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Knime QSAR-ready Standardization workflow

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@kmansouri kmansouri released this 03 Feb 21:01
· 3 commits to master since this release
2.5.8
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Standardization workflow for QSAR-ready chemical structures pretreatment.

Latest updates:

  • The workflow is made smart:
    - Processes input files (SDF, Mol, smi, xls, csv) automatically
    - All parameters are defined as input then the nodes are configured automatically
    - Upgraded to KNIME 4.5 paltform
  • The workflow is now using Indigo v2.0 (compatible with KNIME 3.7 and newer).

Availability of the workflow:

  • KNIME Hub: https://kni.me/w/5TRvnGfMJsgTkcZu

  • Docker container from KNIME 4.1 image (with all dependencies): https://hub.docker.com/r/kamelmansouri/qsar-ready
    https://hub.docker.com/r/kamelmansouri/qsar-ready_cmd

  • Full KNIME zip file (4.5) with all dependencies for a new installation (just unzip and use):
    - Windows: knime_4.5.1_QSAR-ready2.5.8.zip
    - Linux: knime_4.5.1_QSAR-ready2.5.8.tar.gz

  • Single workflow file that can be imported directly into an existing KNIME installation
    - Based on KNIME 4.1 (works on 4.1 and above): QSAR-ready_2.5.8_knime_4.1.knwf
    - Based on KNIME 4.5 (works on all newer installations): QSAR-ready_2.5.8_knime_4.5.knwf
    Input:

  • Mol/SDF file with chemical structures in 2D or 3D

  • Smiles structures in .txt, .csv or .xls/xlsx

Output:

  • SDF file with standardized structures in Kekule form (includes provided IDs, original structures, Salts/solvents, Inchi codes, and keys)
  • SDF file with standardized structures in aromatic form (includes provided IDs, original structures, Salts/solvents, Inchi codes, and keys)
  • SDF file with standardized structures in 3D form (includes provided IDs, original structures, Salts/solvents, Inchi codes, and keys)
  • Smiles file (.smi) with standardized structures (Kekule form)
  • CSV file with structures that failed standardization with a specified error flag (parsing and valence errors, inorganics, mixtures...)
  • CSV file with salts/solvent information that can be used in OPERA (in command line) for optimal prediction results (MP and logP models)

The parameters selected by default are suggested for use in OPERA.

All configuration required is available in the input component. The workflow will then adapt and run autonomously.

The workflow can also be executed in batch mode using the command line:
[knime path]\knime -reset -nosplash -nosave -application org.knime.product.KNIME_BATCH_APPLICATION -workflowDir="[knime path]\knime-workspace\QSAR-ready_2.5.8" -workflow.varaiable=cmd_input,"[input path]\inputfile",String

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