kamelmansouri/qsar-ready_cmd repository overview

Standardization workflow for QSAR-ready chemical structures pretreatment. Performs required structure standardization tasks (related to salts/solvents, tautomers/mesomers, mixtures, inorganics, metals, aromaticity, 2D/3D...) prior to QSAR modeling or prediction. Starts from structures in SDF or smiles format and produces:

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)

This image is based on kamelmansouri/knime and kamelmansouri/knime-workflow-base

To run the image with the QSAR-ready workflow:

(sudo) docker run -v /my/local/data/dir:/data kamelmansouri/qsar-ready_cmd:2.5.6 file-upload=/data/data.sdf

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

To Show additional workflow information and available variables:

(sudo) docker run kamelmansouri/qsar-ready_cmd --info

(sudo) docker run kamelmansouri/qsar-ready_cmd --vars

For more information visit:

https://github.com/NIEHS/QSAR-ready⁠

https://github.com/kmansouri/QSAR-ready⁠

https://kni.me/w/_iyTwvXi6U3XTFW1⁠

https://www.knime.com/denbicibi-contributions⁠