The following script reads in an .sd file and replaces every alcohol oxygen with a Yttrium atom. Then saves a new .sd file with the name provided by \$outFile. This new .sd file can be used as input for the De Novo Library Generation protocol to generate a link library where the 'Atom Types to Consider as Link Sites' would then be defined as 'Y' and the 'Atom types to be Remapped' would be 'O'. In other words, this script enables the user to specify all alcohol oxygens as the link sites.
Note, users may want to consider this script as a template for defining other atom types as the link sites.