Descriptor calculation software accepts various data formats for chemical structure representations.
The formats for chemical structure were more developed, more useful, embedded in software.
SMILES, SDF, and InChI strings are common structural representation formats for chemical entities, which can be directly used for structure search operations or the generation of physico-chemical properties.
The main format used for chemical structure representation in our classification algorithm is the SMARTS format [28].
While attempts have been made to provide a standard format for storing chemical data, including most notably the development of Chemical Markup Language (CML) [2 6], an XML dialect, such formats have not yet achieved widespread use.
The supported input file format for the chemical structures to be analyzed is the MDL MOL/SDF format and these are sequentially read in order to employ suitable memory allocation according to the size of the molecule.
The early design decision to adopt the Standard InChI as a normalizing key was based on the belief that this standard has become the preferred structural format for defining chemical uniqueness in the context of biological activity.
A major goal of the DSSTox project is to encourage the use of the DSSTox data format (including DSSTox Standard chemical structure fields and standardised SDF (structure data format)) for publishing chemicals and their associated toxicity data files.
There are multiple available representation formats for a chemical compound including a systematic name (e.g., IUPAC Name), a molfile connection table [1], and string representations such as various flavors of SMILES [2] and the InChI [3].
