R3mCalculate

A function to calculate the molecular descriptor R3m (R-GETAWAY third order autocorrelation index weighted by atomic mass).

### R3mCalculate ###

Authors: Kevin DeBoyace, Mustafa Bookwala

A function to calculate the molecular descriptor R3m.

This function calculates the molecular matrix (M), geometry matrix (G), molecular influence matrix (H), and influence distance matrix (R). This is accomplished by calling the following subfunctions: ImportSDF, MolecMatrix, EuclidDistance, MolecInfluenceMatrix, and InfluenceDistanceMat. This function currently only works for SDF files. Other file formats can be converted to SDF using OpenBabel. When the code is run, the user is prompted to select an SDF file. Next, the molecule is plotted using the PlotMolecule function to ensure the 3D coordinates are reasonable. Finally, the R3m value is calculated and output to the command window and workspace.

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NOTE: The R3mCalculate function is the primary function. The other functions and scripts are referenced by this function. The user will only need to run the R3mCalculate function:

e.g. [R3m] = R3mCalculate;

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References:

[1] Todeschini, R.; Consonni, V., Molecular Descriptors for Chemoinformatics, Volume

41 (2 Volume Set). 2nd ed.; John Wiley & Sons: 2009.

[2] Consonni V, Todeschini R, Pavan M, Gramatica P 2002. Structure/response

correlations and similarity/diversity analysis by GETAWAY descriptors. 2. Application

of the novel 3D molecular descriptors to QSAR/QSPR studies. Journal of chemical

information and computer sciences 42(3):693-705.

[3] Tetko, I. V.; Gasteiger, J.; Todeschini, R.; Mauri, A.; Livingstone, D.; Ertl, P.;

Palyulin, V. A.; Radchenko, E. V.; Zefirov, N. S.; Makarenko, A. S. Virtual

computational chemistry laboratory–design and description. J. Comput. Aided Mol.

Des. 2005, 19, (6), 453-463.

[4] DeBoyace, K.; Buckner, I. S.; Gong, Y.; Ju, T.-c. R.; Wildfong, P. L. D. Modeling

and Prediction of Drug Dispersability in Polyvinylpyrrolidone-Vinyl Acetate Copolymer

Using a Molecular Descriptor. J. Pharm. Sci. 2018, 107, (1), 334-343.

R3m can also be calculated online with appoximately 1600 other descriptors at http://www.vcclab.org/lab/edragon/

Author: Kevin DeBoyace

ss Wildfong Lab

Duquesne University

Last Updated: January 2019