Reaction Templates

For large factorial datasets, reaction templates are a mechanism to quickly enumerate a set of reactions based on a spreadsheet of values.

Step 1: Create a template reaction

Use the ORD Interactive Editor to create a new dataset and fill out a single reaction (feel free to enter dummy values for fields that vary in the dataset). Download the reaction pbtxt by clicking the “download” button on the reaction editor page.

Here’s an example reaction.

Step 2: Mark the variable fields in the template

Open a text editor such as Notepad (Windows) or TextEdit (Mac) and replace the template fields with variable placeholders. Each variable name should match a column in the data spreadsheet and start and end with $. For instance:

...
products {
  identifiers {
    type: SMILES
    value: "C"  <-- Change "C" to "$product_smiles$" (with quotes).
  }
  is_desired_product: true
  measurements {
    analysis_key: "19f NMR of crude"
    type: YIELD
    uses_internal_standard: true
    percentage {
      value: 50.0  <-- Change 50.0 to $product_yield$ (without quotes).
      precision: 4.8
    }
  }
...

Here’s the templated version of the earlier example.

Step 3: Prepare the accompanying spreadsheet

The spreadsheet can be a CSV or Excel file. There should be a column for each of the variables defined in the previous step (the $ markers are not required). Here’s an example spreadsheet.

Some datasets may not include all reaction components in every example. In these cases, the corresponding cell(s) in the spreadsheet should be left empty (see templating.py for details):

If after templating, any identifier does not have a defined value, remove the identifier.
If a compound doesn’t have any identifiers, remove that compound.
If a compound amount is undefined/NaN, remove that compound.
If an input has no components, remove that input.

Step 4: Enumerate the dataset

Use the ORD Interactive Editor by selecting the “Enumerate” tab on the main page and following the instructions to upload the template and spreadsheet.