Rcpi (version 1.8.0)

extractDrugBCUT: BCUT -- Eigenvalue Based Descriptor

Description

BCUT -- Eigenvalue Based Descriptor

Usage

extractDrugBCUT(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 6 columns:

• BCUTw-1l, BCUTw-2l ... - n high lowest atom weighted BCUTS
• BCUTw-1h, BCUTw-2h ... - n low highest atom weighted BCUTS
• BCUTc-1l, BCUTc-2l ... - n high lowest partial charge weighted BCUTS
• BCUTc-1h, BCUTc-2h ... - n low highest partial charge weighted BCUTS
• BCUTp-1l, BCUTp-2l ... - n high lowest polarizability weighted BCUTS
• BCUTp-1h, BCUTp-2h ... - n low highest polarizability weighted BCUTS

Details

Eigenvalue based descriptor noted for its utility in chemical diversity. Described by Pearlman et al. The descriptor is based on a weighted version of the Burden matrix which takes into account both the connectivity as well as atomic properties of a molecule. The weights are a variety of atom properties placed along the diagonal of the Burden matrix. Currently three weighting schemes are employed:

• Atomic Weight
• Partial Charge (Gasteiger Marsilli)
• Polarizability (Kang et al.)

References

Pearlman, R.S. and Smith, K.M., Metric Validation and the Receptor-Relevant Subspace Concept, J. Chem. Inf. Comput. Sci., 1999, 39:28-35.

Burden, F.R., Molecular identification number for substructure searches, J. Chem. Inf. Comput. Sci., 1989, 29:225-227.

Burden, F.R., Chemically Intuitive Molecular Index, Quant. Struct. -Act. Relat., 1997, 16:309-314

Kang, Y.K. and Jhon, M.S., Additivity of Atomic Static Polarizabilities and Dispersion Coefficients, Theoretica Chimica Acta, 1982, 61:41-48

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
mol = readMolFromSmi(smi, type = 'mol')
dat = extractDrugBCUT(mol)
head(dat)