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--- compounds [2023/11/20 15:48] – created shankar
+++ compounds [2024/03/22 12:08] (current) – shankar
@@ Line 1: / Line 1: @@
 ====== Compounds======
-From enviPath Wiki
+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.
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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).
+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 Ketcher chemical structure editor or by providing the structure as SMILES or Molfile.
+  * 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, where each node in the pathway corresponds to a compound.
+  * Alternatively, compounds are created during [[pathway_prediction|pathway prediction]], where each node in the pathway corresponds to a compound.
-  *
-Retrieved from "https://wiki.envipath.org/index.php?title=Compounds&oldid=147"