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R3mCalculate

version 1.0.0 (11.8 KB) by Kevin
A function to calculate the molecular descriptor R3m (R-GETAWAY third order autocorrelation index weighted by atomic mass).

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Updated 03 Jan 2019

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### R3mCalculate ###

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
Wildfong Lab
Duquesne University

Last Updated: January 2019

Cite As

Kevin (2019). R3mCalculate (https://www.mathworks.com/matlabcentral/fileexchange/69891-r3mcalculate), MATLAB Central File Exchange. Retrieved .

DeBoyace, Kevin, et al. “Modeling and Prediction of Drug Dispersability in Polyvinylpyrrolidone-Vinyl Acetate Copolymer Using a Molecular Descriptor.” Journal of Pharmaceutical Sciences, vol. 107, no. 1, Elsevier {BV}, Jan. 2018, pp. 334–343, doi:10.1016/j.xphs.2017.10.003.

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MATLAB Release Compatibility
Created with R2018a
Compatible with any release
Platform Compatibility
Windows macOS Linux
Acknowledgements

Inspired: GetAtomCoords

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