Specification of Different Options
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You may specify additional options on the Options tab. Specific options are displayed in a short title, but by moving the mouse over the selected one, its detailed description appears in a yellow tooltip (a detailed description of these options can be found here also):
- Options related to Query structure
Here you can select the types of atoms an R-group can be connected to:
- 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.
- Options related to 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 (e.g. two R1 atoms), these nodes represent identical ligand structures by default. If this option is checked in, 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.
- Attachment Symbol
- None: no attachment symbol will be displayed in the output.
- Attachment mark: Special marker is used to define attachment points in R-group nodes.
- Any-atom symbol: Any atom symbol (A) is used to define attachment points in R-group nodes, this is the default option. In the results numbers also displayed representing 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 map label: Attachment symbol is an atom label representing the corresponding R-group ID as: R1, R2, R3,...
- Display in Output
- Targets: In the column before the results of the R-group decomposition process target structures, which matched the query, will also be displayed.
- 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, Run button becomes active.
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