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 1κ descriptor [tc00]
can be defined as :
Equation 5-1. Kier shape 1
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:
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 2κ 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 3κ 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.
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.