One of the most common pieces of feedback we have received in regards to facilitating better search capabilities for our spectroscopy users (specifically mass spectrometrists) is to allow our users to define what elements can be and cannot be contained within a molecular formula. In the near future we will roll out a more complete solution (under development) for expert spectroscopists but for the time being we are providing this solution for all of our users.

Under the Advanced Search tab it is now possible to “Search by Elements”. Two periodic tables are displayed by selecting the checkbox. These allow selection of “Elements which MUST be present in the compounds” and “Elements which MUST NOT be present in the compounds”. The graphic below shows the form of the interface.

Included and Excluded Elements

With this type of search it is possible to show that the database contains the following example subsets:

1) 10,659 deuterated molecules
2) 1628 tritiated molecules
3) 20 with BOTH deuterium and tritium!
4) 4994 containing Arsenic

Watch this space for how the search will be improved even further meanwhile we hope you find this enhancement of value.

As we unveil new capabilities on the ChemSpider site we clearly perform a lot of our own testing…we ARE the testing team before we push new functionality to the general users. That said, a number of you are very committed to providing us with ongoing feedback and thereby sharing the testing across the community. For this we thank you. When there has been a dedicated effort in any particular month to help “stress-test” new capabilities we like to acknowledge those who help push them…it is to the benefit of all users.

As we announced earlier this week we removed ACD/Labs’ Name to Structure batch as the background processing engine for SMILES and InChI generation and replaced it with the Openbabel open source component. The transition has been seamless and ACD/Labs staff have helped us test the conversion engine this week by pushing many SMILES and InChI strings through the system. In all cases, according to our log files, the conversions worked without fail and as expected. We officially declare this transition tested and thank ACD/Labs for their dedicated support to facilitate the transition.

Watch out for the promised structure deposition next. The development has been published as a beta capability and is presently in the hands of a few selected users for “exercise”. If you are interested in helping to test the Structure Deposition process please contact us at

Likely the majority of you in the Open Source and cheminformatics world will know of Open Babel. In the development teams’ own words “Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.” We have now implemented OpenBabel on the services page for the conversion of SMILES strings and InChI strings to chemical structures. Previously the conversion of chemical names, trade names, SMILES and InChI was supported by utilizing the ACD/Labs Name to Structure batch software in a service transaction mode. As previously discussed we are no longer using this application and have replaced the SMILES and InChI conversion with OpenBabel. We were very impressed by the ease of implementation and certainly the community dialog and support around this Open Source component. Our thanks to the community supporting Open Babel. We are committed to giving back any developments we add.

In terms of Name to Structure conversion originally in place with ACD/Labs Name to Structure this is now rather name “look-up” through the millions of names, synonyms and registry numbers we have on the index.

Open Babel Structure Generation

A recent enhancement allowing searches to distinguish between single and multi-component structure handling should be of value to a number of users but especially mass spectrometrists, of which we have many it appears. Thanks to all of you Mass Spectrometrists we will be putting some additional focus into enabling searches that facilitate your queries. This is the first….use the Advanced Search and select whether you want single, multi-component or both searched when searching on formula or the various forms of masses. Next up will be the ability for you to select which elements to include/exclude from the formula for the searches. Enjoy…give us more feedback…we’re listening.

Single and Multi Component Searching