====== Compounds======

In enviPath, a compound object stores the structure of a chemical compound. Compounds are assigned to [[packages|Packages]], compounds with equal structure exist only once in each package. Therefore, a compound is identified by its canonical [[http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html|SMILES]] representation (Absolute SMILES created with the CDK library). Compounds provide connections to other enviPath objects like, e.g., [[pathways|pathways]] and [[reactions|reactions]], as well as a reference to the corresponding [[https://www.ncbi.nlm.nih.gov/pccompound|PubChem]] entry.

===== Available compounds=====

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

===== Creating compounds =====


  * Compounds can be created manually by drawing the structure with the [[https://web.archive.org/web/20201128144903/https://lifescience.opensource.epam.com/ketcher/|Ketcher chemical structure editor]] or by providing the structure as SMILES or Molfile.
  * Alternatively, compounds are created during [[pathway_prediction|pathway prediction]], where each node in the pathway corresponds to a compound.