Setting up a relationship between the reactants and the products

1. Open the Schema Editor: right-click on the schema header and select Edit Schema from the drop-down menu.

2. Create a relationship between the product table and the first reactant table:

   1. Navigate to "Entities" tab within the Schema Editor

   2. Right-click on the products table of the reaction and select New Relationship...

      

   3. Select "New Many-to-One Relationship" from the relationship type drop-down menu

   4. The "From" table must be the output table, containing the results; for this table the Field must be set to "Reactant 1 CdId"

   5. The "To" table must be the one containing molecules for reactant 1; for this table the Field must be set to "CdId"

   6. Click Finish

      

3. Create another relationship between the product table and the second reactant table following the above steps (using the corresponding values of the second reactant table instead of the first one)

   1. 

4. Include the child entities in the data tree:

   1. Navigate to "Data trees" tab within the Schema Editor

   2. Right-click on the products table and select Manage Child Entities...

   3. In the drop-down menu select the Relationship for which you would like to create the new edge. Create edges for both new relations.

   4. Ensure the checkboxes next to both child entities are selected and click Finish
      

      You can skip this part if you had included the entities in the data tree during the creation of the relationship, by clicking Next and selecting the entity checkbox in the Update Data Tree dialog.

5. The resulting data tree in the schema editor should look as shown below

   

Creating a form view

1. In the Project Window right-click on the data tree containing the products and select New View...

2. Set the View type to "Empty Form View" in the dialogue and click Finish

3. Go to Design mode by clicking on the Design button in the upper left corner of the Form View

4. Add three Molecule panes to the form through the corresponding button in the top toolbar, or through the r-click drop-down menu. Resize and reposition them according to your needs

5. Bind the result structure to the results structure and the two reactant structures to the relevant reactant structures by using the "Bind widget to field" menu item in the right-click menu of the widgets

   

6. Rename the two reactant molecule panes to "Reactant 1" and "Reactant 2", respectively. It can be done in the Customize Widget Settings right click menu

   

7. Click on Browse in the top left corner of the view to see the result of the above steps

   

Calculating properties of the products

In this sub-section the calculation of simple and complex properties will be shown. To add a new calculated property to the table containing the results follow the steps below:

1. Go back to grid view of the products table

2. Click the New Chemical Terms Field... button on the top toolbar in Browse mode or add it through the ... button menu

   

3. Select logD from the favourites and adjust the pH argument of the chemical terms function in the editor. Click Finish

4. Add a new Chemical Terms Field and select Lead likeness from the favourites.

5. Try to edit the complex expression predicting Lead likeness

6. Click Finish

7. Add a new Chemical Terms Field

8. Use the following expression in the editor to give a custom score to the structures:

   (mass <= 400) +

   (logP <= 4) +

   (donorCount <= 5) +

   (acceptorCount <= 9) +

   (rotatableBondCount() >= 5) +

   (largestRingSystemSize() < 50)

9. Set the field Name to Score

10. Set the field Type to Integer

    

11. Click Finish

Visualizing properties

Using the copied and the calculated property fields this section will show how this data can be viewed in Instant JChem using the Chart Widgets.

1. Open the Form View of the products

2. Go to Design mode

3. Right-click on the form and select Histogram

   

4. Select MolWeight as the Value to Bin and set the number of bins to 20 in the Histogram Customization dialog

   

5. Click OK; resize and reposition the chart widget. Switch back to Browse mode to see the result.

   

To create a synthesis matrix-like plot (i.e. a scatter plot showing which Reactant 1 molecules react with which Reactant 2 molecules) follow the steps below.

1. Go back to Design mode

2. Using the above steps add a new Scatter Plot

3. Use Index 1 as X field, Index 2 as Y field in the Main tab of Scatter plot Customization window

   

4. Use the Score as Category field in the Data Points tab of Scatter plot Customization window

   

5. Using Score as the Category field will automatically color the scatter plot according to the values in this field: