Convert MOL files to SMILES via standard I / O

Introduction

I created a python script to convert a MOL file to SMILES. This is ubiquitous, but I read a MOL file (MOL format string) from standard input and spit out SMILES to standard output. As a result, the result can be obtained without going through the file, and it can be used more easily.

environment

• Python3.6
• RDKit 2019.03.3.0

Source

The source is as follows.

Mol2SMILESConvertor.py

import sys
from rdkit import Chem


def main():
    f = sys.stdin
    mol_block = ""
    for line in f:
        mol_block += line

    mol = Chem.MolFromMolBlock(mol_block)
    smiles = Chem.MolToSmiles(mol)
    print(smiles)


if __name__ == "__main__":
    main()

How to use

The usage is explained using the following MOL file as an example.

test.mol

2,3,6-PCB
     RDKit          2D

 15 16  0  0  0  0  0  0  0  0999 V2000
    1.2990   -0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2990    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2990   -0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.0008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2978   -3.7529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3380   -3.1546    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.2955   -5.2529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3337   -5.8546    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0048   -6.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3026   -5.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3002   -3.7488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3385   -3.1472    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  2  0
 12 13  1  0
 13 14  2  0
 14  7  1  0
 14 15  1  0
M  END
$$$$

If you cat the above MOL file and feed it to this script, you will get SMILES as follows. It's easy.

$ cat test.mol |python bin/Mol2SMILESConvertor.py
Clc1ccc(Cl)c(-c2ccccc2)c1Cl

Other

--It would be even more convenient to read an SDF file (SDF format character string) containing multiple compounds and output multiple SMILES at once.