combine_mol2sdf: Combine multiple mol files into a single sdf file and remove...

In QizhiSu/mspcompiler: Compile Mass Spectral Libraries from Various Sources

Combine multiple mol files into a single sdf file and remove duplicates

Description

combine_mol2sdf offers a way to combine multiple mol files in to a single sdf file removing duplicates.

Usage

combine_mol2sdf(input, output, use_filename = FALSE)

Arguments

input	The location of the exported *.MOL folder from Lib2NIST, e.g., "/home/nist.MOL".
output	The location where the sdf file will be stored and its name, e.g., "/home/exported.sdf".
use_filename	In case you want to use the file name as the Molecule_Name in the sdf file, please use use_filename = TRUE. This is useful when you draw your own chemicals which might not have Molecule_Name in the .MOL files. With this option, you can use the name of the .MOL files.

Details

The msp file exported from NIST format by the Lib2NIST software has no SMILES which is used for viewing the structure in MS-DIAL and is crucial as well if you want to predict retention index (RI) for compounds with no experimental RI (in the case of EI library). Chemical structure of each compound in the NIST library can be exported as a mol file. Every library entry will have one corresponding mol file. All these mol files will be stored in a folder with ".MOL" suffix. This function aims to combine all these mol files into a single sdf file which can be then used for retrieve SMILES for each entry. This function supports parallel computing.

Value

It will return no value but only creates a sdf file.

QizhiSu/mspcompiler documentation built on May 7, 2024, 4:25 a.m.