extrDrugWHIM: Calculate Holistic Descriptors Described by Todeschini et al.

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

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.

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.

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

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

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

sdf = system.file('sysdata/test.sdf', package = 'BioMedR')
mol = readMolFromSDF(sdf)
dat = extrDrugWHIM(mol)
head(dat)

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.