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.

Value

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

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.

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')
# \donttest{
mol = readMolFromSmi(smi, type = 'mol')
#> Error in parseSmiles(smi): The package "rcdk" is required to parse SMILES
dat = extractDrugFragmentComplexity(mol)
#> Error in evaluateDescriptor(molecules, type = "FragmentComplexityDescriptor",     silent = silent): The package "rcdk" is required to compute molecular descriptors
head(dat)# }
#> Error: object 'dat' not found