Purpose of 1.3 multiplier in checking covalent bonds

[ljmartin]

Thanks for the great script.

Would someone please explain the purpose of the GetRCovalent covalent radius being multiplied by 1.3? ie: https://github.com/jensengroup/xyz2mol/blob/2b9f96836dde5c983bd6dd7266c1f422e8bbb436/xyz2mol.py#L392 thanks

[cstein]

Hi Martin,

When you want to test of there is a covalent bond between to pairs of atoms you use the covalent radii of the atoms and check if the distance between the pair of atoms is shorter. It turns out that using only the covalent radii (from GetRCovalent) will not find bonds that are slightly longer then their equilibrium distance. So you add this fudge factor of 1.3 to make sure you also get those.

[ljmartin]

Great, thanks!