extractDrugChiPathCluster {Rcpi} | R Documentation

## Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6

### Description

Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6

### Usage

    extractDrugChiPathCluster(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 path cluster descriptors. The code currently evluates the simple and valence chi chain descriptors of orders 4, 5 and 6. 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 6 columns named `SPC.4`, `SPC.5`, `SPC.6`, `VPC.4`, `VPC.5`, `VPC.6`:

- `SPC.4` - Simple path cluster, order 4

- `SPC.5` - Simple path cluster, order 5

- `SPC.6` - Simple path cluster, order 6

- `VPC.4` - Valence path cluster, order 4

- `VPC.5` - Valence path cluster, order 5

- `VPC.6` - Valence path 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 = extractDrugChiPathCluster(mol)
    head(dat)

[Package Rcpi version 1.24.0 Index]