Nav: Home

Software library to serve for faster chemical reaction processing

May 13, 2019

Big Data has become ubiquitous in recent years, and especially so in disciplines with heterogeneous and complex data patterns. This is particularly true for chemistry. In some ways, chemical compounds may be compared with synonyms in linguistics because one particular compound can be represented in various ways. To further complicate things, some of them don't even have a specific structure and only exist as an amalgamation of forms turning into each other. That's why it's important to know whether we are dealing with different compounds or with different representations of the same one.

Sometimes, databases also have errors arising from general unawareness of software features or just general inattentiveness. Special software is needed to detect and correct such errors.

In the case of organic chemistry, reactions are notoriously difficult to analyze. That's why reaction data in chemoinformatics is much less developed than information about single molecules.

Laboratory of Chemoinformatics and Molecular Modeling (Kazan Federal University) has been working on this problem since 2013. The efforts have so far been funded by the Government of Russia and Russian Science Foundation. The group includes from the University of Strasbourg, University of North Carolina, Moscow State University, Palacky University Olomouc, and Helmholtz Center in Munich.

Kazanites have learned to predict reaction characteristics, find optimal reaction conditions, detect and correct data errors. As a result, a unique database of reaction characteristics has arisen. Currently, it includes 3.5 million entries. KFU is the only Russian member of Reaxys R&D Collaboration, a collective working on chemical databases.

In this new project, titled CGRtools, KFU researchers solved a number of problems to better handle reaction information. The software library is significantly richer in functionality than all the existing tools. CGRtools supports molecules and reaction as objects being the only tool supporting CGRs. CGRtools treats chemical objects similarly to standard Python data types like integers, strings, etc. Every chemical object is hashable due to atom numbering canonicalization. The objects support transparent class inheritance which augments existing functionalities - methods and attributes - without breaking up existing ones.

Importantly, the library is in free access at https://github.com/cimmkzn/CGRtools.
-end-


Kazan Federal University

Related Chemistry Articles:

Better chemistry through tiny antennae
A research team at The University of Tokyo has developed a new method for actively controlling the breaking of chemical bonds by shining infrared lasers on tiny antennae.
Chemistry in motion
For the first time, researchers have managed to view previously inaccessible details of certain chemical processes.
Researchers enrich silver chemistry
Researchers from Russia and Saudi Arabia have proposed an efficient method for obtaining fundamental data necessary for understanding chemical and physical processes involving substances in the gaseous state.
The chemistry behind kibble (video)
Have you ever thought about how strange it is that dogs eat these dry, weird-smelling bits of food for their entire lives and never get sick of them?
Top 10 chemistry start-ups
Starting a new chemistry-based company is one part discovery, one part risk.
More Chemistry News and Chemistry Current Events

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Rethinking Anger
Anger is universal and complex: it can be quiet, festering, justified, vengeful, and destructive. This hour, TED speakers explore the many sides of anger, why we need it, and who's allowed to feel it. Guests include psychologists Ryan Martin and Russell Kolts, writer Soraya Chemaly, former talk radio host Lisa Fritsch, and business professor Dan Moshavi.
Now Playing: Science for the People

#537 Science Journalism, Hold the Hype
Everyone's seen a piece of science getting over-exaggerated in the media. Most people would be quick to blame journalists and big media for getting in wrong. In many cases, you'd be right. But there's other sources of hype in science journalism. and one of them can be found in the humble, and little-known press release. We're talking with Chris Chambers about doing science about science journalism, and where the hype creeps in. Related links: The association between exaggeration in health related science news and academic press releases: retrospective observational study Claims of causality in health news: a randomised trial This...