extractDrugChiChain {Rcpi} | R Documentation

## Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7

### Description

Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7

### Usage

    extractDrugChiChain(molecules, silent = TRUE)

### Arguments

`molecules` | Parsed molucule object.
`silent` | Logical. Whether the calculating process should be shown or not, default is `TRUE`.

### Details

Evaluates chi chain descriptors. The code currently evluates the simple and valence chi chain descriptors of orders 3, 4, 5, 6 and 7. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

### Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 10 columns, in the following order:

- `SCH.3` - Simple chain, order 3

- `SCH.4` - Simple chain, order 4

- `SCH.5` - Simple chain, order 5

- `SCH.6` - Simple chain, order 6

- `SCH.7` - Simple chain, order 7

- `VCH.3` - Valence chain, order 3

- `VCH.4` - Valence chain, order 4

- `VCH.5` - Valence chain, order 5

- `VCH.6` - Valence chain, order 6

- `VCH.7` - Valence chain, order 7

### Note

These descriptors are calculated using graph isomorphism to identify the various fragments. As a result calculations may be slow. In addition, recent versions of Molconn-Z use simplified fragment definitions (i.e., rings without branches etc.) whereas these descriptors use the older more complex fragment definitions.

### Author(s)

Nan Xiao <https://nanx.me>

### Examples

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

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

[Package Rcpi version 1.20.1 Index]