Name to Structure User Guide

Chemaxon's naming toolkit capabilities allow you to generate chemical structures from many kinds of chemical names and identifiers.

Supported names include

• IUPAC names, CAS names and generally systematic names

• Common names (e.g. Toluene)

• Drug names (e.g. Paracetamol, Doliprane)

• Acronyms (e.g. ATP for "Adenosine Triphosphate")

• CAS Registry Numbers^® (Note that this feature uses a webservice, read the notice about CAS Registry Numbers^® for more information.)

• For systematic names:

  • Chains

  • Monocycles

  • Retained/traditional names for ring systems with and without heteroatoms

  • Spiro ring systems

  • All cases of von Baeyer nomenclature for bridged ring systems

  • Fused ring systems

  • Ethers, esters, oximes, ...

  • Common characteristic groups

  • Ionic compounds

  • Compounds with one radical

  • Unlimited number of atoms and rings

  • All atom types

  • Substitutive and multiplicative nomenclatures

  • Stereochemistry

Current limitations

• Molecules containing multiple radicals (e.g. ethane-1,2-diyl) are not supported yet.

• Names containing isotopes are not supported yet.

Corporate IDs and custom dictionaries

It is possible to extend the Name to Structure conversion, for instance to support corporate IDs such as ABC0001234, or to make use of common name dictionaries in addition to the default one. This can be done by connecting to a webservice or by creating a custom dictionary file.

Name to Structure Conversion in MarvinSketch

There are different ways how you can import a name directly into MarvinSketch and convert it to a chemical structure.

• A simple method is to select the name in the text of any page and drag&drop or copy&paste it to MarvinSketch.

OR

• Select the "Import Name" (Ctrl+Shift+N) option from the File menu, and write the name into the text field and click the "Import" button (Ctrl+I).

Name to Structure Conversion in MarvinView

Open a text file with the .name extension containing the names (one per row). MarvinView will open all the structures.

Name to structure conversion from command line

As a command line tool, you can use MolConverter for name to structure conversion. Examples:

1. Converting test.name name file to MOL file:

   molconvert mol test.name -o test.mol

2. Converting test.name name file to test.smi SMILES file which also contains the name of the structures:

   molconvert smiles:n test.name -o test.smi

The behavior of Name to Structure can be controlled using format options.

Structure to Name conversion

Marvin can also convert structures to names.

See also

• Name to Structure format options

• Name to Structure Developer Guide

• Document to Structure is used to find names in documents and free text

License information

Name import is only available for a single molecule with the free MarvinSketch desktop application. For batch conversion (with MarvinView, MolConverter, API, ...) you need the "Name to Structure" licence.