rdkit

RDKit convert Mol file sdf v3000 to v2000

I have a Mol (sdf) file with a few chemicals in v3000 format. How do I convert it to Mol (sdf) file in v2000 format using RDKit?

Any help is appreciated.

Solution

  • RDKit will write v2000 format by default unless v3000 is specified, so you can just read in the SDF in v3000 format and write to v2000:

    from rdkit import Chem

supplier = Chem.SDMolSupplier('v3000.sdf')
writer = Chem.SDWriter('v2000.sdf')

for molecule in supplier:
    writer.write(molecule)

writer.close()

    Suppose you wanted to do the opposite:

    supplier = Chem.SDMolSupplier('v2000.sdf')
writer = Chem.SDWriter('v3000.sdf')
writer.SetForceV3000(True)

for molecule in supplier:
    writer.write(molecule)

writer.close()