R-group Decomposition
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R-group decomposition is a special kind of substructure search that aims at finding a central structure (scaffold) and identify its ligands at certain attachment positions. The query molecule consists of the scaffold and ligand attachment points represented by R-groups. These R-groups are simple R-group atoms without R-group definitions in most cases.
| 1. | Click on the R-Group Decomposition ribbon button (in case of Office 2007 and 2010) or select the R-Group Decomposition JChem menu item (in case of Office 2003) to open the R-Group Decomposition form. |
| 2. | The R-group decomposition wizard appears. |
| 3. | Specify the query structure by: |
| o | Clicking on the Browse button to open a file. It is indicated if the format of the selected file cannot be recognized by the system (red exclamation mark with tooltip). |
| o | Dragging the file containing the query structure over the picture box. |
| o | Entering a file name with path. It is indicated if the specified file does not exists (red exclamation mark with tooltip). |
| o | Double-clicking on the picture box to open the structure editor and drawing the structure for the query. |
| o | Paste a structure from the clipboard by using the Paste right-click menu item over the picture box. |
| o | The system remembers the previously specified query structure within a session. The previously specified query structure is displayed on the R-Group Decomposition form automatically at the following opening so it can be reused with or without modifications for a second, third, etc. R-group decomposition process for different target structures. |
| 4. | Specify the target structures: |
| o | Select a file by clicking on the button. It is indicated if the format of the selected file cannot be recognized by the system (red exclamation mark with tooltip). |
| o | Enter a file name with path. It is indicated if the specified file does not exists (red exclamation mark with tooltip). |
| o | Select a worksheet which contains the target structures. |
| o | Select a structure column. The first structure column is selected by default. It is indicated if there are no structures on the selected worksheet or the structure column header is empty (red exclamation mark with tooltip). |
| 5. | Specify the destination where to put the results: |
| o | New columns right from the target structures: it is the default selected option if there are target structures on the active worksheet. The results will be inserted between column Structure and ID in this case. |
| o | To Different Location: It is possible to specify a workbook and a worksheet for the results. |
| o | Select an existing workbook from the combo box. The active workbook is selected by default. |
| o | Select an existing worksheet from the combo box for the import. The active worksheet is selected by default. |
| o | It is also possible to create a new worksheet for the import and type in the name for the new sheet. It is indicated if the entered sheet name already exists or blank or contains not allowed characters (red exclamation mark with tooltip). |
| o | Data Placement - Append option: It is possible to put the results to a worksheet which is not empty. The results can be appended to the existing structures and data from the specified cell. |
| o | Data Placement - Overwrite option: It is possible to overwrite the existing structures and data on a worksheet by the results. |
| o | Data Placement - Start: It is possible to specify a starting cell for the process. The column and row number can be specified or the active cell can be selected as starting cell. |
| 7. | You may specify additional options on the Options tab. |
Undefined R-atom in query matches
| o | only an undefined R-atom in target. |
| o | a group of one or more connected atoms, including at least one heavy atom. |
| o | a group of one or more connected atoms, which can also be a single H atom. |
| o | a group of one or more connected atoms, which can also be a single H atom or the empty set. |
Attachment symbol
| o | None: decomposition without any attachment symbol. |
| o | Attachment point: decomposition with attachment symbol - a small mark besides the attachment atom. |
| o | Any-atom: decomposition with attachment symbol - an any-atom is attached to the attachment atom representing the connection to the scaffold. |
| o | Atom map representing the corresponding R-group index. |
| o | An atom label representing the corresponding R-group index. |
Output Style
| o | Include Header: display query structure on the result sheet. |
| o | Include Target: display the target structures on the result sheet. |
| o | Include Scaffold: display the scaffold structure on the result sheet. |
| 7. | Clicking the Run button starts the decomposition process. |
| 8. | The progress and other information is displayed on the Progress tab. |
| 9. | The process may be stopped by clicking on the Stop button. |
| 10. | When finished, the Stop button is replaced by the Close button. |
| 11. | Clicking Close button closes the R-group decomposition wizard. The results of the R-group decomposition process are displayed on the selected worksheet. |
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