Matteo Floris, Egon Willighagen, Rajarshi Guha, Miguel Rojas and Christian Hoppe
This dictionary describes descriptors used in quantitative structure activity relationship (QSAR) programs. This document contains MathML [MATHML] equations and can best be viewed with a MathML aware browser, like Mozilla and FireFox [Mozilla] .
[Entries] [Bibliography] [Final Notes]
Constitutional Descriptors
Electronic Descriptors Geometrical Descriptors Topological Descriptors Molecular Descriptors
Definition
Descriptor that returns the number of amino acids in an atom container.
Classification
This descriptor is a Constitutional Descriptor
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Contributed by: Egon Willighagen. Created on: 2006-01-15.
Definition
Descriptor based on the number of aromatic atoms of a molecule.
Classification
This descriptor is a Constitutional Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor based on the number of aromatic bonds of a molecule.
Classification
This descriptor is a Constitutional Descriptor
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Contributed by: , Egon Willighagen. Created on: 2004-11-26.
Definition
Descriptor that calculates the number of not-Hs substituents of an atom.
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor that returns the hybridization state of an atom.
Classification
This descriptor is a Molecular Descriptor
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Definition
Descriptor that returns the hybridization state of an atom.
Description
The calculation find a SIMPLE WAY the molecular geometry for following from
Valence Shell Electron Pair Repulsion or VSEPR model and at the same time its
hybridization of atoms in a molecule.
Classification
This descriptor is a Molecular Descriptor
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Contributed by: . Created on: 2006-05-08.
Definition
Descriptor that calculates the sum of the atomic polarizabilities (including implicit hydrogens).
Description
Polarizabilities derive from periodic tables.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: , Egon Willighagen. Created on: 2004-11-26.
Definition
Descriptor that calculates the valence of an atom.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Eigenvalue based descriptor noted for its utility in chemical diversity
described by Pearlman et al.
[PEA99]
.
Classification
This descriptor is a Molecular Descriptor
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Contributed by: , . Created on: 2005-01-27.
Definition
Descriptor based on the number of bonds of a certain bond order.
Classification
This descriptor is a Constitutional Descriptor
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Contributed by: , Egon Willighagen. Created on: 2004-11-26.
Definition
Descriptor that calculates bond-pi Partial charge of a bond.
Description
Calculation is calculated determining the difference the Partial Pi
Charge on atoms A and B of a bond. Based in Gasteiger Charge.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2006-05-08.
Definition
Descriptor that calculates bond-sigma Partial charge of a bond.
Description
Calculation is calculated determining the difference the Partial Sigma
Charge on atoms A and B of a bond. Based in Gasteiger Charge.
Classification
This descriptor is a Electronic Descriptor
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Definition
Descriptor that calculates bond-total Partial charge of a bond.
Description
Calculation is calculated determining the difference the Partial Total
Charge on atoms A and B of a bond. Based in Gasteiger Charge.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2006-05-08.
Definition
Descriptor that calculates the sum of the absolute value of the difference between atomic
polarizabilities of all bonded atoms in the molecule (including implicit hydrogens).
Description
Polarizabilities derive from periodic tables.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: , Egon Willighagen. Created on: 2004-11-26.
Definition
Descriptor that calculates of bond-Polarizability of a bond.
Description
Calculation is calculated determining the difference the Sigma
electronegativity on atoms A and B of a bond.
Classification
This descriptor is a Electronic Descriptor
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Definition
Descriptor based on the number of bonds on the shortest path between two atoms.
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor that calculates the carbon connectivity index (order 0).
Description
While the atomic connectivity is calculated as the sum of
$\frac{1}{$ {{d}_{i}}^{\mathrm{0.5}}$}$
over all heavy atoms i with degree greather than zero, carbon connectivity index
takes into account only carbon atoms with degree greather than zero.
Relations
Is a Modification Of: Connectivity index (order 0)
Classification
This descriptor is a Topological Descriptor
Implementations
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Definition
Descriptor that calculates carbon connectivity index (order 1).
Description
While the atomic connectivity is calculated as the sum of
$\frac{1}{$ {$ \left($ {d}_{i}$$ {d}_{j}$\right)$}^{\mathrm{0.5}}$}$
over all bonds between heavy atoms i and j, the carbon connectivity index
takes into account only bonds between carbon atoms.
Relations
Is a Modification Of: Connectivity index (order 1)
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor that calculates 29 Charged Partial Surface Area (CPSA) descriptors.
Description
The CPSA's were developed by Stanton et al.
