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pathways [2024/04/11 10:20] – [Pathways] strichpathways [2024/04/23 11:32] (current) – shankar
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 A pathway stores the biodegradation of compounds. A pathway can either be predicted or created manually by adding compounds and reactions. When predicting a pathway enviPath tries to apply a set of [[rules|transformation rules]] to the compound at hand, starting with the root compound, and will add the transformation product(s) to the pathway. If two different rules predict the same compound the pathway will only have one compound but there will be two connections from the educt to the product. Each connection represents a reaction. For every product a compound will be generated and added to package unless it is already present there. