MoSS

This node searches for frequent molecular fragments in a set of molecules. The algorithm used is Christian Borgelt's MoSS implementation.

Options

Column with molecule structure: Select the column in the input table that contains the molecule strings (Smiles, SLN or SDF).
Column with class labels: Select the column in the input table that contains the class labels (must be a string column). In the list below you can choose which values of the class column form the two groups (active or inactive) used during the search.

Ignore pure carbon fragments: Prevents the search for fragments that only consists of carbon atoms.
Use ring mining: If enabled, ring of the specified sizes are treated as singles entities which makes the search much faster and also avoids finding fragments with partial rings.
Minimum focus support: Sets the minimum number of fragments - a fraction of the number of input molecules in the active class - a fragment must occur in in order to be frequent and thus reported.
Maximum complement support: Sets the maximum number of fragments - a fraction of the number of input molecules in the inactive class - a fragment may occur in in order to be reported.
Minimum fragment size: The minimum size (number of bonds) a fragment must have in order to be reported.
Maximum fragment size: The maximum size (number of bonds) a fragment may have in order to be reported.

Start with core: Provide a Smiles string that is used as a seed for starting the search. All found fragments will contain the core.
Canonical Form pruning: Turns canonical form pruning on or off.
Equivalent fragment pruning: Turns equivalent sibling pruning on or off.
Perfect extension pruning: Turns perfect extension pruning on or off.
Find chains of variable lengths: Enables the search for fragments that are equal except the length of their carbon chains.
Fragment extension mode: Choose between the two possible ways to extend a fragment during the search.
Maximum embeddings used: Sets the upper limit on the number of extension that are stored in memory

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To use this node in KNIME, install the extension KNIME Chemistry Add-Ons from the below update site following our NodePit Product and Node Installation Guide:

v5.4

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

Plugin provider: KNIME AG, Zurich, Switzerland

Plugin version: 5.4.0.v202407231408

On NodePit since: 2024-12-06

Last update: 2024-12-21

KNIME versions: Since v3.6

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