Using gemmi. Simple case

[orex]

Hello, Marcin.
I want you use your project in my program supercell (https://github.com/orex/supercell) for reading and storing cif files. At the moment I'm using openbabel for this, but this is heavy library and I have a lot of problems with it (for example in CI/CD). I would like to have something lightweight. C++ header only library sounds perfectly fine.
I went through your documentation and code, but I can't found directly how to make a few simple steps.

1. Read cif file.
2. Convert it to P1.
3. fract->cart
4. Do some processing.
5. Store unitcell (Eigen::Matrix3d), list of coordinates (+atom num, Label etc) to file.

The best answer for me will be is an example tool, which convert cif to supercell_cif.

Thank you in advance.

Best,
Kirill.

[wojdyr]

Is it for small molecule CIF?

1. see https://gemmi.readthedocs.io/en/latest/mol.html#small-molecules
2. I think expanding to P1 was considered, but there is no such function yet. There is a function to expand NCS (NCS – non-crystallgraphy statistics – is probably MX-specific).
3. Position pos = cell.orthogonalize(fractional);
4. n/a
5. Writing small molecule structures is not supported - it hasn't been a priority. Gemmi can write mmCIF files, PDB files and CIF files in a generic way. The latter could be used to write small molecule CIFs.

[orex]

Thank you very much for your quick response. I will check the options.