You can specify additional options on the Options tab. This tab consists of the following parts:
Display in Output
You can specify the type of atom to which an R-group can be connected.
A heavy atom: Undefined R-atom in query matches a group of one or more connected atoms, including at least one heavy atom.
A heavy atom or H: Undefined R-atom in query matches a group of one or more connected atoms, which can also be a single H atom.
A heavy atom or H atom or empty set: Undefined R-atom in query matches a group of one or more connected atoms, which can also be a single H atom or the empty set.
You can specify the general R-group settings.
Allow bridging R-groups: We call bridging R-atom matching when two R-atoms match the same group of target atoms. It can be forbidden or allowed with this option.
R-group equality check: When the query contains R-group nodes with the same R-group IDs, for example, two R1 atoms, these nodes represent identical ligand structures by default. If this option is selected different structures are allowed to match these nodes.
Display all hits for R-groups: In some cases, more than one decomposition results are possible for a specific target. By default, only one decomposition for each target (corresponding to the first search group hit) is presented in the output. If this option is selected, all possible decomposition results are listed.
Align hits as query: the result structures of the R-group decomposition process are aligned the same as the query structure. The option is selected by default.
You can select the type of attachment symbol.
None: No attachment symbol will be displayed in the output.
Attachment mark: A special marker is used to define attachment points in R-group nodes.
Any-atom symbol (A): Any atom symbol (A) is used to define attachment points in R-group nodes, this is the default option. In the results, numbers are also displayed to represent the corresponding R-group index.
R-group index=Atom map number: Attachment symbol is the atom map number representing the corresponding R-group index (works only with mapped structures).
R-group index=Atom label: Attachment symbol is an atom label representing the corresponding R-group IDs as R1, R2, R3, and so on.
Display in Output
You can specify the type of data to be included in the output besides the results of the R-group decomposition process.
Targets: Target structures will be displayed next to the results of the R-group decomposition process (only matching ones).
Non-matching targets: Rows containing non-matching targets will be inserted among the results of the R-group decomposition process (keeping their order in the original sheet).
Scaffolds: Scaffold structures will be displayed next to the results of the R-group decomposition process.
After specifying all options, click the Run button to start the process.