210
Descriptor Ontology
20090719
Egon Willighagen
Atomic Descriptors
20051118
Data Feature
Molecular Descriptors
20051118
Descriptor
A feature (descriptor) is an algorithm that operates on a chemical
entity (commonly atoms and molecules)
and returns a numerical or nominal (descriptor) value which described
certain information on that entity.
Implementation
Algorithm
20090707
Atomic Descriptors
Data Representation
Category
Protein Descriptor
A descriptor specifically designed for characterizing proteins
20061102
Descriptor Value
One or more output values calculated by an Implementation
of a certain Algorithm for a certain molecule.
Contributor
Is Classified As
Is A
Requires
Instance Of
20060926
Kier & Hall SMARTS
Rajarshi Guha
Topological Descriptor
20050207
Descriptor reflecting the molecular connectivity without geometry information.
DescriptorCategories
20051118
Traditionally, the Estate indices are obtained by identifying a set of
fragments and then evaluating the Estate index from them. However it has
been shown by Butina (Molecules, 2004, 9, 10041009) that the frequency
of occurrence of the fragments can lead to QSAR models that perform as well
as those based on the original Estate indices. This descriptor generates
counts for 35 fragments. Descriptor names are prefixed with "khs."
Counts the number of occurrences of the Estate fragments
Chi Cluster Indices
Both the simple and valence versions of this descriptor are evaluated
20061113
Evaluates the Kier & Hall Chi cluster indices of orders 3,4,5,6 and 7
20050207
Geometrical Descriptor
Any descriptor derived from the threedimensional structure of the molecule.
This descriptor is described by Katritzky et al.
.
Gravitational Index
Descriptor characterizing the mass distribution of the molecule.
20041124
Gasteiger, J.
Saller, H.
Berechnung der Ladungsverteilung in konjugierten
Systemen durch eine Quantifizierung des
Mesomeriekonzeptes
Angew. Chem.
1985
97
699701
Ertl, P. and Rohde, B. and Selzer, P.
Fast Calculation of Molecular Polar Surface Area as a Sum of
FragmentBased Contributions and Its Application to the Prediction of
Drug Transport Properties
J. Med. Chem.
2000
43
20
37143717
10.1021/jm000942e
20061113
Evaluates the Kier & Hall Chi path cluster indices of orders 4,5 and 6
Both the simple and valence versions of this descriptor are evaluated
Chi PathCluster Indices
Weighted path descriptors
20060115
The weighted path (molecular ID) descriptors described by Randic. They characterize molecular branching.
20041126
Matteo Floris
Descriptor that calculates carbon connectivity index (order 1).
Carbon connectivity index (order 1)
While the atomic connectivity is calculated as the sum of
1
(
d
i
d
j
)
0.5
over all bonds between heavy atoms i and j, the carbon connectivity index
takes into account only bonds between carbon atoms.
Miguel Rojas
Bond Sigma Electronegativity
Descriptor relating to the electronic distribution in a molecule.
Electronic Descriptors
20050207
20060508
Descriptor that calculates of bondPolarizability of a bond.
Calculation is calculated determining the difference the
Sigma electronegativity on atoms A and B of a bond.
Eccentric Connectivity Index
20050319
The eccentric connectivity index for a hydrogen supressed molecular graph is given by the
expression
$${\xi}^{c}=\sum _{i=1}nE\left(i\right)V\left(i\right)$$
where E(i) is the eccentricity of the i
^{th}
atom (path length from the
i
^{th}
atom to the atom farthest from it) and V(i) is the vertex degree of the
i
^{th}
atom.
A topological descriptor combining distance and adjacency information.
Peter MurrayRust
Descriptor reflecting the molecular composition of a compound without
connectivity and geometry information.
20050207
Constitutional Descriptor
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 Hbond donors and more than 10 Hbond acceptors;
its molecular weight is over 500.
its LogP is over 5;
Lipinski's Rule of Five
This Class contains a method that returns the number failures of the
Lipinski's Rule Of Five.
20050127
Calculation is calculated determining the difference the
Partial Sigma Charge on atoms A and B of a bond. Based in
Gasteiger Charge.
Descriptor that calculates bondsigma Partial charge of a
bond.
20060508
Bond Partial Sigma Charge
20060508
Atomic Hybridization VSEPR
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.
Descriptor that returns the hybridization state of an atom.
20061112
Evaluates the Kier & Hall Chi chain indices of orders 3,4,5 and 6
Both the simple and valence versions of this descriptor are evaluated
Chi Chain Indices
Descriptor that counts the number of rings in the molecules. Optionally,
it counts the number rings with a specified number of ring atoms.
20090723
Ring Count
20050207
This Class contains a method that returns the sigma electronegativity for a given atom.
Sigma electronegativity is given by
X
=
a
+
b
q
+
c
(
q
2
)
,
where a, b and c are Gasteiger Marsili parameters, and q is the sigma charge.
