extractDrugChiCluster {Rcpi} | R Documentation

## Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6

### Description

Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6

### Usage

    extractDrugChiCluster(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 cluster descriptors. 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 8 columns, the order and names of the columns returned is:

- SC.3 - Simple cluster, order 3

- SC.4 - Simple cluster, order 4

- SC.5 - Simple cluster, order 5

- SC.6 - Simple cluster, order 6

- VC.3 - Valence cluster, order 3

- VC.4 - Valence cluster, order 4

- VC.5 - Valence cluster, order 5

- VC.6 - Valence cluster, order 6

### 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 = extractDrugChiCluster(mol)
    head(dat)

[Package Rcpi version 1.16.2 Index]