The formal definition of atom properties is given in chapter Chapter 2. Is this atom a hydrogen acceptor atom α_{acceptor}(G,V,A_{chem}JOELib,kernelID).
We used here the interpretation of Böhm/Klebe [bk02]. Atom in conjugated environment α_{conj}(G,V,A_{chem}JOELib,kernelID) [wfz04a,wfz04b,fwz04].
Table 51. SMARTS definitions for assigning the conjugated atom property flag SMARTS  Description 

a  Aromatic atoms  *=,#*,=*=,#*  All butadien analogues  [N,P,O,S]=,#*[*;!H0]  alpha, beta unsaturated (pi effect)  *=,#*[F,Cl,Br,I]  alpha, beta unsaturated (sigma effect)  *=,#*[N,P,O,S;!H0]  alpha, beta unsaturated (pi effect, tautomer) 
Is this atom a hydrogen donor or acceptor atom α_{don,acc}(G,V,A_{chem}JOELib,kernelID).
We used here the interpretation of Böhm/Klebe [bk02]. Is this atom a hydrogen donor atom α_{donor}(G,V,A_{chem}JOELib,kernelID).
We used here the interpretation of Böhm/Klebe [bk02]. Is this atom a ring atom α_{inRing}(G,V,A_{chem}JOELib,kernelID). Is this atom a terminal carbon atom α_{methylen}(G,V,A_{chem}JOELib,kernelID). Is this atom a negative charged atom α_{negative}(G,V,A_{chem}JOELib,kernelID). Is this atom a positive charged atom α_{positive}(G,V,A_{chem}JOELib,kernelID). Electronegativity after Pauling. Calculation of atom partial charges (GasteigerMarsili) α_{GM}(G,V,A_{chem}JOELib,kernelID) [gm78].
The Partial Equalization of Orbital Electronegativities (PEOE) sigma charges of atoms can be calculated using
an iterative algorithm. There exists a dependency between the electronegativity
χ_{i,A}
and the charge q_{A}
of an atom:
Equation 511. Orbital electronegativity based on atom charge
where i is the orbital and A the atom. The algorithm requires the polynomial coefficients a_{i},
b_{i},
c_{i} the damping factor α
and the maximal number of iterations N_{max}.
Because the amount of charge transferred at each iteration is damped with an exponentially decreasing factor the convergence is
guaranteed. Graph potentials α_{GP}(G,V,A_{chem}JOELib,kernelID) [wy96] or rotational symmetry descriptor. Only the connection table
is needed to calculate the external rotational symmetry, or topological equivalent atoms.
Equation 512. Graph potentials
where v_{i} is the valence (vertex degree) of the atom
i. Intrinsic topological state α_{Istate}(G,V,A_{chem}JOELib,kernelID) [tc00,wfz04b].
Equation 513. Intrinsic topological state
where L_{i} is the principal quantum number,
δ_{i}^{ν}
is the number of valence electrons, and δ_{i}
is the number of sigma electrons of the
ith atom a_{i}.
Last changes: 08.12.2010, 16:50 CET
(UTC/GMT +1 hour) wegner.
http://www.ra.cs.unituebingen.de/software/joelib/tutorial/descriptors/atomProperties.html
© 2003 University of Tübingen, Germany
