Structure Checker


We often encounter chemical structures with issues. The majority are caused by human mistakes, legacy structure representations and workarounds. Structure Checker is an interactive tool to detect and fix these issues using ChemAxon’s JChem technology. It comes with numerous checkers and fixers to search and correct various structural issues. The correction process can be manual, completely automatic, or somewhere in between. Structure checker can operate in batch and provide flags for problems which cannot be automatically corrected.

Helps drawing chemically correct structures

Structure-with-error Structure-issues-found-small Structure-fixed-small

Structure validation during drawing

Structure Checker is integrated into Marvin. If we regard MarvinSketch as an editor of the chemical language, then Structure Checker is its spellchecker. Whenever you have a structure on the canvas, issues are automatically discovered and highlighted. It also prompts you with a solution. This gives the chemists a highly customizable tool to continuously supervise their structure drawing.

Checkers for various structural issues

Structure Checker comes with over 40 checkers. Most are for detecting mild structural drawing problems or special structural features, e.g. invalid bond lengths, overlapping atoms/bonds, molecule charge, etc. However, there is a group called error checkers, which deal with more significant structural errors, such as incorrect chiral flags, invalid valences, OCR errors, and so forth. Furthermore, there is a substructure checker that can be configured to transform a given substructure defined by SMARTS string.

Check and fix chemical structures

A Structure Checker process consists of two steps: checking and fixing. Firstly, it checks the structure for issues based on the user selected checkers. Secondly, the issues found will be fixed either manually by the user or automatically by built-in fixers. However, not all checkers have a fixer because there is no single solution such as with empty structures, racemate representations etc.

Integration in different applications

Easily accessible

Structure Checker is available as a standalone, Java based application. It is platform independent and can be used via a wizard-like graphical user interface or via the API or command line, for batch operation. As previously described, it is part of MarvinSketch. In Chemical Terms, ChemAxon’s universally supported language for combining and manipulating structure properties, which make Structure Checker available in Instant JChem, JChem for Excel and JChem for SharePoint. Workflow management tools, like KNIME and Pipeline Pilot also integrate the Structure Checker engine.


Advanced reporting capabilities

When structures are checked in a batch process it is important to get a report to summarize the process. Structure Checker can give a detailed report on the issues found, fixer or fixers applied and flag molecules with needing a chemists review to resolve.

Write your own checkers and fixers

As all other ChemAxon applications, Structure Checker also has a full featured Application Programming Interface (API) in Java and in .NET, making this solution integratable into in-house or third-party applications. This means that you are able to write your own checkers and fixers according to your needs. If you have to handle chemical features which cannot be done by the built-in checkers and fixers, then with some programming you can easily implement them and extend Structure Checker. Read more…


Configurable structure checking

The user is free to choose any combinations of checkers available for customized usage. After completing the setup of the checker list, the configuration can be saved to an XML file to be reloaded in the future. The same XML configuration file can also be used in other platforms, such as command-line, KNIME and so forth.

Register errorless structures

When it comes to compound registration it is crucial to store structures that are free of drawing errors and incorrect features. Structure Checker can be a useful and integral part of a registration system. It can serve as a filter to check and automatically fix incoming structures and in the case of ambiguity, prompt the registrar to fix manually.


Comparison with Standardizer

One might raise the question after getting familiar with Standardizer and Structure Checker why there are two different tools for a very similar problem. The reason for the separation can be understood easier if one thinks of the philosophy and the goal of the two applications. While Standardizer is for creating canonical structure representations in an automated way for a consistent chemical database, Structure Checker is rather an interactive tool that lets the user manually decide the resolution in certain cases.

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