QSAR.sf.net Descriptor Dictionary

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]

Table of Contents

Constitutional Descriptors

Entries

Amino Acids Count (aminoAcidsCount)

• Definition
  Descriptor that returns the number of amino acids in an atom container.

  Classification
  This descriptor is a Constitutional Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2006-01-15.

Aromatic Atoms Count (aromaticAtomsCount)

• Definition
  Descriptor based on the number of aromatic atoms of a molecule.

  Classification
  This descriptor is a Constitutional Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Aromatic Bonds Count (aromaticBondsCount)

• Definition
  Descriptor based on the number of aromatic bonds of a molecule.

  Classification
  This descriptor is a Constitutional Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2004-11-26.

Atomic Degree (atomDegree)

• Definition
  Descriptor that calculates the number of not-Hs substituents of an atom.

  Classification
  This descriptor is a Topological Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Atomic Hybridization (atomHybridization)

• Definition
  Descriptor that returns the hybridization state of an atom.

  Classification
  This descriptor is a Molecular Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Atomic Hybridization VSEPR (atomHybridizationVSEPR)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Atomic Polarizabilities (apol)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2004-11-26.

Atomic Valence (atomValence)

• Definition
  Descriptor that calculates the valence of an atom.

  Classification
  This descriptor is a Electronic Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

BCUT (BCUT)

• Definition
  Eigenvalue based descriptor noted for its utility in chemical diversity described by Pearlman et al. [PEA99] .

  Classification
  This descriptor is a Molecular Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: , . Created on: 2005-01-27.

Bond Count (bondCount)

• Definition
  Descriptor based on the number of bonds of a certain bond order.

  Classification
  This descriptor is a Constitutional Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2004-11-26.

Bond Partial Pi Charge (bondPartialPiCharge)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Bond Partial Sigma Charge (bondPartialSigmaCharge)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Bond Partial Total Charge (bondPartialTCharge)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Bond Polarizabilities (bpol)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2004-11-26.

Bond Sigma Electronegativity (bondSigmaElectronegativity)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Bonds to Atom (bondsToAtom)

• Definition
  Descriptor based on the number of bonds on the shortest path between two atoms.

  Classification
  This descriptor is a Topological Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Carbon connectivity index (order 0) (chi0C)

• 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
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Carbon connectivity index (order 1) (chi1C)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Charged Partial Surface Area (CPSA)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-05-16.

Charged Partial Surface Area (eccentricConnectivityIndex)

• 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
  Search implementations on Google.com

Contributed by: . Created on: 2005-03-19.

Connectivity index (order 0) (chi0)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Connectivity index (order 1) (chi1)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Covalent Radius (covalentRadius)

• Definition
  Descriptor that returns the covalent radius of a given atom.

  Classification
  This descriptor is a Molecular Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Distance to Atom (distanceToAtom)

• Definition
  Descriptor that calculates the 3D distance between two atoms.

  Classification
  This descriptor is a Geometrical Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Effective Polarizability (effectivePolarizability)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2004-11-26.

Element Count (atomCount)

• Definition
  Descriptor based on the number of atoms of a certain element type.

  Classification
  This descriptor is a Constitutional Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Gravitational Index (gravitationalIndex)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , . Created on: 2004-11-24.

Gravitational Index (Square and Cube Roots) (gravitationalIndex_SquareAndCubeRoots)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , . Created on: 2004-11-25.

Hydrogen Bond Acceptors (hBondacceptors)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , . Created on: 2004-11-26.

Hydrogen Bond Donors (hBondDonors)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Inductive atomic hardness (atomicHardness)

• 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
  Search implementations on Google.com

Contributed by: . Created on: 2005-04-21.

Inductive atomic softness (atomicSoftness)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-04-21.

Kier and Hall kappa molecular shape indices (kierValues)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Largest Aliphatic Chain (largestAliphaticChain)

• Definition
  Descriptor that returns the number of atoms in the longest aliphatic chain.

  Classification
  This descriptor is a Topological Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-1-03.

Largest Chain (largestChain)

• Definition
  Descriptor that returns the number of atoms in the largest chain.

  Classification
  This descriptor is a Topological Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-1-03.

Largest Pi System (largestPiSystem)

• Definition
  Descriptor that returns the number of atoms in the largest pi system.

  Classification
  This descriptor is a Topological Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-1-03.

Lipinski's Rule of Five (lipinskifailures)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2005-01-27.

Molecular Weight (weight)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2005-01-27.

