More recent octahedral embed that can handle carbenes

[alex-l-m]

Updated octahedral-embed that can handle the new molecule class. Should be harmless to merge into the existing repo since it just adds functionality that the existing repo doesn't use.

[xiangchenjhu]

Since there are now eight new *.mol2 files in /modules/octahedral_embed/, should the original four *.mol files in /modules be removed?

[alex-l-m]

Yes, I didn't notice thee redundancy, but those original four can be deleted.

To double-check this, I looked at how octahedral_embed finds the mol2 files. It checks its own path variable, which is:

In [2]: from bluephos.modules.octahedral_embed import __path__

In [3]: print(__path__)
['/home/alexlm/repos/bluephos/bluephos/modules/octahedral_embed']

So only the mol2 files in that directory should be necessary. Which means you can delete the mol2 files in bluephos/modules.

[xiangchenjhu]

Yes, I didn't notice thee redundancy, but those original four can be deleted.

To double-check this, I looked at how octahedral_embed finds the mol2 files. It checks its own path variable, which is:

In [2]: from bluephos.modules.octahedral_embed import __path__

In [3]: print(__path__)
['/home/alexlm/repos/bluephos/bluephos/modules/octahedral_embed']

So only the mol2 files in that directory should be necessary. Which means you can delete the mol2 files in bluephos/modules.

Thanks for the clarification! Could you make this change directly in this PR to keep everything self-contained? Thanks!

[alex-l-m]

Yes, I made the change to the PR.

I also confirmed that I can run the pipeline with those files deleted, and it can run xTB without errors.

[xiangchenjhu]

Thanks

[xiangchenjhu]

Great! Thanks!

[xiangchenjhu]

@alex-l-m A formatting issue was detected during the lint check in /octahedral_embed/init.py. Please run ruff format . to correct it. Thanks!

[xiangchenjhu]

Need formatting this file (ruff format)

[xiangchenjhu]

Looks good, Thanks!