Speedy SMILES Convert to Scaffold

This node converts SMILES strings to a scaffold representation. By default, all atoms are represented as 'C' (i.e. carbon), and the output is a SMILES string. However, when 'Any Atom' ('*' in SMILES) is used, and the 'Keep Aromatic atoms aromatic' option is selected, then a SMARTS cell is returned, using the SMARTS 'A' and 'a' atoms, as these are not valid SMILES. See the individual options below for details.

NB, no canonicalisation of the output is attempted , and so if grouping molecules by identical scaffold is required, then the output should subsequently be passed into a toolkit for canonicalisation

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

Options

Select SMILES column: The SMILES column, containing molecules
Remove input columns: If checked, then the input column is removed
Use 'Any Atom' (* or A/a) symbols: See above for details
Keep Explicit H's: Any [H] atoms, or 'D' and 'T' pseudoatoms for [2H] and [3H] are preserved. NB no other isotopic, atom class or other atom properties are maintained on these atoms, and H's specified as e.g [C3H] will be discarded. If this option is not set, then they will be treated as any other atom, and so will appear as 'C' or '*' in the output.
Keep Bond Orders: If this option is checked, any bond symbols present in the input will be removed in the output (including explicit single bonds between aromatic atoms not in rings)
Keep Aromatic atoms aromatic: An atom represented as aromatic in the SMILES (specifically, a lower-case non-bracketed organic subset atom, or a bracketed atom starting with a lower case letter - i.e. not just 'as' and 'se' as bracketed 2-character elements) will be represented as an aromatic 'c' or 'a', otherwise it will be represented as 'C' or 'A'. See also above.
Keep Chirality: If this option is selected, then and '@' chirality settings on atoms are preserved (including '@@', '@@@' - the Daylight specification is ambiguous as to whether this should be allowed for e.g. @OH3 - and the @TH1/@OH1 etc forms)

Input Ports

: Input Table containing a SMILES Column

Output Ports

: SMILES or SMARTS scaffold representation

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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.v202405281205

On NodePit since: 2024-07-11

Last update: 2024-11-15

Tags: Streamable

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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