JOELib Tutorial: A Java based cheminformatics/computational chemistry package | ||
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The formal definition of atom properties is given in chapter Chapter 2.
Is this atom a hydrogen acceptor atom αacceptor(G,V,Achem|JOELib,kernelID). We used here the interpretation of Böhm/Klebe [bk02].
Atom in conjugated environment αconj(G,V,Achem|JOELib,kernelID) [wfz04a,wfz04b,fwz04].
Table 5-1. SMARTS definitions for assigning the conjugated atom property flag
SMARTS | Description |
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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 αdon,acc(G,V,Achem|JOELib,kernelID). We used here the interpretation of Böhm/Klebe [bk02].
Is this atom a hydrogen donor atom αdonor(G,V,Achem|JOELib,kernelID). We used here the interpretation of Böhm/Klebe [bk02].
Is this atom a ring atom αinRing(G,V,Achem|JOELib,kernelID).
Is this atom a terminal carbon atom αmethylen(G,V,Achem|JOELib,kernelID).
Is this atom a negative charged atom αnegative(G,V,Achem|JOELib,kernelID).
Is this atom a positive charged atom αpositive(G,V,Achem|JOELib,kernelID).
Atom mass.
Valence.
Van der Waals volume.
Conjugated electrotopological state [wz03,wfz04b].
Ii is the intrinsic state of atom i (the Section called Intrinsic topological state) and k the distance influence. The distance influence is reduced by the conjugated topological distance where Ci is the conjugated atom i (the Section called Atom in conjugated environment) of the molecule.Electrogeometrical state αEGstate(G,V,Achem|JOELib,kernelID) [wz03,wfz04b].
Ii is the intrinsic state of atom i (the Section called Intrinsic topological state) and k the distance influence.Electron affinity.
Electronegativity after Pauling.
Electrotopological state αEstate(G,V,Achem|JOELib,kernelID) [tc00,wfz04b].
Ii is the intrinsic state of atom i (the Section called Intrinsic topological state) and k the distance influence.Calculation of atom partial charges (Gasteiger-Marsili) αGM(G,V,Achem|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 χi,A and the charge qA of an atom:
where i is the orbital and A the atom.The algorithm requires the polynomial coefficients ai, bi, ci the damping factor α and the maximal number of iterations Nmax. Because the amount of charge transferred at each iteration is damped with an exponentially decreasing factor the convergence is guaranteed.
Graph potentials αGP(G,V,Achem|JOELib,kernelID) [wy96] or rotational symmetry descriptor. Only the connection table is needed to calculate the external rotational symmetry, or topological equivalent atoms.
where vi is the valence (vertex degree) of the atom i.Intrinsic topological state αIstate(G,V,Achem|JOELib,kernelID) [tc00,wfz04b].
where Li is the principal quantum number, δiν is the number of valence electrons, and δi is the number of sigma electrons of the ith atom ai.