May 20 2013
Chemical Find&Replace tool allows you to find an arbitrary chemical fragment with one or more
attachment point(s) and replace it with another fragment with the same number of attachment points.
To find a substructure and replace it with something else:
- Select the column in which the molecular structures are displayed. The column
is usually called "mol".
- Right click on the "mol" column header and select Find and Replace. A data entry box as shown below will be displayed.
- Click on the Molecular Editor button at the end of the Find What: data entry box.
- The ICM Molecular Editor will be displayed. Draw the substructure you wish to search for and replaced.
- Draw the pattern and mark attachment points with R1,R2.... R-groups can be added by right clicking at the attachment point and selecting the R-group from the drop down options.
- Close the ICM Molecular Editor and the string will be displayed.
- Repeat with the "Replace With:" data entry box. Make sure the same number of R1,R2... labels are drawn.
- Click the Find Next button and then Replace or Replace All. When a substructure to replace is identified it will be colored red.
NOTE: There are a number of keyboard shortcuts which can be used to draw chemicals. Also please note
that an aromatic bond in the source molecule will not match a double bond in the replacement pattern.
Here is an example: