Reaction-Based Enumeration Panel — Define Reactants Step

Define the reactant libraries to be used when enumerating the reaction. Each R group in the set of reactions can be assigned a library.

See Reaction-Based Enumeration Panel for an overview of the panel.

  • Using
  • Features
  • Additional Resources

Using the Define Reactants Step

The primary goal of this step is to decide which parts of the final product you want to enumerate. This is done by selecting a library for each of the reactant groups that you want to enumerate, and selecting the original reactant, or not making a choice, for the groups that you want to hold fixed. For example, you might want to keep the core of a structure fixed and enumerate the attachments to the core. Alternatively, you might want to keep the peripheral groups fixed and vary the core. Both of these can be done by the choice of the reaction scheme and the choice of which groups to vary and which to fix.

Define Reactants Step Features

Reactions table

This table shows diagrams of each reaction in the sequence. You can select a row in the table to set up reactants for the reaction in that row.

Reactants section

Define the reactants for the reaction, by selection of a library and applying filters.

Reactant N option menus

These option menus allow you to select the source for each of the reactants. The choices are:

  • Internally defined library for the reactant (the default).
  • Reactant Library—opens the Reactant Library Dialog BoxManage Reactant Libraries Panel so you can choose from the current set of libraries. This dialog box shows the libraries that are in the installation as well as the ones you have defined.
  • Original Reactant—use the fragment from the original reactant. Selecting this option fixes the fragment, so that it will not be enumerated. This option is only present if you defined the reaction using the PathFinder analysis.
  • File—opens a file browser so you can load a library from an external file.
  • Project Table (Selected Entries)—use the entries that are selected in the Project Table or Entry List as the reactants. This is useful if you want to use the output from one enumeration as input for the next enumeration.

There is no default if you sketched the reaction, and the menu item is labeled - Select -, to indicate that you must make a choice.

Reactant filter option menus

These option menus allow you to apply filters to the structures for each of the reactants. The choices are:

Options section

Set options for the enumeration in this section.

Property Filter button

Filter the output structures based on properties of the reactants and products. Opens the Filter Options Dialog Box.

SMARTS Filter button

Filter the output structures based on matches to SMARTS patterns. Opens the Filter by SMARTS Dialog Box.

Allow multiple products per reaction step option

Allow multiple products to be generated in each reaction step for reactants that have multiple R-group attachment points. The title of each product is appended with a product index and total number of products from the synthesis. For example, a two-step chlorination route starting from propane generates the following products:

CCC(Cl)Cl propane [1/4]
CC(Cl)CCl propane [2/4]
ClCCCCl propane [3/4]
CC(C)(Cl)Cl propane [4/4]

The total number of products from a given set of starting materials is also stored as a Maestro property, num products.

This option is selected by default. If it is deselected, only the first product from each reaction step is kept.

Maximum number of products option and text box

Specify the maximum number of products to generate in the enumeration. The products are generated by random sampling of the combinations of reactants, and continues until the requested number of products is generated, or there are no more reactant combinations, or the number of combinations tried exceeds 100 times the specified maximum number of products. The same seed is used for the random sampling by default, to ensure reproducibility of the enumeration results. This option is selected by default.

If this option is deselected, random sampling is turned off and an exhaustive enumeration is performed. Depending on the library size and the number of sites enumerated, the resulting library sizes could exceed the capacity and lifetime of your computer, so use this setting with caution.

Back button

Click this button to return to the Reaction Setup step.

Enumerate button

Run the enumeration. Opens the Enumerate - Job Settings Dialog Box, in which you can choose the host, set the number of subjobs and number of processors, name the job, and direct the output. When the settings are made, click Run to run the job.

The output file format can be selected, from Maestro and SMILES. Only Maestro format is available if you choose to incorporate the job results into Maestro. SMILES format allows you to run much larger enumerations, as the space taken by the output per structure is a lot smaller than for Maestro format.

You can click Write to write the job files out to the working directory, along with a shell script that has the command for running the job. The files are named using the job name as a base name. This capability is useful for copying the job files to a remote server for execution, or for submitting the jobs to a queue.

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