Quick Fix to Bondi radii

[dunphysd]

Describe the bug
Current buried volume calculations include H-atoms by default. However, the Bondi radii for H-atoms (1.20 A) is not the radii used on popular buried volume tools such as SambVca. Instead, a radius of 1.10 A is used as "carbon bonded to hydrogen". Given the widespread use of SambVca as a tool for buried volume calculations, this discrepancy may cause confusion when different Vbur volumes are produced with SEQCROW.

On a separate note, I am not aware of any way to turn off H-atom inclusion, this would also be a good feature to add given they are frequently omitted in literature reported buried volumes.

To Reproduce
Steps to reproduce the behavior:

1. Calculate buried volume in SEQCROW as you would normally, making sure there is some H-atom contribution to the buried volume
2. Calculate buried volume using SambVca on the same .xyz file, making sure to include H-atoms in the Vbur calculation
3. Compare values. SEQCROW will consistently produce a larger Vbur value due to the larger H-atom radius
   Expected behavior
   The buried volume produced by SEQCROW should match that of SambVca

[ajs99778]

I can add an option for SambVca radii in the next update. I think I want to leave Bondii radii as just what was published in the Bondii paper. In the meantime, the UMN radii for main group elements differ by about 0.01 compared to the SambVca radii. The main group elements are taken from here: https://doi.org/10.1021/jp8111556 (see table 12). I will probably also add an option to use each atom's 'radius' attribute in case someone wants to use their own radii.

Even with consistent radii, I want to note that there could still be discrepancies between the two software depending on how dense of a grid is used.

To ignore hydrogens, you can omit them from the ligand selection. If you're using the tool, this could look like

1. select the ligand(s)
2. deselect hydrogen atoms (e.g. run the command ~select H)
3. click "set ligand to current selection"
4. change selection to the metal center and click "calculate % buried volume"

The process with the command would be similar.

[ajs99778]

I've added an option to use SambVca radii for calculating buried volume. It will be in the next patch. If you'd like to preview it, instructions for installing from github are here: https://github.com/QChASM/SEQCROW?tab=readme-ov-file#github. Using custom radii is still on the to-do list.