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