Fragments to MMPs

This Node Is Deprecated — This version of the node has been replaced with a new and improved version. The old version is kept for backwards-compatibility, but for all new workflows we suggest to use the version linked below.
Go to Suggested ReplacementFragments to MMPs

This node implements the Hussain and Rea algorithm for finding Matched Molecular Pairs in a dataset. The node takes an input table of fragments generated either by the MMP Molecule Fragment node and generates an output table of matched molecular pairs (MMPs)

The node requires two SMILES input columns, representing the 'key' (unchanging atoms) and 'value', and a string column containing the ID. The node will attempt to auto-guess these column selections based on the default names for the columns output by the fragment node.

Optionally, the user can specify that the table is pre-sorted by keys. If this option is selected, then the user can allow checking of the output for correct sorting, in which case, the node will fail if an earlier key is found again later in the table. This method uses less memory, as the entire input table does not have to be loaded into memory. For anything other than small datasets, the user is recommended to pre-sort the input table by key, and then use this setting.

Any attachment point fingerprint(s) generated during fragmentation are passed through and attached to the appropriate transformations

This node was developed by Vernalis Research. For feedback and more information, please contact knime@vernalis.com

1.J. Hussain and C Rea, " Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large datasets ", J. Chem. Inf. Model. , 2010, 50 , 339-348 (DOI: 10.1021/ci900450m ).

Options

Select the Fragment Key column
Select the column containing the fragment 'keys'
Keys are sorted
Use this option if the keys column is pre-sorted. See above for details
Check keys are sorted
It is strongly recommended to use this option if specifying that keys are pre-sorted, in order to avoid missing MMPs from the dataset if a sorting error has occurred.
Select the ID column
Select the column containing the parent molecule IDs
Select the Fragment Value column
Select the column containing the fragment 'values'

Output Settings

Remove Explicit H's from output
Explicit hydrogens will be removed from the output if selected
Show unchanging portion
A SMILES cell will be included showing the 'key' resulting in the fragmentation pattern
Show number of changing atoms
The number of heavy atoms (not including 'A', the attachment point) will be included for Left and Right fragments
Show ratio of constant / changing heavy atoms
The ratio of constant / changing heavy atoms (not including 'A', the attachment point) will be included for Left and Right fragments
Show reverse-direction transforms
The transformations will be duplicated in the 'reverse' direction, e.g. A-->B and B-->A
Include Reactions SMARTS
In addition to the SMIRKS representation of the transformation, the transform is shown in an rSMARTS representation with atom mappings. Using this option without the 'Track Connectivity' option selected will produce nonsense rSMARTS!

Input Ports

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Fragmented molecule key-value pairs

Output Ports

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Matched pair transformations

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Installation

To use this node in KNIME, install the extension Vernalis KNIME Nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

Plugin provider: Vernalis Research, UK
Plugin version: 1.36.7.v202408051613
On NodePit since: 2024-07-11
Last update: 2024-10-30
Tags: Deprecated
KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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