a reliable chemical name conversion and mining engine
ChemAxon offers a powerful naming engine that can convert chemical and biochemical structures and names in various formats bi-directionally. In addition to IUPAC and traditional name support, it also recognizes common names and CAS registry numbers. It can reference a local user customizable dictionary or a web service to convert corporate IDs, or arbitrary texts to structures. Chinese name to structure support was added since version 5.12; Japanese support is now available in version 6.3.

Reliable chemical name conversion

Structure to Name Conversion – IUPAC, common names

Naming allows the user to generate an IUPAC name from a structure according to the latest IUPAC conventions. In addition, traditional names can also be generated if applicable. Radicals, natural products, or peptide sequences are also supported. Working with Structures - Common Names

Name to Structure Conversion – IUPAC, common names, CAS

Supported names:
  • IUPAC name (English, Chinese and Japanese)
  • Systematic names
  • Common names
  • Drug commercial names
  • CAS name
  • CAS registry number (via a public webservice)
Working with Structures

Asian Language Support

To accommodate the fast growing scientific literature in Asian language, ChemAxon has released Chinese and Japanese Name to Structure (CN2S, JN2S) conversion tool. It is not only an enhancement to our Naming engine, but also to other products (e.g. Document to Structure) powered by Naming. With CN2S and JN2S, extracting chemical information from Chinese and Japanese literature is now achievable.
With CN2S, extracting chemical information from Chinese literature is now achievable. Working with Structures

User Customizable Dictionary

Have a list of obscure common names not in our dictionary? Or want to convert corporate compound IDs to structures? No problem. Naming supports User Customizable dictionary import. SMILES and customized texts can be stored in a local file, and Naming can reference this information for the conversion. Starting with version 5.12, Naming can also call a webservice for customized conversions. Working with Structures

Use Naming with Other Products

Naming in MarvinSketch

In the Sketching Tool MarvinSketch, IUPAC names can be interactively generated and displayed on the canvas. Both IUPAC and traditional names can also be generated and visualized in a separate window. Working with Structures - Common Names

Batch Conversion of Chemical Names

Naming can perform batch conversion between multiple structures and names bi-directionally using MolConverter or Cxcalc in command-line mode.

Working with Structures - Common Names
Batch conversion of a large collection of structures to names or names to structures can be achieved in various ways. In all cases, all formats supported by Marvin are acceptable as input. Names and structures can be automatically generated into columns in Instant JChem and JChem for Office. Our SharePoint add-on, JChem for SharePoint, also uses Naming to index chemical information from SharePoint documents.  When using Naming with other ChemAxon products a separate naming license will be required.
In an Oracle database, names and structures can be automatically converted using JChem Cartridge. The Naming engine can also be applied via the Marvin API in customized applications. Within Workflow Tools: Naming is available for workflow tools, such as Pipeline Pilot and KNIME Within Our Partners’ Applications: Naming has been implemented into our partners’ applications. For example, Linguamatics and ChemAxon have been working together in the ChiKEL project to enhance text mining in chemistry. Working with Structures

Document to Structure and Chemicalize — text mining for chemistry

Extract Chemistry from Documents

Powered by Naming, Document to Structure (D2S) is a versatile application to extract different types of chemical information from documents in various formats (PDF, PPT, Doc, Xls, Txt, HTML, etc.). D2S also applies text OCR and image OSR technologies to extract information from non-searchable PDF documents. Once the structure is converted, the location of that structure is also returned. All these features make D2S an excellent choice for text mining, patent analysis and internal document management. Learn more about Document to Structure » EUREKA's Eurostars ProgrammeDevelopment sponsored by EUREKA’s Eurostars Programme – find chemical structures on the web

We offer the functionalities in Document to Structure as a free public tool called, to extract chemical information from webpages and documents. Chemicalize’s Webpage Viewer allows viewing of any webpage with all recognized chemical information highlighted and 2D structure images shown when moused over. All structures are summarized on the top of the page, and can be downloaded. The Document Viewer brings the same capabilities to PDF files: view them in your browser and see all recognized structures in the text. For more information please visit


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