[CPSA]
and
are related to the Polar Surface Area descriptors.
This implementation uses a numerical algorithm to obtain surface areas
and obtains partial charges using the Gasteiger-Marsilli algorithm.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2005-05-16.
Definition
Descriptor that calculates the eccentric connectivity index for a
hydrogen supressed molecular graph.
Description
Descriptor combining distance and adjacency information. This descriptor is
described by Sharma et al. and has been shown
to correlate well with a number of physical properties.
Classification
This descriptor is a Topological Descriptor
Implementations
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Contributed by: . Created on: 2005-03-19.
Definition
Descriptor that calculates atomic connectivity index (order 0).
Description
Atomic connectivity is calculated as the sum of
$\frac{1}{$ {{d}_{i}}^{\mathrm{0.5}}$}$
over all heavy atoms i with degree greather than zero.
Relations
Is Modificated Into: Carbon connectivity index (order 0)
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor that calculates atomic connectivity index (order 1).
Description
Atomic connectivity is calculated as the sum of
$\frac{1}{$ {$ \left($ {d}_{i}$$ {d}_{j}$\right)$}^{\mathrm{0.5}}$}$
over all bonds between heavy atoms i and j.
Relations
Is Modificated Into: Carbon connectivity index (order 1)
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor that returns the covalent radius of a given atom.
Classification
This descriptor is a Molecular Descriptor
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Contributed by: . Created on: 2006-05-08.
Definition
Descriptor that calculates the 3D distance between two atoms.
Classification
This descriptor is a Geometrical Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor that calculates the effective polarizability of a given heavy atom.
Description
Polarizabilities are assigned to the heavy atom by Polarizability class.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: , Egon Willighagen. Created on: 2004-11-26.
Definition
Descriptor based on the number of atoms of a certain element type.
Classification
This descriptor is a Constitutional Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor characterizing the mass distribution of the molecule.
Description
This descriptor is described by Katritzky et al.
[KAT96]
.
Relations
Is Modificated Into: Gravitational Index (Square and Cube Roots)
Classification
This descriptor is a Molecular Descriptor
This descriptor is a Geometrical Descriptor
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Contributed by: , . Created on: 2004-11-24.
Definition
Descriptor characterizing the mass distribution of the molecule as the square
or cube root of the gravitational index.
Description
This descriptor is described by Wessel et al.
[WES98]
.
Relations
Is a Modification Of: Gravitational Index
Classification
This descriptor is a Geometrical Descriptor
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Contributed by: , . Created on: 2004-11-25.
Definition
Descriptor that calculates the number of hydrogen bond acceptors.
Description
As defined by Daylight website,
[DAY01]
, a H-bond acceptor is a heteroatom with no positive charge, note that negatively
charged oxygen or sulphur are included. Excluded are halogens, including F,
heteroaromatic oxygen, sulphur and pyrrole N. Higher oxidation levels of N,P,S are excluded.
Note P(III) is currently included. Zeneca's work would imply that (O=S=O) shoud also be excluded.
Classification
This descriptor is a Electronic Descriptor
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Definition
Descriptor that calculates the number of hydrogen bond donors.
Description
As defined by Daylight website,
[DAY01]
, a H-bond acceptor
must have an N-H bond, an O-H bond, or a F-H bond
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
This class calculates the atomic hardness of a given atom.
Description
Inductive atomic hardness of an atom in a polyatomic system can be defined
as the resistance to a change of the atomic charge.
This descriptor is described by Cherkasov
[CHER2003]
.
Classification
This descriptor is a Electronic Descriptor
Implementations
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Contributed by: . Created on: 2005-04-21.
Definition
This class calculates the atomic softness of a given atom.
Description
Inductive atomic softness of an atom in a polyatomic system can be defined
as as charge delocalizing ability.
This descriptor is described by Cherkasov
[CHER2003]
.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2005-04-21.
Definition
Descriptor that calculates Kier and Hall kappa molecular shape indices.
Description
Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs.
First kappa shape index is given by
$\frac{$ {$ n(n-1)$}^{2}$}{$ {m}^{2}$}$,
second kappa shape index is given by
$\frac{$ $ (n-1)$$ {$ (n-2)$}^{2}$$}{$ {{p}_{2}}^{2}$}$
and third kappa shape index is given by
$\frac{$ $ (n-1)$$ {$ (n-3)$}^{2}$$}{$ {{p}_{3}}^{2}$}$
for odd n and
$\frac{$ $ (n-3)$$ {$ (n-2)$}^{2}$$}{$ {{p}_{3}}^{2}$}$
for enev n,
where n denotes the number of atoms in the hydrogen suppressed graph, m is the number of bonds in the hydrogen
suppressed graph. Also, let p2 denote the number of paths of length 2 and let p3 denote the number of paths of length 3
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2004-11-26.
