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Pharmacophore (local files)

This Node Is Deprecated — This node is kept for backwards-compatibility, but the usage in new workflows is no longer recommended. The documentation below might contain more information.

KRIPO stands for Key Representation of Interaction in POckets .

Retrieve Kripo pharmacophores from local Kripo pharmacophores database file.

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

Kripo Fragment Identifiers: The column containing the Kripo identifiers
Pharmacophores database (Selected File): Location of Kripo pharmacophores database file (*.h5)

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 pharmacophore.

Popular Predecessors

Popular Successors

Pharmacophore from molecule100 %

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Installation

To use this node in KNIME, install the extension 3D-e-Chem KNIME nodes from the below update site following our NodePit Product and Node Installation Guide:

v4.2

A zipped version of the software site can be downloaded here.

Plugin provider: Netherlands eScience Center

Plugin version: 3.0.0.v202102121204

On NodePit since: 2020-07-13

Last update: 2024-12-12

Tags: Deprecated

KNIME versions: From v3.6 to v4.3

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