1 / 10

Chemical Naming

Chemical Naming. Daniel Bonniot, PhD. October 2008. Naming history. Structure to Name since 2007 Name to Structure since 2008 (Marvin/JChem 5.1) ‏ Document to Structure: in progress. Structure to IUPAC Name. Usage Plugin in MarvinView and MarvinSketch

floyd
Download Presentation

Chemical Naming

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Chemical Naming Daniel Bonniot, PhD October 2008

  2. Naming history • Structure to Name since 2007 • Name to Structure since 2008 (Marvin/JChem 5.1)‏ • Document to Structure: in progress

  3. Structure to IUPAC Name Usage • Plugin in MarvinView and MarvinSketch • Label updated in real-time in MarvinSketch • Batch: Save As: IUPAC Name in MarvinView • Batch: command line (molconvert, cxcalc)‏ • Instant JChem 2

  4. Structure to IUPAC Name Evaluation • Test on random molecules from PubChem • Semi-automatic testing with manual inspection • Names generated for 99.9% of the structures • Correct name for 99.6%

  5. Structure to IUPAC Name Future work • Complex fused rings • Specialized nomenclatures (e.g. sugars) depending on demand • Extend traditional nomenclature

  6. Name to Structure Usage • Paste a name in MarvinView and MarvinSketch • Automatic format recognition • Open IUPAC Name file in MarvinView or MarvinSketch (.name extension)‏ • Import name file into InstantJChem database • Batch from command line (molconvert)‏

  7. Name to Structure Evaluation • ChemAxon name import on ChemAxon generated names: • Name imported in 87.3% of the cases • Correct structures: 95.6% • ChemAxon name import on LexiChem generated names: • Name imported in 81.4% of the cases • Correct structures: 89% (+4% where only stereochemistry is wrong)‏

  8. Document to Structure • Find chemical names in a text document (PDF, HTML, ...)‏ • Convert those names into chemical structures • As required: extract them, annotate the document, ... • Demo web service website adds annotations to any public webpage: http://www.chemicalize.org

  9. Visit othertechnical presentations MarvinSketch/Viewhttp://www.chemaxon.com/MarvinSketch_View.ppt MarvinSpacehttp://www.chemaxon.com/MarvinSpace.ppt Calculator Pluginshttp://www.chemaxon.com/Calculator_Plugins.ppt Structural Searchhttp://www.chemaxon.com/Structural_Search.ppt JChem Basehttp://www.chemaxon.com/JChem_Base.ppt Instant JChemhttp://www.chemaxon.com/conf/Instant_JChem.ppt JChem Cartridgehttp://www.chemaxon.com/JChem_Cartridge.ppt Standardizerhttp://www.chemaxon.com/Standardizer.ppt Screenhttp://www.chemaxon.com/Screen.ppt JKlustorhttp://www.chemaxon.com/JKlustor.ppt Fragmenterhttp://www.chemaxon.com/Fragmenter.ppt Reactor http://www.chemaxon.com/Reactor.ppt

  10. Find out more Product descriptions & links www.chemaxon.com/products.html Forum www.chemaxon.com/forum Presentations and posters www.chemaxon.com/conf Download www.jchem.com/licensefrset.html

More Related