Hi Markus,You can generate the RXN file output from the rxn object via ReactionToRxnBlock, like this Python code:
>>> from rdkit import Chem >>> from rdkit.Chem import AllChem >>> rxn = AllChem.ReactionFromSmarts('CC(=O)O.OCC>>CC(=O)OCC') >>> AllChem.ReactionToRxnBlock(rxn) '$RXN\n\n RDKit\n\n 2 1\n$MOL\n\n RDKit \n\n 4 3 0 0 0 0 0 0 0 0999 V2000\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 6 0\n 2 3 2 0\n 2 4 6 0\nM END\n$MOL\n\n RDKit \n\n 3 2 0 0 0 0 0 0 0 0999 V2000\n 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 6 0\n 2 3 6 0\nM END\n$MOL\n\n RDKit \n\n 6 5 0 0 0 0 0 0 0 0999 V2000\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 6 0\n 2 3 2 0\n 2 4 6 0\n 4 5 6 0\n 5 6 6 0\nM END\n' >>>Writing an RDF file is quite like writing an SD file, except that the molfile entry is replaced with an RXN file entry. The syntax for data fields is a bit different too. Data fields can be used to describe agents, conditions, etc. but there is no fixed vocabulary (that I know of) for e.g. specifying "this is an agent". Hence, exchanging and parsing RDF files can be ... interesting.
Cheers -- Jan Holst Jensen On 2019-09-03 11:59, Markus Grimm via Rdkit-discuss wrote:
Dear all,I'm trying to generate .rxn files or one single .rdf file from a csv file where I have a bunch of reactions smiles stored. I know how to instantiate a rxn object but I no idea how to safe this to several .rxn files or a RDF file.I already asked this question last Friday but unfortunately I did not receive any answer. So I'm wondering is it even possible?Thank you very much for your support. Best regards, Markus
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