Compounds

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In enviPath, a compound object stores the structure of a chemical compound. Compounds are assigned to Packages, compounds with equal structure exist only once in each package. Therefore, a compound is identified by its canoncial SMILES representation (Absolute SMILES created with the CDK library). Compounds provide connections to other enviPath objects like, e.g., pathways and reactions, as well as a reference to the corresponding PubChem entry.

Available compounds

A list of all available compounds is provided here: http://envipath.org/compound. To view all compounds of a particular package, select the package first, then the compounds within this package (http://evipath.org/package/<id>/compound).

Creating compounds

  • Compounds can be created manually by drawing the structure with the Ketcher chemical structure editor or by providing the structure as SMILES or Molfile.
  • Alternatively, compounds are created during pathway prediction, where each node in the pathway corresponds to a compound.