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RDKit Open 3D Alignment

RDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

Aligns the 3D model of two structures based on their shape and three-dimensional conformation. The structure taken from table 1 will be aligned to a reference structure taken from table 2. If reference table 2 contains only a single row all query molecules of table 1 will be aligned to this single structure. If reference table 2 contains more than one row, the alignment will be performed row by row until one of the tables has no more rows to process. If the passed in molecules have no conformation, it will be calculated.

Options

Query RDKit Mol column (table 1)
The input column of table 1 with RDKit Query Molecules to be aligned.
Reference RDKit Mol column (table 2)
The input column of table 2 with RDKit Reference Molecules to base the alignment on. If the table contains only a single row all query molecules of table 1 will be aligned based on this. If the table contains more than one row, the alignment will be performed row by row until one of the tables has no more rows to process.
New column name for aligned molecule
The name of the new column, which will contain the aligned molecule.
Remove source column
Set to true to remove the specified source column of table 1 from the result table.
New molecule column name
The name of the new column, which will contain the aligned molecule.
New column name for Row IDs of reference used molecule
The name of the new column, which will contain the row id of the used reference molecule of table 2.
New column name for RMSD information
The name of the new column, which will contain the root-mean-square deviation (RMSD) for the aligned molecule.
New column name for score information
The name of the new column, which will contain the score for the aligned molecule.

Advanced

Allow reflection
Set to true to allow reflection of structure parts during the alignment process.
Maximal number of iterations
The maximal number of iterations used in the alignment process.
Accuracy
Determines how accurate the alignment process shall work (0 - most accurate, 3 - least accurate).

Input Ports

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The table with the molecules to be aligned.
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The table with the reference molecules to base the alignment on.

Output Ports

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Aligned molecules

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:

KNIME 4.2

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

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