Dragon molecular descriptors

"The molecular descriptor is the final result of a logic and mathematical procedure which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment." (Handbook of Molecular Descriptors, R.Todeschini and V.Consonni, Wiley-VCH, 2000).


Molecular descriptors play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, health research and quality control, they being obtained when molecules are transformed into a molecular representation allowing some mathematical treatment. Many molecular descriptors have been proposed derived from different theories and approaches with the aim of predicting biological and physico-chemical properties of molecules [R.Todeschini and V.Consonni, Handbook of Molecular Descriptors, Wiley-VCH, Weinheim (GER), 2000].


The information content of a molecular descriptor depends on the kind of molecular representation that is used and on the defined algorithm for its calculation. There are simple molecular descriptors derived by counting some atom-types or structural fragments in the molecule, other derived from algorithms applied to a topological representation (molecular graph) and usually called topological or 2D-descriptors, and there are molecular descriptors derived from a geometrical representation that are called geometrical or 3D-descriptors.


All the molecular descriptors must contain, to varying extents, chemical information, must satisfy some basic invariance properties and general requirements, and must be derived from well-established procedures which enable molecular descriptors to be calculated for any set of molecules. It is obvious – almost trivial - that a single descriptor or a small number of descriptors cannot wholly represent the molecular complexity or model all the physico-chemical responses and biological interactions. As a consequence, although we must get used to living with approximate models (nothing is perfect!), we have to keep in mind that "approximate" is not a synonym of "useless".


The field of molecular descriptors is strongly interdisciplinary and involves a variety of different theories. For the definition of molecular descriptors, a knowledge of algebra, graph theory, information theory, computational chemistry, theories of organic reactivity and physical chemistry is usually required, although at different levels. For the use of the molecular descriptors, a knowledge of statistics, chemometrics, and the principles of the QSAR/QSPR approaches is necessary in addition to the specific knowledge of the problem.


The 29 logical molecular descriptors blocks (and their sub-blocks) calculated by Dragon are:


1.Constitutional descriptors
1.1.Basic descriptors


2.Ring descriptors
2.1.Basic descriptors


3.Topological indices
3.1.Vertex degree-based indices
3.2.Distance-based indices
3.3.MTI indices
3.4.Path/walk indices
3.5.E-state indices
3.6.Centric indices


4.Walk and path counts
4.1.Walk counts
4.2.Self-returning walk counts
4.3.Path counts
4.4.Multiple path counts
4.5.ID numbers


5.Connectivity indices
5.1.Kier-Hall molecular connectivity indices
5.2.Solvation connectivity indices
5.3.Randic-like connectivity indices


6.Information indices
6.1.Basic descriptors
6.2.Indices of neighborhood symmetry


7.2D matrix-based descriptors
7.1.Adjacency matrix
7.2.Topological distance matrix
7.3.Laplace matrix
7.4.Chi matrix
7.5.Reciprocal squared distance matrix
7.6.Detour matrix
7.7.Distance/detour matrix
7.8.Barysz matrices
7.9.Burden matrices


8.2D autocorrelations
8.1.Broto-Moreau autocorrelations
8.2.Centred Broto-Moreau autocorrelations
8.3.Moran autocorrelations
8.4.Geary autocorrelations
8.5.Topological charge autocorrelations


9.Burden eigenvalues
9.1.Largest eigenvalues
9.2.Smallest eigenvalues


10.P_VSA-like descriptors
10.2.Molar Refractivity
10.4.Van der Waals volume
10.5.Sanderson electronegativity
10.7.Ionization Potential
10.8.Intrinsic State


11.ETA indices
11.1.Basic descriptors


12.Edge adjacency indices
12.1.Spectral indices
12.2.Connectivity-like indices
12.3.Spectral moments


13.Geometrical descriptors
13.1.Size indices
13.2.Shape indices
13.3.Delocalization-degree indices
13.4.COMMA descriptors


14.3D matrix-based descriptors
14.1.Geometrical distance matrix
14.2.Reciprocal squared geometrical distance matrix
14.3.Distance/distance matrix


15.3D autocorrelations
15.1.TDB autocorrelations


16.RDF descriptors
16.2.Weighted by mass
16.3.Weighted by van der Waals volume
16.4.Weighted by Sanderson electronegativity
16.5.Weighted by polarizability
16.6.Weighted by ionization potential
16.7.Weighted by I-state


17.3D-MoRSE descriptors
17.2.Weighted by mass
17.3.Weighted by van der Waals volume
17.4.Weighted by Sanderson electronegativity
17.5.Weighted by polarizability
17.6.Weighted by ionization potential
17.7.Weighted by I-state


18.WHIM descriptors
18.1.Directional descriptors
18.2.Global descriptors


19.GETAWAY descriptors
19.1.Basic descriptors


20.Randic molecular profiles
20.1.Molecular profiles
20.2.Shape profiles


21.Functional group counts
21.1.Basic descriptors


22.Atom-centred fragments
22.1.Basic descriptors


23.Atom-type E-state indices
23.1.E-State sums
23.2.Atom-type counts


24.CATS 2D
24.1.Basic descriptors


25.2D Atom Pairs
25.1.Weighted topological atom pairs
25.2.Binary Atom Pairs
25.3.Frequency Atom Pairs


26.3D Atom Pairs
26.1.Weighted geometrical atom pairs


27.Charge descriptors
27.1.Basic descriptors


28.Molecular properties
28.1.Basic descriptors


29.Drug-like indices
29.1.Basic indices