Improved handling of CIF files

• Handle symmetry when given just the spacegroup name
• For CIF files with alternate structures (proteins?) automatically pick the highest occupancy alternates.

Bugfix: Primitive cell handling

Needed to track the numbers and identity of atoms in the conventional cell and primitive cell to be able to handle e.g. charges and spins on the atoms.

This is the same as 2022.7.23; however, PyPi seemed to have a glitch, so seeing if a new release will fix it. The downloadable file for e.g. condaforge was empty https://pypi.io/packages/source/m/molsystem/molsystem-2022.7.23.tar.gz

Bug fix: output MMCIF for systems with no bonds.

What's Changed

• Corrected writing systems with no bonds to MMCIF files. by @paulsaxe in #45

Full Changelog: 2022.5.7...2022.5.23

Improved handling of CIF files

Improved handling of CIF and MMCIF files to better support e.g. PDB files.

Added space group symmetry

Add handling of space group symmetry, which allows using e.g. the primitive cell in computations and also is necessary for band structure paths, phonons, etc.

Further improvements in CIF handling

Fixed issues where the atom type label had extra characters beyond the element.

Bugfix: CIF files

There was an issue reading CIF files that had atom labels and not atom types.

Fixed problem with charge systems and SMILES

Fixed a problem that prevented getting the charge for systems created from SMILES

Bugfix: molecules with formal charges

There was an error handling molecules with formal charges, i.e. nitromethane CN+[O-] from SMILES caused by adding the formal_charge attribute to the atoms even if it existed. This was due to a typo in the code and is fixed in this release.

Bugfix: PDB files

PDB files with unattached atoms were written with incorrect CONECT records. This caused other problems, such as packmol_step crashing on such systems. This release corrects the problem.