Calculate Complexity of a System

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Description

Calculate Complexity of a System

Usage

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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.

Author(s)

Nan Xiao <http://nanx.me>

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

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

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

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