extractDrugWHIM {Rcpi} | R Documentation

## Calculate Holistic Descriptors Described by Todeschini et al.

### Description

Calculate Holistic Descriptors Described by Todeschini et al.

### Usage

    extractDrugWHIM(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)

Nan Xiao <https://nanx.me>

### 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/OptAA3d.sdf', package = 'Rcpi')

    mol = readMolFromSDF(sdf)
    dat = extractDrugWHIM(mol)
    head(dat)

[Package Rcpi version 1.20.1 Index]