenger]

Thanks, I'll give it a try.
I'm trying to get rid of the mview proprietary tool.

[François Bérenger]

Sometimes, I would like mols2grid to just be able to visualize some molecules in a browser.
Either the molecules are SMILES in a file; or in a mol2 or sdf file.
I still think a basic CLI to visualize a bunch of molecules, not requiring any Python programming from the end-user would be nice.

[François Bérenger]

If you know mview from chemaxon, than that's what I'd like but in open-source.

[François Bérenger]

I had written one in the past, as you suggested, but it is now broken:
https://github.com/UnixJunkie/molenc/blob/master/bin/molenc_mview.py

mols2grid.save(mols, output='caff.html', template="table", prerender=True)

Gives me:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In [4], line 1
----> 1 mols2grid.save(mols, output='caff.html', template="table", prerender=True)

File ~/usr/miniconda/lib/python3.11/functools.py:909, in singledispatch.<locals>.wrapper(*args, **kw)
    905 if not args:
    906     raise TypeError(f'{funcname} requires at least '
    907                     '1 positional argument')
--> 909 return dispatch(args[0].__class__)(*args, **kw)

File ~/usr/miniconda/lib/python3.11/site-packages/mols2grid/dispatch.py:298, in _(mols, **kwargs)
    294 @save.register(Series)
    295 @save.register(list)
    296 @save.register(tuple)
    297 def _(mols, **kwargs):
--> 298     template, kwargs, render_kwargs = _prepare_kwargs(kwargs, "save")
    299     output = kwargs.pop("output")
    300     return MolGrid.from_mols(mols, **kwargs).save(
    301         output, template=template, **render_kwargs
    302     )

File ~/usr/miniconda/lib/python3.11/site-packages/mols2grid/dispatch.py:24, in _prepare_kwargs(kwargs, kind)
     20 """Separate kwargs for the init and render methods of MolGrid"""
     21 template = kwargs.pop("template", _SIGNATURE["render"]["template"].default)
     22 render_kwargs = {
     23     param: kwargs.pop(param, sig.default)
---> 24     for param, sig in _SIGNATURE[f"to_{template}"].items()
     25 }
     26 if kind == "display":
     27     render_kwargs.update(
     28         {
     29             param: kwargs.pop(param, sig.default)
     30             for param, sig in _SIGNATURE["display"].items()
     31         }
     32     )

KeyError: 'to_table'

[François Bérenger]

Software that was working in the past, but doesn't anymore makes me feel very sad.

[Cédric Bouysset]

For the KeyError, that's because there were some breaking changes (here the renaming of the possible values for template from pages/table to interactive/static) between v1 and v2. You can either:

• pin your dependencies to mols2grid<2 and keep your code as is,
• or mols2grid>=2,<3 but using template=static,
• or don't pin anything and use either template=table or template=static depending on the version of mols2grid installed with mols2grid.__version__.

For the CLI, yeah I can see some use case for it, but I have some other priorities for this package and rarely enough time to spare unfortunately. I remember you opening PR #54, apologies for not giving feedback on that. If you're still up for it I can make some suggestions and guide you to integrate it as an actual CLI tool.

[François Bérenger]

I could repair molenc_mview.py, thanks!