Group Limits Section
Synapse generates candidate chemicals by assembling
design groups into new molecular structures. The Design
Groups Section is used to specify these design groups as
well as the limits on their occrrence in new molecular
For example, the previous image shows that seven groups
can be used to generate new molecular structures. It
also shows that every new molecular structure must have
between 0 and 2 =CH- groups.
Example: Specifying design groups
Open the MKS Chemical Design Examples document. Save
a "working" copy of the document. (See documentation on
Copying Documents for
Change to the Combinatorial Designs chapter and navigate to
the page displaying the "Example Chemical Design C01".
Click the left mouse button on the Design Groups Section's
table control. The application activates the Design Groups
Limits Dialog. (See documentation on the
Groups Limits Dialog for
Click the left mouse button on the row of the
Design Groups Limits Dialog's table control that lists
the -F group. Then
press the dialog's Edit button. The application
activates the Design Group Limits Dialog.
Change the Minimum Limit from 0 to 2 and the Maximum
limit from 6 to 2. These changes
now require every candidate molecular structure
to have exactly two fluorine atoms. Then, press
the dialog's OK button.
The updated limit will be changed in the Design Groups
Limits Dialog. Press the dialog's Save button to
store these values into the current document.
Clicking the right mouse button on the Design Groups
Section's table control displays the commands menu.
The menu's commands enable you to edit, copy, cut and paste
values to and from the edit control. See
Common Menu Commands for
documentation on these commands.
Example: Design candidate chemicals
Ensure the Example Chemical Design C01 design
we just modified in the previous example is the
Select the Design Candidates command from the
chapter's Commands menu.
The application activates the Combinatorial Chemical
Design dialog. Press the dialog's Start button. Synapse
will begin assembling and testing candidate molecular
Once the design is completed, press the dialog's
Save button to store the candidates into the
Eighteen chemical candidates were designed in the
previous combinatorial design. These are shown in the
These eighteen chemical candidates all have exactly two
fluorine atoms as well as other design groups within
the entered limits.