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Chem_​RDF_​fixer_​converter

Clean and convert broken RDF files (e.g. from Reaxys or SciFinder )

Clean potentially broken .rdf files (usually "empty" reactions) stemming e.g. from a Reaxys or Scifinder export.
Also prevents error from Erlwood Chem File Reader (note: this file reader is only available up to V4.2.x).
Therefore, a csv files of the rdf contents is also created.

Update Version 20221222. Spresi output support. Some code cleaning.
N.b.: Spresi contains mol based structures in fields other than the reaction as well, these are not converted into the csv.

Works in all Knime V4.x, not tested in 3.x

Uses a Python node, i.e. Python installation required.
Python requires Rdkit in your Python installation.

Output contains columsn with filenames of newly created fixed RDF and resulting CSV files.
Number of columns may vary, this is due to nature of the RDF data.

Even if you don't have or use Erlwood, the resulting CSV files may be parsed & used elsewhere & independently.

Update: Now includes a minimal mol sanitization else errors prevent the csv creation and crashes all, even though the rdf itself does get fixed.










Clean & convert potentially broken chemical .rdf files.e.g. from Reaxys, Scifinder, ICSynth exports Also prevents error from Erlwood Chem File Reader* (*ChemFileReader only available up to Knime 4.2.x) RI.SESweden Load and covert files. Output table contains new filenamesRequires Python >= 3.6 install Requirement: Python RDKIT-install Continue workflow hereor use files in anotherworkflow depending onneeds Input: RDF files (path to) Output: On disc: converted RDF files and resulting csv files. N.B.: CSV may contain differing number of columns! In Knime: two colums containing resulting new file names N.B.:resulting csvfiles areindependent ofKnime Versionsor Erlwoodinstall! top level directorywith.RDF files(subdirs allowed)(optional)keep newfile names onlyCall the built-inrdffixer module Note: the Knime Versiondoesn't filter previouslyanalysed _fixedfiles compared to thepure Python versionhence the duplicate checkerbefore this nodetop: only ".rdf" filesbottom: filters out "_fixed"shows up as empty (red cross)actually not necessary,the filter inside should be enoughList Files(deprecated) Column Filter Python Script (1⇒1)(deprecated) duplicate"fixed" checker Clean & convert potentially broken chemical .rdf files.e.g. from Reaxys, Scifinder, ICSynth exports Also prevents error from Erlwood Chem File Reader* (*ChemFileReader only available up to Knime 4.2.x) RI.SESweden Load and covert files. Output table contains new filenamesRequires Python >= 3.6 install Requirement: Python RDKIT-install Continue workflow hereor use files in anotherworkflow depending onneeds Input: RDF files (path to) Output: On disc: converted RDF files and resulting csv files. N.B.: CSV may contain differing number of columns! In Knime: two colums containing resulting new file names N.B.:resulting csvfiles areindependent ofKnime Versionsor Erlwoodinstall! top level directorywith.RDF files(subdirs allowed)(optional)keep newfile names onlyCall the built-inrdffixer module Note: the Knime Versiondoesn't filter previouslyanalysed _fixedfiles compared to thepure Python versionhence the duplicate checkerbefore this nodetop: only ".rdf" filesbottom: filters out "_fixed"shows up as empty (red cross)actually not necessary,the filter inside should be enoughList Files(deprecated) Column Filter Python Script (1⇒1)(deprecated) duplicate"fixed" checker

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: ferna
Created at: 2020-11-13
On NodePit since: 2021-04-27
Last update: 2024-11-21
Created with KNIME version: v4.3.2
Tags: rdfreaction data filechemical reaction filescifinderreaxysicsynthspresi

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