Add RDFile support

[tkzv]

Is your feature request related to a problem? Please describe.
RDFile format (RDF) is not supported.

Describe the solution you'd like
I occasionally need a batch converter from SDF and RDF to SMILES to quickly view structures in console. OpenBabel works fine for SDF.

RDF belongs to the same family of formats as SDF and RXN, and seems to be their combination. I believe, its implementation can reuse what already is available for SDF and RXN.

Describe alternatives you've considered
As far as I know, there are no free software to read and write RDFs. I use ACD/Labs Specrus DB client to convert them to SDFs.

Additional context
Wikipedia has following links to format specifications:
https://web.archive.org/web/20210219065450/https://discover.3ds.com/sites/default/files/2020-08/biovia_ctfileformats_2020.pdf
https://discover.3ds.com/sites/default/files/2020-08/biovia_ctfileformats_2020.pdf

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[nbehrnd]

@tkzv

As far as I know, there are no free software to read and write RDFs.

I presume MDL reaction files and MDL RD files are syntactically the same, because then DataWarrior (seminal publication here) can both read and write them, e.g., to build combinatorial libraries. That is, e.g. you define a Diels-Alder reaction with a RDF file, and the program then permutates dienes and dienophiles to yield the corresponding products, all organized in a (chemistry aware) spreadsheet / array of data. See for instance the documentation here.

The program requires Java for which the installer provide a suitable engine, then runs in either in Linux, MacOS, or Windows. The source code is in the public on GitHub, for instance GUI and auxiliary libraries. See for instance Isabelle Giraud's tutorial.

example.zip

[tkzv]

I presume MDL reaction files and MDL RD files are syntactically the same

Different enough for RXN filter of OpenBabel to skip records without reactions.

DataWarrior (seminal publication here) can both read and write them

Thanks, but judging from the overview, it is a visual interactive program rather than a tool for bulk batch processing.