A combinatorial chemical design uses entered groups, limits, and constraints to design molecular structures possessing a set of desired physical properties. The Combinatorial Chemical Design dialog collects all these inputs from the current chemical design and then generates and tests candidate chemical structures.

The dialog enables you to start and view the progress of a combinatorial chemical design. The dialog diplays constraints, candidate properties, designed candidates, and each candidate's molecular structure.

1	Constraint Bar Graphs: the results of applying each constraint to the generated candidates are reported in a bar graph. Results are reported sequentially. Thus, the first bar graph shows the results of applying the first constraint to generated candiates. The second bar graph shows the results of applying the second constraint to those candidates that satisfied the first constraint. See below for additional details.
2	Bar Graphs Scale Control: moving the scale control to the left or right either decreases or increases the scale of the bar graphs. It is often useful to increase the scale to examine regions of the graph in which only a few values occur.
3	Constraint Profile Graphs: each valid candidate's constraint values are plotted on a set of profile graphs. Note that only the constraint values of completely valid candidates are graphed. See below for additional details.
4	Prefix Control: the value entered into this control will be used to form a name for each design candidate.
5	Start Index Control: the value entered into this control will be used to append a numerical suffix to the name formed for each design candidate.
6	Comment Control: the entered comment will be assigned to each design constraint. Often the comment documents the time and name of the design.
7	Date, Phrase, Set Buttons: these buttons provide standard operations to add to your comment. Pressing the Date button inserts the current date and time into the comment control. Pressing the Phrase button inserts the stored 'common phrase' into the comment control. Pressing the Set button enables you to change the 'common phrase'. (See documentation on the Set Phrase dialog for details.
8	Start Button: pressing this button begins the design process. Candidates are generated, their properties estimated, and these estimates used to evaluate each design constraint.
9	Background Button: pressing this button causes the design process to run in the background. This enables you to continue using Synapse for other tasks. Note that a combinatorial design can consume a great amount of computer processing power. Running several designs in the background could significantly slow down your computer.
10	Stop Button: pressing this button stops the design process. At times, you may have to wait a few seconds for Synapse to finish a calculation before it responds to the Stop command.
11	Detail Button: activates the Chemical Candidate Detail Dialog which shows the candidate's constraint values, structure, name, and comments.
12	Valid Candidates List Control: displays all the valid candidates of the current design.
13	Auto Display Control: if this control is checked then the dialog will automatically highlight the last candidated generated and display its molecular structure in the Candidate Structure control. Note that selecting a candidate with the mouse will automatically uncheck this control.
14	Progress Bar Control: displays a graphical measure of progress. Note that the evaluation of candidates is not equal. Some candidates take more time to evaluate than others. Thus, although the progress bar provides information on how many more candidates still need to be evaluated, it is not a good measure of the amount of time that will take.
15	Progress Controls: displays values for the total number of candiates evaluated, the total number of candidates found to be valid, and the percentage of candidates found to be valid.
16	Candidate Structure Controls: displays the molecular structure of candidate currently selected in the Valid Candidates list. See below for additional documentation.

1	Constraint Name: the constraint's name is displayed in the graph's upper left corner. The name is either a function name or a 'functional form' depending upon how the constraint was entered.
2	Valid Percentage: the percentage of candidates that satisfied this constraint is displayed at the graph's center top as a percentage.
3	Center Green Bar Region: the graph displays the constraint's goal value at the center of its axis. The three central green bars record candidates whose values are within the minimum and maximum constraint limits.
4	Left Red Bar Region: the graph defines the left red bar region by subtracting the width of the valid constraint region from the minimum constraint value. In equation form this region includes values: from {MAX - (MAX - MIN)} to MIN
5	Right Red Bar Region: the graph defines the right red bar region by adding the width of the valid constraint region to the maximum constraint value. In equation form this region includes values: from MAX to {MAX + (MAX - MIN)}
6	Lower Red Bar: the graph allocates any value less than the lower limit of the left red bar region minimum to the lower red bar.
7	Upper Red Bar: the graph allocates any value greater than the uppper limit of the right red bar region maximum to the upper red bar.

1	Constraint Name: the constraint's name is displayed on the upper left of each profile axis. The name is either a function name or a 'functional form' depending upon how the constraint was entered.
2	Blue Diamond: the blue diamond corresponds to the constraint's goal value.
3	Minimum Value: the left number corresponds to the constraint's minimum limit.
4	Maximum Value: the left number corresponds to the constraint's maximum limit.
5	Candidate Curve: lines connecte each candidate's constraint values are drawn through each of the graph's axes.

• Copy Structure to Text: this menu contains two submenus:
  • SMILES Notation: converts the entered structure into a SMILES string and then copies this string to the clipboard
  • Mol File Format: converts the entered structure into the contents of a mol file and then copies this text to the clipboard.
• Write Text to File: converts the entered structure into the contents of a mol file and then writes these contents into a text file.
• Copy Structure: copies the candidate's structure to the clipboard for pasting into other structure controls or into other applications.
• Form Formula: generates the chemical's formula and displays it in the Formula from Structure Dialog.

Topic	Description
Getting Started using Synapse	provides a quick tour of Synapse's capabilities including examples of chemical product design.
Getting Started using Cranium	provides a quick tour of Cranium's capabilities including a discussion of structure editing.
Estimating Chemical Properties	a short video demonstrating how to estimate the physical properties of chemicals using either Synapse or Cranium.
Estimating Mixture Properties	a short video demonstrating how to estimate the physical properties of mixtures using either Synapse or Cranium.