Definition
Descriptor that returns the number of atoms in the longest aliphatic chain.
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2006-1-03.
Definition
Descriptor that returns the number of atoms in the largest chain.
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2006-1-03.
Definition
Descriptor that returns the number of atoms in the largest pi system.
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2006-1-03.
Definition
This Class contains a method that returns the number failures of the
Lipinski's Rule Of Five.
Description
The Rule of 5 got its name from the cutoff values for each of the four parameters that define the potential of
a drug candidate for good absorption: all of these values are close to five or a multiple of five.
The original definition, given by Christopher A. Lipinski, says that poor absorption (or permeation) is more likely when:
the molecule has more than 5 H-bond donors and more than 10 H-bond acceptors;
its molecular weight is over 500.
its LogP is over 5;
Classification
This descriptor is a Constitutional Descriptor
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Contributed by: , Egon Willighagen. Created on: 2005-01-27.
Definition
Descriptor based on the weight of atoms of a certain element type.
If no element is specified, the returned value is the Molecular Weight
Classification
This descriptor is a Molecular Descriptor
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Contributed by: , Egon Willighagen. Created on: 2005-01-27.
Definition
Descriptor that calculates the principal moments of inertia and ratios
of the principal moments. Als calculates the radius of gyration.
Classification
This descriptor is a Geometrical Descriptor
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Contributed by: , Egon Willighagen. Created on: 2005-02-07.
Definition
Descriptor that calculates pi partial charges in pi-bonded systems of an heavy atom.
Description
Calculation is based on Gasteiger H.Saller (PEPE)
[SALLER]
.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2006-05-08.
Definition
Descriptor that calculates sigma partial
charges in sigma-bonded systems (PEOE) of an heavy atom.
Description
Calculation is based on Gasteiger Marsili (PEOE)
[MARSILI]
.
Classification
This descriptor is a Electronic Descriptor
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Definition
Descriptor that calculates total partial
charges of an heavy atom.
Description
Calculation is based on MMFF94.
Classification
This descriptor is a Electronic Descriptor
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Definition
Descriptor that calculates total partial
charges of an heavy atom.
Description
Calculation is based on Partial Equalization of Orbital Electronegativity method (PEOE)
from Gasteiger. They are obtained by summation of the results of the calculations
on sigma- and pi-charges.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2006-05-08.
Definition
Descriptor that returns the period in the periodic table of an atom belonging to an atom container
Classification
This descriptor is a Constitutional Descriptor
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Contributed by: . Created on: 2005-02-07.
Definition
Descriptor that calculates the Petitjean Number of a molecule.
Description
According to the Petitjean definition, the eccentricity of a vertex corresponds to the
distance from that vertex to the most remote vertex in the graph. The distance
is obtained from the distance matrix as the count of edges between the two vertices.
If ${r}_{i}$
is the largest matrix entry in row i of the distance matrix D, then the radius
is defined as the smallest of the ${r}_{i}$.
The graph diameter D is defined as the largest vertex eccentricity in the graph.
Petitjean Number is the value of
$\frac{$ (\mathrm{diameter}-\mathrm{radius})$}{\mathrm{diameter}}$.
Classification
This descriptor is a Topological Descriptor
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Definition
Descriptor that evaluates the Petitjean shape indices.
Description
These original Petitjean number was described by Petitjean and considered
the molecular graph. This class also implements the geometric analog
of the topological shape index described by Bath et al.
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2006-01-14.
Definition
Descriptor that check if two atoms have pi-contact (this is true when there is one and
the same conjugated pi-system which contains both atoms, or directly linked neighboors of the atoms).
Classification
This descriptor is a Constitutional Descriptor
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Definition
This Class contains a method that returns the pi electronegativity for a given atom.
Description
Pi electronegativity is given by
$X=a+bq+c$ \left($ {q}^{2}$\right)$$,
where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge.
Classification
This descriptor is a Electronic Descriptor
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Definition
This Class contains a method that returns 1 if the protons is directly bonded to an aromatic system,
it returns 2 if the distance between aromatic system and proton is 2 bonds,
and 0 for other positions.
Classification
This descriptor is a Constitutional Descriptor
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Definition
This Class contains a method that returns true if the protons is directly bonded to a pi system.
