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Speedy SMILES Convert to Scaffold

StreamableVernalis Speedy SMILES extension for KNIME Workbench version 1.30.1.v202103301200 by Vernalis (R&D), UK

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

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Input Table containing a SMILES Column

Output Ports

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SMILES or SMARTS scaffold representation

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

KNIME 4.3

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

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Developers

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