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 aliphatic hydroxy groups.

Number of aromatic bonds.

Fraction of rotatable bonds.

Geometrical 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 hydrophobic groups.

The Kier shape ^{1}κ descriptor [tc00]
can be defined as :

**Equation 5-1. Kier shape 1**

**P**_{max} is the maximum number of paths of length 1.
**P**_{min} 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:

**Equation 5-2. Kier shape 1 (alternative formulation)**

**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 ^{2}κ descriptor [tc00]
can be defined as :

**Equation 5-3. Kier shape 2**

**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 ^{3}κ descriptor [tc00]
can be defined as :

**Equation 5-4. Kier shape 3**

**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].

Number of chlorine atoms.

Number of fluorine atoms.

Number of nitrogen atoms.

Number of phosphorus atoms.

Number of -NO_{2} groups.

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.

Zagreb index 1 [tc00].

**Equation 5-5. Zagreb index 1**

where **a** are all atoms of the hydrogen depleted graph and
is the vertex degree.

Zagreb index 2 [tc00].

**Equation 5-6. Zagreb index 2**

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**.