Classification
This descriptor is a Constitutional Descriptor
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Definition
Descriptor that calculates partial charges of an heavy atom and its protons.
Description
Calculation is based on Gasteiger Marsili (PEOE)
Classification
This descriptor is a Electronic Descriptor
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Definition
Calculation of RDF proton descriptor based on
[GAST2002]
.
Description
A given proton is represented by 5 different descriptors.
The first one has the form
${g}_{H}(r)=\sum $ {p}_{i}{e}^{$ -B{$ (r-{r}_{i})$}^{2}$}$$
where i denotes an atom up to four not rotatable bonds away from the target proton,
p is the partial atomic charge of the atom i, B is a smoothing parameter,
${r}_{i}$ is the
3D distance between proton and atom i, and r is a running variable.
The second one is a topological form of the first one, where i is an atom up to the fifth sphere,
${p}_{i}$ is the
partial atomic charge of atom i, and ${r}_{i}$
is now the sum of bond length on the shortest path between the proton and atom i.
The third one has the form
${g}_{D}(r)=\sum $ \frac{1}{$ {{r}_{\mathrm{D,i}}}^{2}$}{e}^{$ -B{$ (r-{a}_{\mathrm{D,i}})$}^{2}$}$$
where i denotes a double bond up to the seventh sphere of nonrotatable bonds centered on the target proton,
and ${r}_{D}$ and
${a}_{D}$ are
geometric variables.
The fourth one has the form
${g}_{S}(r)=\sum $ \frac{1}{$ {{r}_{\mathrm{S,i}}}^{2}$}{e}^{$ -B{$ (r-{a}_{\mathrm{S,i}})$}^{2}$}$$
where i denotes a single bond up to the seventh sphere of nonrotatable bonds centered on the target proton,
and ${r}_{S}$ and
${a}_{S}$ are
geometric variables.
The last one has the form
${g}_{3}(r)=\sum $ {e}^{$ -B{$ (r-{a}_{\mathrm{3,i}})$}^{2}$}$$
where i denotes an atom three nonrotatable bonds away from the target proton and belonging to a
six-membered ring, and ${a}_{3}$ is
a dihedral angle in radian units.
Each values is returned as atom property.
Classification
This descriptor is a Topological Descriptor
This descriptor is a Geometrical Descriptor
This descriptor is a Electronic Descriptor
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Definition
Descriptor that calculates the number of nonrotatable bonds on a molecule.
Description
The number of rotatable bonds is given by the SMARTS specified by Daylight on
[DAY01]
.
Classification
This descriptor is a Molecular Descriptor
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Definition
This Class contains a method that returns the sigma electronegativity for a given atom.
Description
Sigma electronegativity is given by
$X=a+bq+c$ \left($ {q}^{2}$\right)$$,
where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge.
Classification
This descriptor is a Electronic Descriptor
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Contributed by: . Created on: 2005-02-07.
Definition
Calculation of topological polar surface area based on fragment
contributions
[ERTL2000]
.
Classification
This descriptor is a Topological Descriptor
This descriptor is a Electronic Descriptor
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Definition
Descriptor that calculates carbon valence connectivity index (order 0).
Description
Let
$$ {v}_{i}$=$ \frac{$ ($ {v}_{i}$-$ {h}_{i}$)$}{$ ($ {z}_{i}$-$ {h}_{i}$-1)$}$$,
where ${p}_{i}$
is the numbers of valence electrons of atom i,
${h}_{i}$
is the number of hydrogens bonded to atom i, and ${z}_{i}$
is the atomic number of atom i.
While the atomic valence connectivity is calculated as the sum of
$\frac{1}{$ {$ \left($ {v}_{i}$\right)$}^{\mathrm{0.5}}$}$
over all heavy atoms i with
${v}_{i}$ greather than 0,
the carbon valence connectivity index takes into account only carbon atoms with ${v}_{i}$ greather than 0.
Classification
This descriptor is a Topological Descriptor
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Definition
Descriptor that calculates carbon valence connectivity index (order 1).
Description
Let
$$ {v}_{i}$=$ \frac{$ ($ {v}_{i}$-$ {h}_{i}$)$}{$ ($ {z}_{i}$-$ {h}_{i}$-1)$}$$,
where ${p}_{i}$
is the numbers of valence electrons of atom i,
${h}_{i}$
is the number of hydrogens bonded to atom i, and ${z}_{i}$
is the atomic number of atom i.
