readMolFromSmi {Rcpi} | R Documentation

## Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List

### Description

Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List

### Usage

    readMolFromSmi(smifile, type = c("mol", "text"))

### Arguments

`smifile` | Character vector, containing SMILES file location(s).
`type` | `'mol'` or `'text'`. `'mol'` returns parsed Java molecular object, used for `'text'` returns (plain-text) character string list. For common molecular descriptors and fingerprints, use `'mol'`. For descriptors and fingerprints calculated by OpenBabel, i.e. functions named `extractDrugOB...()` , use `'text'`.

### Details

This function reads molecules from SMILES strings and return parsed Java molecular object or plain text list needed by `extractDrug...()` functions.

### Value

A list, containing parsed Java molecular object or character strings.

### Author(s)

Nan Xiao <https://nanx.me>

### See Also

See `readMolFromSDF` for reading molecules from SDF files and returning parsed Java molecular object.

### Examples

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

    mol1 = readMolFromSmi(smi, type = 'mol')
    mol2 = readMolFromSmi(smi, type = 'text')

[Package Rcpi version 1.20.1 Index]