When you perform a graphical chemical design, you draw molecular structures while Synapse evaluates your entered physical property constraints. The results of this constraint evaluation are displayed graphically for you interpretation. If all constraints are satified, the entered molecular structure represents a new candidate chemical. If all constraints are not satified, the entered molecular structure is not a valid candidate.

However, even if some contraints are not satisified, you may still wish to retain the entered structure for further investigation. For example, you might want to contiue to modify the structure at a later time, you might want to create a modifed design with different design elements and bond types, or you might want to modify the design constraints to make the current structure a satisfactory candidate.

The Intermediate Candidates Section displays those candidates that do not satisfy all constraints. The section contains one large table field displaying the candidate's name, the number of invalid constraints, the overall distance and the individual distances.

1	The name of the candidate.
2	The number of constraints the candidate does not satisfy. (Note that viable canidates, i.e., candidates that satisfy all constraints, can also be saved as intermediate candidates.)
3	The overall distance between constraint goal values and this candidate's values.
4	The distance between constraint 01's goal value and this candidate's constraint 01 value.
5	The distance between constraint 02's goal value and this candidate's constraint 02 value.

The distances displayed for candidates are calculated using a simple Euclidean distance formula:

distance = (Σ(goal_i-value_i)²)^½

in which goal_i is the goal value of constraint i and value_i is the value of constraint i evaluated for the current candidate. When the distance is reported for a single constraint, the above equation is equivalent to the absolute value of the distance between the constraint's goal value and the candidate's constraint value.

At present, overall distance calculations are unweighted and unscaled. Thus, the distance calculated for a critical constraint whose values vary exponentially is weighted the same as the distance of a marginal constraint that varies linearly.

To take full advantage of distance calculations, you should formulate your constraints to all vary linearly and be of similar orders of magnitude. Often, this can be done by thoughtful consideration of units of measure. For example, instead of comparing a vapor pressure constraint's distance measured in Pa with a surface tension constraint's distance measured in N/m, you might consider changing the units used in the constraints to kPa and dyn/cm. Thus, instead of comparing a distance of 20,000 Pa with a distance of 0.03 N/m, you would be comparing a distance of 20 kPa with a distance of 30 dyn/cm.

Clicking the left mouse button on the section's table control activates the Intermediate chemical Candidates dialog. This dialog enables you to edit, delete, sort, and bookmark chemical candidates.

1	Table Control: the dialog's table control displays the current list of intermediate candidates. Clicking the left mouse button on a table row selects that table row. Clicking and holding the left mouse button down and then dragging the mouse will select several table rows. Double-clicking the left mouse button on a row selects the row and edits the contents of that row.
2	Edit Button: pressing the dialog's Edit button activates the Chemical Candidate dialog. See below for documentation.
3	Sort Button: the dialog's Sort button will be enabled if two or more rows are selected. Pressing the Sort button will activate the Sort Attribute dialog. This dialog enables you to sort chemical candidates in ascending or descending order by name, overall distance, constraint distance, or validity.
4	Clear Button: pressing the dialog's Clear button deletes the selected candidates from the list.
5	Undo Button: pressing the dialog's Undo button reverses the effect of the previous change.
6	Select All: selects all candidates displayed in the table control.
7	Copy Button: copies all selected candidates attributes to the clipboard for pasting into other applications.
8	Bookmark Button: activates the Select Bookmark dialog which enables you to add the selected candidates to a bookmark set. (See Using Bookmarks for documentation.)
9	Save Button: pressing the Save button stores all candidates into the current document.

Clicking the left mouse button on the section's table control activates the Intermediate Chemical Candidates dialog. Selecting a chemical candidate from the dialog's table control and pressing the Edit button activates the Chemical Candidate dialog.

1	Summary Control: the dialog's summary control displays either 'All Constraints Valid' or 'Invalid Constraints' depending upon the results of applying constraints.
2	Constraints Table Control: displays the results of each constraint evaluation on a profile graph. See below for details.
3	Structure Control: displays the candidate's molecular structure. You can move atoms to reformat the structure but atoms and bonds cannot be added or removed.
4	Name Control: displays and enables editing of the candidate's name. This control can accept any valid text value.
5	Comments Edit Control: displays and enables editing of the comments associated with this candidate.
6	Date, Phrase, and Set Buttons: the Date button inserts the current date and time into the Comments Control. The Phrase button inserts the current user's 'Personal Phrase' into the Comments Control. The Set Button activates the Set Phrase Dialog which enables you to change your personal phrase.
7	Next and Prev Buttons: these buttons enable you to easily view or edit the candidate before or after the current candidate in the list of candidates. Note that once the current candidate's name or comments have been changed, the Next and Prev buttons become disabled.

The candidates displayed in the Intermediate Candidates Section can be viewed, sorted and deleted. Only a candidate's name, comments and structure's appearance can be edited. Candidates can only be added by performing a graphical design.

1. Open the MKS Chemical Design Examples document. Save a "working" copy of the document. (See documentation on Copying Documents for details.)
2. Change to the Graphical Designs chapter and navigate to the page displaying the "RI Matching Fluid Design G01".
3. Scroll to the Intermediate Candidates Section and click the left mouse button on the section's large table control. The application activates the Intermediate Chemical Candidates dialog. (See documentation on the Intermediate Chemical Candidates Dialog for details.)
4. The example design already has several intermediate candidates. Click the left mouse button one of the displayed entries and press the dialog's Edit button. The application activates the Chemical Candidate dialog.

   The image above shows that the displayed candidate satisfies two of the three imposed constraints. The candidate's refractive index was too low to satisfy the first constraint.

5. You can arrange the candidate's molecular structure, i.e., moving atoms is allowed but adding or deleting atoms or bonds is not. You can also change the candidate's name and comments.
6. When you are done editing, press the dialog's OK button.

Constraint graphs are used throughout Synapse to display the results of a constraint evaluation.

1	The name of the constraint, e.g., Refractive Index at 20°C in this example.
2	The value of the constraint evaluated for the current candidate, e.g., 1.4101E+00 in this example. The value will be displayed in green if the value is within the constraint's limits. The value will be displayed in red if the value is outside of the constraint's limits.
3	The constraint's lower limit, e.g., 1.000E-04 for the Vapor Pressure at 20°C constraint shown in this example.
4	The constraint's goal value, e.g., 2.000E-01 for the Vapor Pressure at 20°C constraint shown in this example. The goal value is displayed in blue.
5	The constraint's upper limit, e.g., 4.000E-01 for the Vapor Pressure at 20°C constraint shown in this example.
6	The constraint's current value is displayed graphically as a green rectangle.
7	The constraint's goal value is displayed graphically as a blue diamond.
8	If the constraint's current value is below the lower limit or above the upper limit, a red arrow will be displayed at the appropriate end of the graph. In this example, the candidate's refractive index was 1.4101E+00 which was below the contraint's lower limit. Thus, a red arrow was displayed at the graph's lower limit indicating that the value was further "to the left" of the lower limit.

Topic	Description
Getting Started using Synapse	provides a quick tour of Synapse's capabilities including examples of chemical product design.
Designing Chemical Products	a short video demonstrating how to use Synapse to design candidate chemicals that satisfy a set of physical property and molecular structure constraints.