While the valence connectivity is calculated as the sum of
$\frac{1}{$ {$ \left($ {v}_{i}$$ {v}_{j}$\right)$}^{\mathrm{0.5}}$}$
over all bonds between heavy atoms i and j, the carbon valence
connectivity index takes into account only bonds between carbon atoms.
Classification
This descriptor is a Topological Descriptor
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Definition
Descriptor that calculates atomic valence connectivity index (order 0).
Description
Let
$$ {v}_{i}$=$ \frac{$ ($ {v}_{i}$-$ {h}_{i}$)$}{$ ($ {z}_{i}$-$ {h}_{i}$-1)$}$$,
where ${p}_{i}$
is the numbers of valence electrons of atom i,
${h}_{i}$
is the number of hydrogens bonded to atom i, and ${z}_{i}$
is the atomic number of atom i.
Valence connectivity is calculated as the sum of
$\frac{1}{$ {$ \left($ {v}_{i}$\right)$}^{\mathrm{0.5}}$}$
over all heavy atoms i with
${v}_{i}$ greather than 0.
Classification
This descriptor is a Topological Descriptor
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Definition
Descriptor that calculates atomic valence connectivity index (order 1).
Description
Let
$$ {v}_{i}$=$ \frac{$ ($ {v}_{i}$-$ {h}_{i}$)$}{$ ($ {z}_{i}$-$ {h}_{i}$-1)$}$$,
where ${p}_{i}$
is the numbers of valence electrons of atom i,
${h}_{i}$
is the number of hydrogens bonded to atom i, and ${z}_{i}$
is the atomic number of atom i.
Valence connectivity is calculated as the sum of
$\frac{1}{$ {$ \left($ {v}_{i}$$ {v}_{j}$\right)$}^{\mathrm{0.5}}$}$
over all bonds between heavy atoms i and j.
Classification
This descriptor is a Topological Descriptor
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Definition
Descriptor that returns the VdW radius of a given atom.
Classification
This descriptor is a Molecular Descriptor
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Definition
Descriptor that calculates the vertex adjacency information of a molecule.
Description
The values is given by
$1+log2*\mathrm{m}$,
where m is the number of heavy-heavy bonds.
If m is zero, then zero is returned.
Classification
This descriptor is a Topological Descriptor
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Definition
Descriptor that evaluates the weighted path descriptors.
Description
These decsriptors were described by Randic and characterize molecular
branching. Five descriptors are calculated, based on the implementation
in the ADAPT software package.
Classification
This descriptor is a Topological Descriptor
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Contributed by: . Created on: 2006-01-15.
Definition
Holistic descriptors described by Todeschini et al
[TOD98]
.
Classification
This descriptor is a Molecular Descriptor
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Definition
This class calculates Wiener path number and Wiener polarity number.
Description
Wiener path number: half the sum of all the distance matrix entries.
Wiener polarity number: half the sum of all the distance matrix entries with a value of 3.
Classification
This descriptor is a Topological Descriptor
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Definition
Prediction of logP based on the atom-type method called XLogP.
Description
For a description of the methodology see
[WANG97]
.
Classification
This descriptor is a Constitutional Descriptor
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Definition
The sum of the squared atom degrees of all heavy atoms.
Classification
This descriptor is a Topological Descriptor
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[CHER2003]
Cherkasov, A.. Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges,
J. Chem. Inf. Comput. Sci..
vol. 43.
2003,
pp. 2039-2047.
10.1021/ci034147w
[CPSA]
Ertl, P., Rohde, B., and Selzer, P.. Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based
Contributions and Its Applications to the Prediction of Drug Transport Properties,
J. Med. Chem..
vol. 43.
200,
pp. 3714-3717.
[DAY01]
Daylight. SMILES on-line tutorial,
http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html.
[ERTL2000]
Ertl, P. and Rohde, B. and Selzer, P.. Fast Calculation of Molecular Polar Surface Area as a Sum of
Fragment-Based Contributions and Its Application to the Prediction of
Drug Transport Properties,
J. Med. Chem.. 43
(20).
2000,
pp. 3714-3717.
10.1021/jm000942e
[GAST2002]
Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J.. Prediction of 1H NMR Chemical Shifts Using Neural Networks,
Anal. Chem.. 74
(1).
2002,
pp. 80-90.
10.1021/ac010737m
[KAT96]
Katritzky, A.R. and Mu, L. and Lobanov, V.S. and Karelson, M.. Correlation of Boiling Points With Molecular Structure. 1. A Training Set of 298 Diverse Organics and a Test Set of 9 Simple Inorganics,
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