Here we collected Frequently Asked Questions about Reactor for you.
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.
No, Reactor uses the reactants of the scheme as queries to find reaction sites in the input molecules. See the the Query Guide for more details on queries.
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.
Reactor, in general, is lightning fast. Although, the exact speed depends on the reaction schema and the calculations defined in the rules, the slowest step is usually writing the results into a hard disk. In case of SMILES output - which is a relatively small molecule description format - the speed can be higher than half million reactions/hour even on an ordinary notebook. In case of a database output, the speed is usually a bit less but it is still possible to generate some millions of compounds overnight.
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Yes, try our working examples.
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 sequental mode, the two first molecules are reacted, then second ones, and so on.
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.
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.
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.
Drug-likeness filters can easily be written in Chemical Terms. Although you could, you should not add a drug-likeness filter (or similar) to the rules. Specific synthesis goals should not appear in the reactions. You can post-filter the products or use Synthesizer (part of Reactor Pro) to specify custom conditions for each reaction step. This will not hurt the integrity and reusability of the reactions.
ChemAxon provides a library of several important preparative reactions for the Reactor users. Download it from the Reactor web-page.
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There are various ways to define that, let's see them by an acylation reaction example:
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 prediciton
Reactor supports virtual reactions:
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)
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