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Fragment information (local files)

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.

Resolving "Library kripodb.canned is missing" error

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.

Options

Identifiers
The column containing the Kripo identifiers
Fragments database (Selected File)
Location of Kripo fragments database, can be the base url of kripodb webservice or a local SQLite file.

Available datasets:

  • Protein Data Bank, use web service at http://3d-e-chem.vu-compmedchem.nl/kripodb or download from here
  • Tiny example dataset, download from here , in 3D-e-Chem VM available at '/data/kripo/tiny/fragments.sqlite'
  • GPCR, All fragments based on GPCR proteins compared with all proteins in PDB, download from here , in 3D-e-Chem VM available at '/data/kripo/gpcr/kripo.gpcrandhits.sqlite'

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

Type of identifier
Can be fragment or PDB code.

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

Table with Kripo fragment identifiers.

Output Ports

Table with Kripo fragment information.

Best Friends (Incoming)

Best Friends (Outgoing)

Update Site

To use this node in KNIME, install 3D-e-Chem KNIME KripoDB nodes from the following update site:

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