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SyGMa Metabolites

Sygma KNIME nodes version 2.0.0.v202102121148 by Netherlands eScience Center

Predict metabolites from parent molecules using Sygma ( https://github.com/3D-e-Chem/sygma ).

Resolving "'sygma' Python package not found" error

This node requires the ' sygma ' Python package.

If the sygma Python package was not installed then go to https://github.com/3D-e-Chem/sygma#installation and follow the installation instructions. To test if the package is installed run sygma --version on the command line, it should print a version number if installed.

If the sygma Python package was already installed then make sure that KNIME is using the same Python executable. In the File menu > Preferences > KNIME > Python make sure the path to the Python executable is the same Python which has the sygma package installed.


Parents molecule column
Column containing molecules which will be metabolized.
Phase 1 cycles
Number of times phase 1 rules should be applied
Phase 2 cycles
Number of times phase 2 rules should be applied

Python options

Use python version
Allows to choose the python version that should be used for executing the kernel. Available installations can be checked under Preferences → KNIME → Python.
Missing values (Int, Long)
By default, Int and Long columns containing missing values are converted to doubles in Python, because doubles are the only numeric type containing a built-in missing value representation (NaN). Converting longs to doubles, however, introduces imprecision. The conversion may be avoided by replacing missing values with so-called sentinel values. To convert missing values to sentinel values before script execution, check the first option, to convert sentinel values back to missing values after script execution, check the second option. To select a sentinel value, click on MIN_VAL (the smallest possible value for the column's data type), MAX_VAL (the largest possible value for the column's data type), or a manually enter an integer in the text field.
Rows per chunk
Large tables are broken into chunks when they are transferred between Python and Java. This option controls how many rows are included in each chunk. The default value is intended for tables containing few columns having numeric types. If larger data types like images or text are transferred, a single chunk may exceed the maximum allowed buffer size. In this case lowering the value of this parameter helps getting reasonably sized chunks.

Input Ports

Parent molecules

Output Ports

Predicted metabolites

Best Friends (Incoming)

Best Friends (Outgoing)


To use this node in KNIME, install Sygma KNIME nodes from the following update site:


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