Simple RDKit Example

This is a simple example showing how you can use a Docker container containing RDKit to process the structures. All it does is calculate the atom count of each molecule, but as such does provide a complete example that can be executed

Option	Value	Comment
Docker image name	informaticsmatters/rdkit	This is a Docker image that contains a full RDKit distribution that we here use from Python
Input media type	chemical/x-mdl-sdfile	Specifies to write the input to a file named input.sdf.gz in MDL’s SD file format
Output media type	chemical/x-mdl-sdfile	Specifies to read the output from a file named output.sdf.gz in MDL’s SD file format
Command	See below	Python script that iterates through the molecules in the SD file, calculates the atom count of the molecule and writes an output file in SD file format.

The script is as follows:

#!/usr/bin/env python

import gzip
from rdkit import Chem

suppl = Chem.ForwardSDMolSupplier(gzip.open('input.sdf.gz'))

outf=gzip.open('output.sdf.gz','w+')
w = Chem.SDWriter(outf)

for mol in suppl:
    if mol is None: continue
    mol.SetIntProp("atom_count_rdkit", mol.GetNumAtoms())
    w.write(mol)

w.close()
outf.close()

Once executed the output should have the number of atoms in the molecule present as the atom_count_rdkit property.