extractDrugFragmentComplexity: Calculate Complexity of a System

In nanxstats/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Calculate Complexity of a System

Description

Calculate Complexity of a System

Usage

extractDrugFragmentComplexity(molecules, silent = TRUE)

Arguments

molecules	Parsed molucule object.
silent	Logical. Whether the calculating process should be shown or not, default is TRUE.

Details

This descriptor calculates the complexity of a system. The complexity is defined in Nilakantan, R. et al. as:

C = abs(B^2 - A^2 + A) + \frac{H}{100}

where C is complexity, A is the number of non-hydrogen atoms, B is the number of bonds and H is the number of heteroatoms.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns one column named fragC.

References

Nilakantan, R. and Nunn, D.S. and Greenblatt, L. and Walker, G. and Haraki, K. and Mobilio, D., A family of ring system-based structural fragments for use in structure-activity studies: database mining and recursive partitioning., Journal of chemical information and modeling, 2006, 46:1069-1077

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')

mol = readMolFromSmi(smi, type = 'mol')
dat = extractDrugFragmentComplexity(mol)
head(dat)

nanxstats/Rcpi documentation built on Sept. 24, 2024, 9:36 a.m.