Reactor - Graphical User Interface (GUI)

Version 5.9.4

Contents

• About Reactor GUI
• Usage
  • Add reaction library
  • Specify reactants
  • Set runtime option
  • Result
• Reaction Editor
• Links

Application (GUI)

Reactor GUI is an easy-to-use, high-end graphical user interface for the Reactor tool of ChemAxon. This GUI allows you to reach all the functions of Reactor without the need of using the command-line with parameters. Reactor provides a handy way to process virtual reactions that rapidly generates compound libraries. Reactions containing rules defined in the Chemical Terms language can provide synthetically feasible products.

Usage

Start Reactor by double-clicking the appropriate icon . (The installation of JChem creates shortcuts to your Desktop or to the Start Menu on Win32, Win64, Unix or Mac / Java 2.)

Step by step:

Add reaction library

First, select a reaction definition from a reaction file. Input reaction file can be added by browsing it from the file system. The format of input files can be MRV, MOL, SDF, SMIRKS, CML, InChI and many others (all features of reaction SMARTS are available). Reactor users can enjoy a library of important synthetic organic reactions predesigned by experts (download full library).

2. Specify reactants

When a reaction is selected, specify the corresponding reactants. You can load reactants from files, import examples, or add your own compounds. Clicking on the button or double clicking on an empty cell will open MarvinSketch in the same window where you can start drawing reactants.

Browsing reactant file

Drawing reactant

3. Set runtime options for reaction processing.

Reactor options

You can set reactor options on the options panel:

• Output file: The output file will contain the generated results (required).The format of output file can be MRV, MOL, SDF, SMILES, CML, InChI and many others.
• Reactant combination:
  • Sequential: combines reactants continuously (first-first, second-second,...) or;
  • Combinatorial: combines all reactants. In combinatorial mode, the input molecules are filtered by matching the reactant in the reaction scheme thus product generation is faster.
• Output type:
  • Product: generates product molecules;
  • Reaction: generates the specific reactions;
  • Fused reaction: All products are included in one reaction if a reaction yields several products (e.g. nitration of toluene). Products appearing in all variations are depicted only once (e.g. H₂O).
• Mapping style (in case of Reaction output type): The output reactions will be mapped.
  • None
  • Changing
  • Complete
  • Matching
• Manual product selection: Offers to select the main product manually if the generation of more products is possibe.
• Ignore errors: The process will skip the erroneous reaction if checked.

Advanced options

• Ratio: Defines the excess of the reactants in case of more than one reagents. This ratio is considered as the number of cycles of the reaction. Zero (0) means an infinite number of cycles. This consideration is also feasible when only one reagent can be set in a reaction. For example, a reaction on a primary amine group will be repeated until all hydrogens are substituted if the ratio coefficient is 0 and will be stopped at a secondary amine if the coefficient is 1.
• Product standardization: You can beautify the resulting compounds with post-standardization. Load a standardizer configuration file, or set configuration locally
• Generate unsuccessful reactions: If a reaction doesn't yield product, the reactants are shown but the output will be an empty structure.
• Unambiguous only: Does not process reactions providing isomers.
• Ignore rules: The set rules of a reaction is ignored (especially for testing).
• Included products: Unchecked products will not be generated (for example to discard eliminated HCl).

Synthesis code options

• Generate synthesis code of a compound that describes the total synthesis in a short text line using the identifiers of the reaction and the reactants. The synthesis code will be added to the output file.
  Example:
  <Field name in scheme>(<Field name in reactant 1>, <Field name in reactant 2>):<Product list index>/<Product index>.

  For example: Friedel-Crafts acylation(AromaticID038, AcidHalideID038):1/1

• Field name in schema: The drop-down menu contains the property fields of the reaction.
• Field name in reactant 1: The drop-down menu contains the property fields of reactant 1.
• Field name in reactant 2: The drop-down menu contains the property fields of reactant 2.

  The selected definitions will specify the relevant parts of the synthesis code.

• Field name in output: The synthesis code will be written to this field of the output file.

Property Copy

This option offers you to copy selected property fields from the reactant(s) to the product or reaction output file.

• Copy from:
  • Click on the field, and select the reactant having the property you would like to copy, or
  • Select Pattern if you want to define individually formatted property field.
• Property name:
  • Click on the field, and select the property you would like to copy to the output file(s), or
  • If you selected Pattern previously, you cannot make selection here.
• Copy as:
  • You can copy the selected property in a different name to the output file(s). Click on the field and rename it.
  • If you selected Pattern previously, define your individual property field according to the general pattern: "<propertyName>=[<text>*#{<moleculeID>.<propertyID>}]*<text>*"
    Example: My Property=The product of #{r1.smiles} and #{r2.name} is:

  Screenshot of the output file with the user defined reactant property field

  

4. Run the reaction and generate products in batch mode.

The Summary window of Reactor outlines the previously set options. You can run Reactor by clicking the Finish button, you can hit Back to make any modifications, or you can exit Reactor.

Reactor Summary window

When Reactor has finished the enumeration process, the result of running is published in text format. Reactor can present a tabular view of the results if you hit the Show results button.

Results

Grid view of the results

 

Reaction Editor

You can set different parameters of your reaction in the reaction editor. For example reactivity, selectivity, exclude rules, etc.

Reaction editor - reaction scheme

Reaction editor - reaction rules

Reaction editor - reaction examples

Reaction editor - reaction properties

See this page for detailed list of reaction properties.

 

Links

Reactor Main Page
Reactor command-line help
Reactor FAQ
Chemical Terms
Chemical Terms functions
Developers guide