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

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