Phillip (& Eric & Tim)
Per our discussions ...
I have added the table of ionic radii to Jmol.
- the table is what Phillip sent me:
Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143
The algorithm is as follows:
- if an atom has no charge, then the covalent radius is used
(data values from OpenBabel)
- if an atom has a charge, then it is looked up in the ionic table
* if it is not found in the ionic table, then the
covalent radius is returned
I now need the following:
- small/simple files with charged atoms in the following formats
* xyz
* mol
* pdb
- confirmation that the existing bonding algorithm will give
acceptable results:
bondingRadius1 + bondingRadius2 + 0.45 angstroms (tolerance)
I will plan to add the scripting command:
spacefill ionic
This will spacefill render the atoms, using the ionic charge radii.
Q: Are we sure that we want this keyword to be 'ionic'? Since, in fact, it
is applied to things that do not have a charge (in which case the covalent
radius is used)
(Someone wondered about the impact this may have on the size of the
JmolApplet ...
The ionic tables only take up 736 bytes.
But, I took this opportunity to change the representation of the vdwRadius
& covalentRadius tables, saving 440 bytes. So the tables ended up with a
net increase of 296 bytes.
I added one byte to each Atom at runtime to store the charge.
Net code impact was probably 30 lines and less than 250 bytes.
Overall ... absolutely painless ;-)
Miguel
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