Reactor
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Overview
Reactor is the virtual reaction engine of Chemaxon’s JChem technology. It supports “smart” reactions (generic reaction equations combined with reaction rules) generating chemically feasible products even in batch mode. The professional version of the tool includes support for multi-step virtual synthesis and filtering of chemically feasible molecules which are not of interest.
Key features:- high performance
- platform independent (Java)
- easy to access (API, command line, cartridge, GUI)
- chemically intelligent
- chemoselectivity (reactive functional groups, activation/deactivation)
- regioselectivity (electronic and steric effects, main product detection)
- stereospecific reactions
- intramolecular reactions
- various atom mapping styles and automapper
- combinatorial reactions
- reverse reaction processing
- generates an entire synthesis tree at once
- wizard-like reaction processing user interface
- reaction editor with integrated rule editor and tester
- synthesis rules for each synthetic step (for on-the-fly filtering of intermediers)
- lots of integratable property predictions (available as options)
- advanced compound dispatching (complex synthesis graphs, trash)
- database, file and memory operation modes
- graphical user interface for browsing the synthesis database
- colored visualization of the original building blocks in the generated library
- compatible (MRV, MOL, SDF, SMILES, RXN, RDF, SMARTS, SMIRKS, INCHI…)
- synthetic reaction library (available as option)
FAQ
What is Reactor?
Reactor is virtual synthesis tool transforming molecules to products according to given reaction schemes. It is part of ChemAxon’s JChem toolkit.
What is Reactor good for?
You can discover the virtual compound space, enumerate combichem libraries, predict metabolites, or create other molecule transformation-based applications with Reactor.
Do I have to do programming for using Reactor?
Not necessarily. Reactor has a simple desktop user interface. Reactor is delivered with full API, you can equip your own applications with virtual synthesis features.
What kind of additional software is needed?
The Reactor functionality is available in various environments: Java, .Net, Web service, SQL function (in case of JChem Cartridge).
Will Reactor run on my system?
Since Reactor is written in pure Java, it can be used on any platforms supported by the Java Runtime Environment version 1.4.2 or later, including most Windows, Mac, Linux and Unix platforms.
Can I run reactions from a Unix shell?
Yes, there is a script and a batch file as well for those who prefer command line tools, just type react.
Which molecular file formats are supported?
Reaction definitions can be written in MRV, RXN, RDF or SMIRKS/SMARTS formats, the molecules in MRV, MOL, SDF, CML, CDX or SMILES.
I am familiar with SMILES and SMARTS, does Reactor support them?
Yes, you can even run a reaction from the command line.
I do not like SMILES and SMARTS, can I use Molfile, SDfiles and Rxnfiles with Reactor?
Yes, Reactor supports lots of formats, the choice is yours.
Is there a limit for number of reactants?
No. Reactor supports monomolecular, bimolecular, trimolecular and even higher order reactions, no limit.
Can I run Reactor in batch mode?
Absolutely, you can generate large libraries in a single step.
What are map numbers?
Map numbers assign the corresponding atoms on the two sides of the reaction arrow of the scheme.
What are orphan atoms?
Orphan atoms appear only on one side of the reaction arrow. They appear or disappear during the reaction.
Which atoms should I map?
By default, Reactor expects, that all atoms having changing bonds are mapped. Orphan atoms must be mapped, since they have changing bonds. However, Reactor can handle other mapping styles too (when orphan atoms must not be mapped), and provides a built in automapper.
Can my reactions contain R-groups?
Yes, the reaction scheme can contain R-group definitions (appearing on both sides of the reaction arrow). Use R-groups as you use them in R-group queries.
Should I mark the substitutable parts with R-atoms in the reaction scheme?
No, Reactor uses the reactants of the scheme as queries to find reaction sites in the input molecules. See the Query Guide for more details on queries.
Is the order of the reactant files important in a multimolecular reaction?
Yes. Reactor follows the visual order of the reactants in the reaction scheme (left to right, top to down). Thus, the leftmost reactant is the first one. Be sure to specify the input files in that order.
How can I evaluate Reactor?
Download the JChem toolkit including Reactor.
Is there a simple desktop GUI for end user chemists for hardcore virtual synthesis?
ChemAxon provides various easy-to-use graphical interfaces for reaction based library enumeration: wizard, Instant JChem add-on, JChem for Excel functions.
What are sequential and combinatorial modes?
Let’s take a bimolecular reaction example, where the reagents are located in two SDfiles. In combinatorial mode, all molecules of the first file are reacted with all molecules of the second file. In sequential mode, the two first molecules are reacted, then second ones, and so on.
What are those “smart” reactions?
A “smart” reaction contains the corresponding “synthetic knowledge” in rules. These rules provide the basis of chemically feasible virtual synthesis.
How can I specify, that a functional group in a reaction is an amine but not amide?
There are various ways to define that, let’s see them by an acylation reaction example:
- Write the reaction scheme in recursive SMARTS.
- [H:4][N;X3;!$(NC=O):3].O=[C:1][Cl:2]>>O=[C:1][#7:3].[Cl:2][H:4]
- Define the reaction scheme with an R-group and set its occurrence to 0.
- Refine the functional group definition in the Reactivity field using the match function of Chemical Terms.
What is the Reactivity rule?
The functional groups of the generic reaction scheme and their required properties can be refined in the Reactivity rule to correctly specify the reactive sites.
What is the Selectivity rule?
The Selectivity rule helps to determine the main product when more than one reactive site is found on a reactant. The region with the highest Selectivity value is considered to provide the main product. Regioselectivities like ortho/para or meta directing are usually defined in the Selectivity rule.
What is the Tolerance rule?
The Tolerance value makes it possible to have more than one main product in certain cases. Take an aromatic electrophilic substitution reaction as an example, in which the electrophilic localization energy on the aromatic ring is the lowest in the para position, but it is almost as negative in the ortho position. If the difference is less than the tolerance, both ortho and para isomers are generated as main products.
What is the Exclude rule?
Use the Exclude rule to skip reactants containing functional groups causing side reactions. For example, you can avoid generating products from molecules having alcohol or amine functionalities, if you exclude starting compounds having nucleophilic groups by this rule.
Can I use Reactor with schemes without any rules defined?
Yes.
Can I skip the rules of a reaction?
Yes, you can skip the rules to examine their effects.
Can I change the rules?
Yes. The rules can be modified to improve the quality of the virtual reactions.
Do you provide ready-to-use synthetic reactions for library enumeration?
The distribution package of JChem contains a virtual reaction library for organic synthesis, demo reactions can be downloaded from this page.
I found, that one of your reactions generates unfeasible products, what should I do?
Please inform us about the problem to be able to provide better virtual reactions for the community.
In what format are the rules written?
The rules are written in Chemical Terms, a simple language containing logic, arithmetic and lots of chemistry related functions to create complex expressions.
What is the difference between reactions in Reactor and transforms in Standardizer?
Standardizer is for the canonicalization and beautification of molecules, Reactor is for feasible virtual synthesis.
Standardizer supports transforms:
- single input molecules
- one input molecule is converted to one output molecule
- all corresponding groups of an input molecule are transformed at once
- no advanced synthetic feasibility prediction
- both unimolecular and multimolecular reactions
- one reaction can produce multiple products (including isomers)
- reacts one reaction site at once (since it affects the reactivity/selectivity features for the next step)
- can generate synthetically feasible products (supports reactivity, selectivity and exclude rules)
