Speedy SMILES Cyclise End Atoms

This node cyclises a SMILES string by connecting the first and last atom with a new single bond by inserting a ring closure

NB No sense-checking is performed, so if the two end atoms are already connected, an addition connection will be added, which will result in many parsers failing to parse.

NB (2) If the 'Remove First Atom' or 'Remove Last Atom' options are selected, then any bond closures associated with them will also be removed, resulting potentially in 'dangling' bonds. In this case, the node should be followed immediately by a ' Speedy SMILES Remove Broken Bonds Filter ' node.

NB (3) An invalid SMILES may be produced when the 'Remove First Atom' option is selected by removing an atom which is followed by a branch, e.g. 'C(CC)OC' would become '(CC)OC' - in which case a missing cell will be returned

NB (4) The mode will use the first unused ring closure index. Formally, SMILES ring closure indices are not supposed to exceed 99, although the OpenSMILES definition proposes this as an extension. However, in the unlikely even that all 99 indices have been used in a SMILES String, then a ring closure index >99 will be used

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


Select SMILES column
The SMILES column, containing molecules
Remove input columns
If checked, then the input column is removed
Remove First Atom
The first atom in the SMILES string should be removed prior to cyclisation
Remove Last Atom
The last atom in the SMILES string should be removed prior to cyclisation

Input Ports

Input Table containing a SMILES Column

Output Ports

Cyclised SMILES Strings

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