3D-e-Chem KNIME KripoDB nodes version 2.3.0.v201707211425 by Netherlands eScience Center
KRIPO stands for Key Representation of Interaction in POckets .
Find Kripo fragment information by their identifier.
Information includes the fragment molecule and it's associated protein identifiers.
This node requires the kripodb Python package.
If the kripodb Python package was not installed then go to https://github.com/3D-e-Chem/kripodb#install and follow the installation instructions. To test if the package is installed run kripodb --version on the command line, it should print a version number if installed.
If the kripodb 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 kripodb package installed. KNIME can use Python version 2 or 3, the node should have the Python version selected which has the Python package installed.
When combining this node with other Kripo nodes make sure the files are from the same dataset.
For example getting a KeyError: '<fragment id>' not found error most likely means the '/data/kripo/pdb/fragments.sqlite' file is out of sync and must be re-downloaded from here
To use this node in KNIME, install 3D-e-Chem KNIME KripoDB nodes from the following update site: