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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

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Chemical Naming

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  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

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