ChemAxon’s naming toolkit capabilities allow you to generate chemical structures from many kinds of chemical names and identifiers.
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:
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
Compounds with one radical
Unlimited number of atoms and rings
All atom types
Substitutive and multiplicative nomenclatures
Molecules containing multiple radicals (e.g.
ethane-1,2-diyl) are not supported yet.
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.
There are different ways how you can import a name directly into MarvinSketch and convert it to a chemical structure.
Open a text file with the
.name extension containing the names (one per row). MarvinView will open all the structures.
As a command line tool, you can use MolConverter for name to structure conversion. Examples:
test.name name file to MOL file:
molconvert mol test.name -o test.mol
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.
Marvin can also convert structures to names.
Document to Structure is used to find names in documents and free text
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.