Moments of Inertia (momentOfInertia)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2005-02-07.

Partial Pi Charge (partialPiCharge)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Partial Sigma Charge (partialSigmaCharge)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Partial Total Charge (MMFF94) (PartialTChargeMMFF94)

• Definition
  Descriptor that calculates total partial charges of an heavy atom.

  Description
  Calculation is based on MMFF94.

  Classification
  This descriptor is a Electronic Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Partial Total Charge (PEOE) (PartialTChargePEOEDescriptor)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Period of an atom (period)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-02-07.

Petitjean Number (petitjeanNumber)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-02-07.

Petitjean Shape Indices (petitjeanShapeIndex)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-01-14.

Pi-contact of two atoms (piContact)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-02-07.

Pi Electronegativity (piElectronegativity)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-05-08.

Proton belonging to an aromatic system (isProtonInAromaticSystem)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-01-27.

Proton belonging to a pi-system (isProtonInConjugatedPiSystem)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-01-27.

Proton Total Partial Charge (protonPartialCharge)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-02-07.

RDF Proton Descriptor (rdfProtonCalculatedValues)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , . Created on: 2005-01-27.

Rotatable Bonds Count (rotatableBondsCount)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-02-07.

Sigma Electronegativity (sigmaElectronegativity)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-02-07.

Topological Polar Surface Area (tpsa)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , . Created on: 2005-01-27.

Valence carbon connectivity index (order 0) (chi0vC)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Valence carbon connectivity index (order 1) (chi1vC)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Valence connectivity index (order 0) (chi0v)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Valence connectivity index (order 1) (chi0v)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2004-11-26.

Van der Waals Radius (vdwradius)

• Definition
  Descriptor that returns the VdW radius of a given atom.

  Classification
  This descriptor is a Molecular Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-01-27.

Vertex adjacency information magnitude (vAdjMa)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2004-11-26.

Weighted Path (weightedPath)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2006-01-15.

WHIM (WHIM)

• Definition
  Holistic descriptors described by Todeschini et al [TOD98] .

  Classification
  This descriptor is a Molecular Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: , . Created on: 2005-01-27.

Wiener Numbers (wienerNumbers)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: . Created on: 2005-01-27.

XLogP (xlogP)

• 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
  Implementations
  Search implementations on Google.com

Contributed by: , . Created on: 2005-01-27.

Zagreb Index (zagrebIndex)

• Definition
  The sum of the squared atom degrees of all heavy atoms.

  Classification
  This descriptor is a Topological Descriptor
  Implementations
  Search implementations on Google.com

Contributed by: , Egon Willighagen. Created on: 2004-11-26.

Bibliography

[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, J. Phys. Chem.. vol. 100. 1996, pp. 10400-10407.
[MARSILI] Gasteiger, J. and Marsili, M.. Iterative Partial Equalization of Orbital Electronegativity- A Rapid Access to Atomic Charges, Tetrahedron. vol. 36. 1980, pp. 3219-3228.
[MATHML] W3C Math Home, http://www.w3.org/Math/.
[Mozilla] Mozilla - Home of the FireFox browser, http://www.mozilla.org/.
[PEA99] Pearlman, R.S. and Smith, K.M.. Metric Validation and the Receptor-Relevant Subspace Concept, J. Chem. Inf. Comput. Sci.. 39 (1). 1999, pp. 28-35.
[SALLER] Gasteiger, J. and Saller, H.. Berechnung der Ladungsverteilung in konjugierten Systemen durch eine Quantifizierung des Mesomeriekonzeptes, Angew. Chem.. vol. 97. 1985, pp. 699-701.
[TOD98] Todeschini, R. and Gramatica, P.. New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design. 1998, pp. 355-380.
[WANG97] Wang, R., Fu, Y., and Lai, L.. A New Atom-Additive Method for Calculating Partition Coefficients, Journal of Chemical Information and Computer Sciences. vol. 37. 1997, pp. 615-621.
[WES98] 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. vol. 38. 1998, pp. 726-735.

Final Notes

This dictionary [$Revision: 170 $] was last modified by [$Author: egonw $] on [$Date: 2005-10-22 14:42:40 +0200 (Sa, 22 Okt 2005) $]. The XML source can be found in CVS

Additions to this dictionary can be send to the QSAR project developers list (qsar-devel). If you find an error on this page, please post a bug report then on this page. In Category you can select the dictionary which contains the error.