Sigma Electronegativity
Descriptor that calculates the number of nonrotatable bonds on a molecule.
The number of rotatable bonds is given by the SMARTS specified by Daylight on
.
Rotatable Bonds Count
20050207
20060115
Ionization Potential
It should be noted that the descriptor values are obtained using a predictive model
and are not calculated directly from the structure
Descriptor that evaluates the ionization potential.
20041126
Atomic Hybridization
Descriptor that returns the hybridization state of an atom.
Aromatic Atoms Count
20041126
Descriptor based on the number of aromatic atoms of a molecule.
20050127
WHIM
Holistic descriptors described by Todeschini et al
.
Hybrid Descriptor
Petitjean Shape Indices
The topological and geometric shape indices described Petitjean and Bath et al.
respectively. Both measure the anisotropy in a molecule.
20060115
Todeschini, R. and Gramatica, P.
New 3D Molecular Descriptors: The WHIM theory and QAR Applications
Persepectives in Drug Discovery and Design
1998
355380
Covalent Radius
20060508
Descriptor that returns the covalent radius of a given atom.
XLogP
20050127
Prediction of logP based on the atomtype method called XLogP.
For a description of the methodology see
.
Let
v
i
=
(
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
1
(
v
i
)
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.
Valence carbon connectivity index (order 0)
Descriptor that calculates carbon valence connectivity index (order 0).
20041126
Largest Chain
Returns the number of atoms in the largest chain
Christian Hoppe
20050207
Descriptor that calculates sigma partial charges in
sigmabonded systems (PEOE) of an heavy atom.
Calculation is based on Gasteiger Marsili (PEOE)
.
20060508
Partial Pi Charge
2006822
Class that returns the complexity of a system. The complexity is defined as @cdk.cite{Nilakantan06}
Fragment Complexity
20050207
Longest Aliphatic Chain
Returns the number of atoms in the longest aliphatic chain
20050421
Inductive atomic softness of an atom in a polyatomic system can be defined
as as charge delocalizing ability.
This descriptor is described by Cherkasov
.
This class calculates the atomic softness of a given atom.
Inductive atomic softness
has 2D Coordinates
Zagreb Index
The sum of the squared atom degrees of all heavy atoms.
20041126
Molecular Distance Edge
20060918
For a description of the methodology see
.
Evaluate molecular distance edge descriptors for C, N and O
Descriptor that calculates the number of notHs substituents of an atom.
20041126
Atomic Degree
Let
v
i
=
(
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
1
(
v
i
v
j
)
0.5
over all bonds between heavy atoms i and j.
Descriptor that calculates atomic valence connectivity index (order 1).
Valence connectivity index (order 1)
20041126
The values is given by
1
+
log
2
*
m
,
where m is the number of heavyheavy bonds.
If m is zero, then zero is returned.
Vertex adjacency information magnitude
Descriptor that calculates the vertex adjacency information of a molecule.
20041126
This descriptor is described by Wessel et al.
.
Gravitational Index (Square and Cube Roots)
20041125
Descriptor characterizing the mass distribution of the molecule as the square
or cube root of the gravitational index.
20041126
Valence connectivity index (order 0)
Descriptor that calculates atomic valence connectivity index (order 0).
Let
v
i
=
(
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
1
(
v
i
)
0.5
over all heavy atoms i with
v
i
greather than 0.
Gasteiger, J.
Marsili, M.
Iterative Partial Equalization of Orbital
Electronegativity A Rapid Access to Atomic Charges
Tetrahedron
1980
36
32193228
Partial Pi Charge
20060508
Calculation is based on Gasteiger H.Saller (PEPE)
.
Descriptor that calculates pi partial charges in pibonded
systems of an heavy atom.
20061112
Both the simple and valence versions of this descriptor are evaluated
Chi Path Indices
Evaluates the Kier & Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7
20050207
Period of an atom
Descriptor that returns the period in the periodic table of an atom belonging to an atom container
Pearlman, R.S. and Smith, K.M.
Metric Validation and the ReceptorRelevant Subspace Concept
J. Chem. Inf. Comput. Sci.
1999
39
1
2835
Calculation is based on MMFF94.
Descriptor that calculates total partial charges of an heavy
atom.
Partial Total Charge (MMFF94)
20060508
Patani, G. A. and LaVoie, E. J.
Bioisosterism: A Rational Approach in Drug Design
Chem. Rev.
1996
96
31473176
20050207
Picontact of two atoms
Descriptor that check if two atoms have picontact (this is true when there is one and
the same conjugated pisystem which contains both atoms, or directly linked neighboors of the atoms).
MoreauBroto Autocorrelation (mass) descriptors
20060115
The MoreauBroto autocorrelation descriptors using atomic weight
Federico Marighetti
20050207
Descriptor that calculates the Petitjean Number of a molecule.
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
(
diameter

