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Symbols not belonging to the periodic table

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jasousa Joined: 30 Sep 2004 Posts: 28 Back to top	Post subject: Symbols not belonging to the periodic table Posted: Wed Apr 23, 2008 6:57 pm  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 $$$$
Zsolt Joined: 11 Jan 2006 Posts: 326 ChemAxon personnel Back to top	Post subject: Posted: Thu Apr 24, 2008 6:44 pm  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
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