Chemical Design Candidates Section
Applicability: Synapse (core versions 0315+)

Chemical candidates are generated by graphical and combinatorial chemical designs. The Design Candidates Section displays these candidates both tabularly and graphically.

Tabular Display of Candidate Chemicals

The section's table control displays each candidate's name and its overall distance measure. Candidates can be edited, deleted and viewed in more detail. However, the only way to add a candidate to the section is by performing a design.

Editing/Viewing Chemical Candidates

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

1
Table Control: the dialog's table control displays the current list of chemical 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
Clear Button: pressing the dialog's Clear button deletes the selected candidates from the list.
4
Undo Button: pressing the dialog's Undo button reverses the effect of the previous change.
5
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.
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.
Editing/Viewing a Chemical Candidate

Clicking the left mouse button on the section's table control activates the 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: since a chemical candidate cannot be saved into the current document unless it satisified all design constraints, the dialog's summary control will always display 'All Constraints Valid'.
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.
Candidate Profile Graphs

Synapse displays design and selection candidates' constraint values on profile graphs. These graphs enable the display of multiple axes and are very useful in identifying correlations between contraints.

1
The name of the constraint, e.g., 'f("Boiling Point", 0, 0)', is displayed at the top left of each profile graph.
2
The goal value of each constraint is shown as a blue diamond on each profile graph axis.
3
The minimum limit of each constraint is shown at the left side of each profile graph axis.
4
The maximum limit of each constraint is shown at the right side of each profile graph axis.
5
The value of the constraint evaluated for the current candidate, e.g., 1.3536E+06 in this example. The value will be displayed in green because it is within the constraint's limits.
6
The constraint's goal value, e.g., 1.318E+06 for the constraint shown in this example. The goal value is displayed in blue.
7
The constraint's current value is displayed graphically as a green rectangle.
Table Field Commands Menu

Clicking the right mouse button within the field's table control activates the field's data commands menu.

The menu's commands enable you to edit, copy, cut and clear values from the table control. See Common Menu Commands for documentation on the commands commonly found on command menus.

Example: Editing tabularly displayed design candidates
  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 Combinatorial Designs chapter and navigate to the page displaying the "Example Chemical Design C01".
  3. Scroll to the Design Candidates Section and click the left mouse button on the section's large table control. The application activates the Chemical Candidates dialog. (See documentation on the Chemical Candidates Dialog for details.)
  4. The example design already has several chemical candidates. Click the left mouse button one of the displayed entries and press the dialog's Edit button. The application activates the Chemical Candidate edit dialog.

    The image shows that the displayed candidate satisfies all of the three imposed constraints.

  5. You can arange the molecular structure by moving atoms. You cannot perform editing commands that change atoms or bonds. You can also change the candidate's name and change or add comments.
Graphical Display of Candidate Chemicals

Synapse displays the properties of each design candidate on profile graphs. These graphs enable the display of multiple axes and are very useful in identifying correlations between contraints.

Examining Profile Graphs

Clicking the left mouse button on the section's profile graph control activates the Profile Graph Exam dialog. This dialog provides many powerful tools for examining and comparing the properties of candidates as well as examining the effect of tightening constraint limits.

See the documentation on the Profile Graph Exam Dialog for details.

Graph Field Commands Menu

Clicking the right mouse button within the graph field's control activates the field's data commands menu.

The menu provides you with two commands:

  • Save Graph to File: prompts you for the name of a jpg file into which the graph's image will be saved.
  • Copy Graph: copies the graph's image to the clipboard for pasting into other applications.
Example: Examining graphically displayed design candidates
  1. Open the MKS Chemical Design Examples document.
  2. Change to the Combinatorial Designs chapter and navigate to the page displaying the "Example Chemical Design C01".
  3. Scroll to the Design Candidates Section and click the left mouse button on the section's large graph control. The application activates the Profile Graph Exam dialog. (See documentation on the Profile Graph Examination Dialog for details.)
  4. The example design already has several chemical candidates. Click the left mouse button one of the candidates displayed in the All Candidates list. The corresponding polyline will be redraw in red in the dialog's graph window.
  5. Similarly, click the left mouse button on one of the polylines displayed in the dialog's graph window. The corresponding candidate will be selected in the All Candidates list.

The Profile Graph Examination Dialog has several other capabilities that are useful for gaining insight into design results and potential design reformulations. See documentation on the Profile Graph Examination Dialog for additional details.

Related Documentation
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.