radius
)
diameter
.
Petitjean Number
Descriptor that calculates the 3D distance between two atoms.
20041126
Distance to Atom
Todeschini, R. and Consonni, V.
Handbook of Molecular Descriptors
2000
352299130
Atomic Polarizabilities
Polarizabilities derive from periodic tables.
Dietz Representation
Representation in which atoms are represented by graph nodes and
bonds by graph edges. Consequently, bonds are always localized
between two atoms.
Graph Representation
Descriptor that calculates the sum of the atomic polarizabilities (including implicit hydrogens).
20041126
Wang, R., Fu, Y., and Lai, L.
A New AtomAdditive Method for Calculating Partition Coefficients
Journal of Chemical Information and Computer
Sciences
1997
37
615621
This algorithm contains a method that returns the pi
electronegativity for a given atom.
20060508
Pi Electronegativity
Pi electronegativity is given by
X
=
a
+
b
q
+
c
(
q
2
)
, where a, b and c are Gasteiger Marsili parameters, and q
is the sigma charge.
Joerg Kurt Wegner
20060908
Acceptors or Donors Field Atoms (Boehm,Klebe)
Force field based definition of hydrogen bond acceptors or donors .
This rule covers amino and hydroxy groups.
Counts the number of acceptor/donor field atoms for a carbonyl oxygen or amino hydrogen probe.
Let
v
i
=
(
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
1
(
v
i
v
j
)
0.5
over all bonds between heavy atoms i and j, the carbon valence
connectivity index takes into account only bonds between carbon atoms.
Descriptor that calculates carbon valence connectivity index (order 1).
Valence carbon connectivity index (order 1)
20041126
The MoreauBroto autocorrelation descriptors using polarizability
MoreauBroto Autocorrelation (polarizability) descriptors
20060115
20050207
Returns the number of atoms in the largest pi chain
Largest Pi Chain
20041126
Descriptor that calculates the number of hydrogen bond acceptors.
Hydrogen Bond Acceptors
This Class contains a method that returns true if the protons is directly bonded to a pi system.
Proton belonging to a pisystem
20050127
has Fractional Unit Cell Coordinates Coordinates
Returns the number of amino acids found in the system
Amino Acid Count
20060115
ALogP
Calculates atom additive logP and molar refractivity values as described by Ghose and Crippen
and
20050127
Todd Martin
A variety of descriptors combining surface area and partial charge information
20050516
Charged Partial Surface Areas
Calculation is calculated determining the difference the
Partial Total Charge on atoms A and B of a bond. Based in
Gasteiger Charge.
20060508
Bond Partial Total Charge
Descriptor that calculates bondtotal Partial charge of a
bond.
Liu, S. and Cao, C. and Li, Z.
Approach to Estimation and Prediction for Normal
Boiling Point (NBP) of Alkanes Based on a Novel Molecular
Distance Edge (MDE) Vector, lambda
Journal of Chemical Information and Computer Sciences
i1998
38
387394
Descriptor that calculates the number of hydrogen bond acceptors.
20041126
As defined by Daylight website, , a Hbond 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.
Hydrogen Bond Acceptors (Daylight)
20050421
Inductive atomic hardness
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
.
This class calculates the atomic hardness of a given atom.
Effective Polarizability
Polarizabilities are assigned to the heavy atom by Polarizability class.
20041126
Descriptor that calculates the effective polarizability of a given heavy atom.
Polarizabilities derive from periodic tables.
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).
20041126
Bond Polarizabilities
20060115
The MoreauBroto autocorrelation descriptors using partial charges
MoreauBroto Autocorrelation (charge) descriptors
Calculates the ratio of length to breadth.
20060926
The descriptor has two values
indicating the maximum and minimumn value of LoB. Note that this method does not
perform any orientation.
Length Over Breadth
Topological Polar Surface Area
Calculation of topological polar surface area based on fragment
contributions
.
20050127
Trinijastic, N.
Chemical Graph Theory
CRC Press
1992
0849342562
Wessel, M.D. and Jurs, P.C. and Tolan, J.W. and Muskal, S.M.
Prediction of Human Intestinal Absorption of Drug Compounds
From Molecular Structure
Journal of Chemical Information and Computer
Sciences
1998
38
726735
Molecular Weight
Descriptor based on the weight of atoms of a certain element type.
If no element is specified, the returned value is the Molecular Weight
20050127
Eigenvalue based descriptor noted for its utility in chemical diversity
described by Pearlman et al.
.
BCUT
20050127
Petitjean, M.
Applications of the radiusdiameter diagram to the classification of topological and
geometrical shapes of chemical compounds
Journal of Chemical Information and Computer Science
1992
32
331337
Descriptor that calculates the valence of an atom.
Atomic Valence
20041126
Counts the number of acceptor field atoms for a carbonyl oxygen probe.
Force field based definition of hydrogen bond acceptors
This rule covers nitril, carbonyl, ether, and amin nitrogens.
Acceptor Field Atoms (Boehm,Klebe)
20060908
Van der Waals radius
20050127
Descriptor that returns the VdW radius of a given atom.
Descriptor that calculates the number of hydrogen bond donors.
As defined by Daylight website, , a Hbond acceptor
must have an NH bond, an OH bond, or a FH bond
Hydrogen Bond Donors (Daylight)
20041126
Aromatic Bonds Count
Descriptor based on the number of aromatic bonds of a molecule.
20041126
Descriptor that calculates partial charges of an heavy atom and its protons.
Calculation is based on Gasteiger Marsili (PEOE)
Proton Total Partial Charge
20050207
Hydrogen Bond Donors
20041126
Descriptor that calculates the number of hydrogen bond donors.
20041126
Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular
graphs.
First kappa shape index is given by
n
(
n

