BioMedR (version 1.2.1)

extrDrugWHIM: Calculate Holistic Descriptors Described by Todeschini et al.

Description

Calculate Holistic Descriptors Described by Todeschini et al.

Usage

extrDrugWHIM(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 17 columns:

• Wlambda1

• Wlambda2

• wlambda3

• Wnu1

• Wnu2

• Wgamma1

• Wgamma2

• Wgamma3

• Weta1

• Weta2

• Weta3

• WT

• WA

• WV

• WK

• WG

• WD

Each name will have a suffix of the form .X where X indicates the weighting scheme used. Possible values of X are

• unity

• mass

• volume

• eneg

• polar

Details

Holistic descriptors described by Todeschini et al, the descriptors are based on a number of atom weightings. There are six different possible weightings:

• unit weights

• atomic masses

• van der Waals volumes

• Mulliken atomic electronegativites

• atomic polarizabilities

• E-state values described by Kier and Hall

Currently weighting schemes 1, 2, 3, 4 and 5 are implemented. The weight values are taken from Todeschini et al. and as a result 19 elements are considered. For each weighting scheme we can obtain

• 11 directional WHIM descriptors (lambda1 .. 3, nu1 .. 2, gamma1 .. 3, eta1 .. 3)

• 6 non-directional WHIM descriptors (T, A, V, K, G, D)

Though Todeschini et al. mentions that for planar molecules only 8 directional WHIM descriptors are required the current code will return all 11.

References

Todeschini, R. and Gramatica, P., New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design, 1998, ?:355-380.

Examples

# NOT RUN {
sdf = system.file('sysdata/test.sdf', package = 'BioMedR')
mol = readMolFromSDF(sdf)
dat = extrDrugWHIM(mol)
head(dat)

# }