Symbols not belonging to the periodic table

If an atom is labeled with a symbol X or Et or R in a mol file, I get properties (e.g. charges) calculated by cxcalc for that atom. What do they mean? Which 'atomic symbols' are accepted by cxcalc? And by standardizer? An example goes below.








Marvin 04230818162D





9 8 0 0 0 0 999 V2000


-3.3125 0.1250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-2.5980 0.5375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0


-1.8836 0.1250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0


-1.1691 0.5375 0.0000 Et 0 0 0 0 0 0 0 0 0 0 0 0


-2.9000 -0.5895 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-3.7250 0.8395 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-4.0270 -0.2875 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-1.8836 -0.7000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


-1.1691 -0.2875 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0


1 2 1 0 0 0 0


2 3 1 0 0 0 0


3 4 1 0 0 0 0


1 5 1 0 0 0 0


1 6 1 0 0 0 0


1 7 1 0 0 0 0


3 8 1 0 0 0 0


3 9 1 0 0 0 0


M END


> <CHARGE>


0.0000;0.0000;0.0000;0.0000;0.0000;0.0000;0.0000;0.0000;0.0000


0.0344;-0.3951;0.0008;0.1118;0.0529;0.0529;0.0529;0.0447;0.0447


0.0344;-0.3951;0.0008;0.1118;0.0529;0.0529;0.0529;0.0447;0.0447





> <ATOM_POLARIZABILITY>


1.1163;0.8321;1.1163;11.3009;0.3944;0.3944;0.3944;0.3944;0.3944





> <ORBITAL_ELECTRONEGATIVITY>


;3.1478;;5.1220;;;;;


8.2983;9.2925;7.9876;7.1386;7.4983;7.4983;7.4983;7.4479;7.4479





$$$$

Hi,





The 'Et' atom in your molecule is a pseudo atom and is not handled correctly by the calculations. We should not calculate properties for pseudo atoms, it's a bug, we ill correct it.





Standardizer can handle correctly molecules with pseudo atoms. In JChem 5.1 a new action will be added to Standardizer which can convert pseudo atoms and alias atoms to abbreviated groups.





Zsolt