The native values like simple atom/group counts and complexity measures are suitable to build primitive QSAR prediction models for structure property relations, which has a good correlation to the molecular complexity. for more biological relevant models we recommend to use transformation based descriptors (the Section called Transformations) based on atom properties (the Section called Atom properties).
Number of acidic groups.
Number of aliphatic hydroxy groups.
Number of aromatic bonds.
Number of basic groups.
Fraction of rotatable bonds.
Geometrical diameter.
Geometrical radius.
Geometrical shape coefficient.
Graph shape coefficient.
Number of Hydrogen Bond Acceptors (HBA) 1. The default SMARTS pattern is: [$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])].
Number of Hydrogen Bond Acceptors (HBA) 2. The default SMARTS pattern is: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])].
Number of Hydrogen Bond Donors (HBD) 1. The default SMARTS pattern is: [!#6;!H0].
Number of Hydrogen Bond Donors (HBD) 2. The default SMARTS pattern is: [$([O;H1,-&!$(*-N=O)]),$([S;H1&X2,-&X1]),$([#7;H;!$(*(S(=O)=O)C(F)(F)F);!$(n1nnnc1);!$(n1nncn1)]),$([#7;-])].
Number of heavy bonds.
Number of heterocycles.
Number of hydrophobic groups.
The Kier shape 1κ descriptor [tc00] can be defined as :
Pmax is the maximum number of paths of length 1. Pmin is the minimum number of paths of length 1 in a molecule graph of same atom number. P1 is the number of paths in the given molecule of length 1. or:
A means the number of nodes in the molecules graph. P1 is the number of paths of length 1 in the given molecule.
The Kier shape 2κ descriptor [tc00] can be defined as :
A means the number of nodes in the molecules graph. P2 is the number of paths of length 2 in the given molecule.
The Kier shape 3κ descriptor [tc00] can be defined as :
A means the number of nodes in the molecules graph. P3 is the number of paths of length 3 in the given molecule.
Octanol/Water partition coefficient (logP) or hydrophobicity [wc99].
Molar refractivity (MR) [wc99].
Molecular weight (MW).
Number of atoms.
Number of boron atoms.
Number of bromine atoms.
Number of bonds.
Number of chlorine atoms.
Number of halogen atoms.
Number of iodine atoms.
Number of fluorine atoms.
Number of nitrogen atoms.
Number of oxygen atoms.
Number of phosphorus atoms.
Number of sulfur atoms.
Number of -NO2 groups.
Number of -OSO atoms.
Polar surface area (PSA) [ers00].
Number of rotatable bonds, where the atoms are heavy atoms with bond order one and a hybridization which is not one (no sp). Additionally the bond is a non-ring-bond.
Number of -SO groups.
Number of -SO2 atoms.
Topological diameter.
Topological radius.
Zagreb index 1 [tc00].
where a are all atoms of the hydrogen depleted graph and
is the vertex degree.
Zagreb index 2 [tc00].
where b are all bonds of the hydrogen depleted graph and
is the vertex degree.
i and j are the atom indices
of the atoms connected to the bond b.