Read charge from PDB files and list charged atoms separately

[jmaglic]

Current status

Charges specified inside PDB files are ignored and charged atoms are treated the same as uncharged ones.

Issue

Some users could be interested in making a distinction between charged and uncharged atoms, and assigning separate radii. The atomic charge is generally considered to change the radius.

Proposed change

When importing PDB files, the charge should be imported alongside the atom type. The charged atom should be listed as a separate item in the atom list, including their charge, e.g., as "Fe2+". The default radius of the charged atom should be obtained as follows:

• First, check whether a radius is listed for the exact atom and charge combination in the radius file. This could be the case if the user decided to modify or change the radius file. If unsuccessful
• look up the radius for the atom without the charge. This will be the default, but the value can be changed in the atom table inside the GUI. If unsuccessful
• the default radius is set to 0

[rlavendomme]

Currently the elements.txt file provides only the vdw radius of elements. If we need to add ionic radii, we have to choose the source of the data. I propose the Shannon radii as a source: R. D. Shannon, Acta Cryst. A 1976, 32, 751-767. https://doi.org/10.1107/S0567739476001551 http://abulafia.mt.ic.ac.uk/shannon/ptable.php

Several ionic radii are reported in this database for some ions (for example metal cations with different coordination geometries). I propose the following for MoloVol default elements.txt file.

• When several ionic radii are reported, the value selected for this table followed the rules in order:
  • labelled "most reliable"
  • coordination number corresponding to the most commonly found metal complexes
  • coordination number corresponding to the charge for non-metals (or lowest value if not applicable)