1
)
2
m
2
,
second kappa shape index is given by
(
n

1
)
(
n

2
)
2
p
2
2
and third kappa shape index is given by
(
n

1
)
(
n

3
)
2
p
3
2
for odd n and
(
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
Kier and Hall kappa molecular shape indices
Descriptor that calculates Kier and Hall kappa molecular shape indices.
20060823
The TAE RECON descriptors for amino acid sequences. Uses precalculated quantum mechanical
parameters to generate a set of 147 descriptors for a given sequence
TAE RECON descriptors for amino acid sequences
Böhm, M. and Klebe, G.
Development of New HydrogenBond Descriptors and Their {A}pplication to Comparative Molecular Field Analyses
J. Med. Chem.
2002
45
15851597
20060926
Characterizes the carbon connectivity in terms of hybridization
This is a port of the ADAPT CTYPES routine and is a count of
carbon atom in different hybridization states and environments
Carbon Types
Bath, P.A. and Poirette, A.R. and Willet, P. and Allen, F.H.
The Extent of the Relationship between the GraphTheoretical and the Geometrical Shape
Coefficients of Chemical Compounds
Journal of Chemical Information and Computer Science
1995
35
714716
Randic, M.
On molecular identification numbers
Journal of Chemical Information and Computer Science
1984
24
164175
Element Count
Descriptor based on the number of atoms of a certain element type.
20041126
has 3D Coordinates
20041126
Descriptor based on the number of bonds of a certain bond order.
Bond Count
20050207
Moments of Inertia
Descriptor that calculates the principal moments of inertia and ratios
of the principal moments. Als calculates the radius of gyration.
20041126
Bonds to Atom
Descriptor based on the number of bonds on the shortest path between two atoms.
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
J. Phys. Chem.
1996
100
1040010407
A given proton is represented by 5 different descriptors.
The first one has the form
g
H
r
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
1
r
D,i
2
e

B
(
r

a
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
1
r
S,i
2
e

B
(
r

a
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
e

B
(
r

a
3,i
)
2
where i denotes an atom three nonrotatable bonds away from the target proton and belonging to a
sixmembered ring, and
a
3
is
a dihedral angle in radian units.
Each values is returned as atom property.
20050127
Calculation of RDF proton descriptor based on
.
RDF Proton Descriptor
has Partial Atomic Charges
Proton belonging to an aromatic system
20050127
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.
20060908
Force field based definition of hydrogen bond donors .
This rule covers amino groups, chloro, bromo and iodo atoms .
Counts the number of donor field atoms for an amino hydrogen probe.
Donor Field Atoms (Boehm,Klebe)
Cherkasov, A.
Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial
Charges
J. Chem. Inf. Comput. Sci.
2003
43
20392047
10.1021/ci034147w
Carbon connectivity index (order 0)
Descriptor that calculates the carbon connectivity index (order 0).
While the atomic connectivity is calculated as the sum of
1
d
i
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.
20041126
Descriptor that calculates bondpi Partial charge of a bond.
Bond Partial Pi Charge
Calculation is calculated determining the difference the
Partial Pi Charge on atoms A and B of a bond. Based in
Gasteiger Charge.
20060508
AiresdeSousa, J. and Hemmer, M.C. and Gasteiger, J.
Prediction of 1H NMR Chemical Shifts Using Neural Networks
Anal. Chem.
2002
74
1
8090
10.1021/ac010737m
Gillet, J. and Willett, P. and Bradshaw, J.
Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms
J. Chem. Inf. Comput. Sci.
1998
38
165179
Daylight
SMILES online tutorial
http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html
20050127
This class calculates Wiener path number and Wiener polarity number.
Wiener Numbers
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.