Naming
Chemical and pharmaceutical companies rely on software-based naming systems for compliance and adding resolution for mining data. ChemAxon offers a powerful naming engine that is able to consistently derive accurate chemical names for nearly any organic, biochemical, or inorganic structure and to generate chemical structures from various sources.
Try online at www.chemicalize.org Download JChem for ExcelDownload Instant JChem Download MarvinDownload JChem BaseReliable chemical name conversion
Structure to Name Conversion – IUPAC, common names
ChemAxon’s naming toolkit capabilities allow you to generate systematic names according to the latest IUPAC naming conventions. However, simple trivial names can also be generated. Generating IUPAC names for radicals, natural products (Methyl-D-Glucoside) or peptides is also supported, residues can be recognised as groups and sequences can be generated accordingly.
MarvinSketch places IUPAC names interactively in the canvas.
While preferred IUPAC names can also be generated and visualized in a separate MarvinView window, this option allows common name generation as well. Naming in a Single fragment mode generates the largest fragment name.
Name to Structure Conversion – IUPAC, common names, CAS
ChemAxon’s naming toolkit capabilities allow you to generate chemical structures from IUPAC names, CAS indices or common names. We are continually expanding our customisable and extendable trivial name compilation. An animation showcasing name import in MarvinSketch is available here.
ChemAxon’s name import works quite similarly to a programming language compiler; the name is first broken into a list of elemental units, or tokens. This can be achieved by recognizing keywords like multipliers (di, tri, etc), cyclo, proper names like meth, eth, prop, but, benzene, etc. Then those units are parsed as a tree, linking together those tokens in a way that expresses their relationship.
For instance, in case of “(2R)-2-methylsulfanyl-3-hydroxybutanedioate”, this expresses that but is the parent of the compound, and the sulfanyl group is one of its substituents, at atom number 2, with methyl a substituent of sulfanyl, without a locant. This tree is depicted graphically as
Batch Structure to Name and Name to Structure Conversion
Naming of a large number of molecules or generating structures from names can be achieved in several ways. In all cases, all formats supported by Marvin are acceptable as input. Names and structures can be automatically computed into columns in Instant JChem databases or JChem for Excel. In MarvinView, names and structures can be generated and converted by importing, saving or exporting. Workflow tools such as Pipeline pilot or Knime also implements ChemAxon’s naming engine. Command line tools such as Molconvert, cxcalc can convert between names and structures. Names and structures stored in an Oracle database can be automatically converted using JChem Cartridge. Naming engine can also be applied via the Marvin API for custom applications.
Document to Structure Add-on – text mining for chemistry
Document to Structure parses HTML, text or PDF files, it recognizes and converts IUPAC names, common names, as well as SMILES and InChI into chemical structures. Document to Structure is an API that also can be called via command line.
Document to Structure not only identifies but also retrieves the position of chemical structures in a file. Document to Structure API is implemented in the free chemicalize.org webapplication enabling users to find chemical structures in webpages. Text mining can be automatized by using document to structure integrated in Knime.
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Development sponsored by EUREKA’s Eurostars Programme |
chemicalize.org – find chemical structures on the web
We have implemented Document to Structure functionality into a free, public browsing tool, called chemicalize.org, to find chemical names and present the corresponding structure images as you browse the web.
The Webpage Viewer allows viewing any webpage with all recognized chemical names highlighted and 2D structure images are generated. When browsing the web from chemicalize.org visited links continue to be transformed, see screen captures below. 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 www.chemicalize.org
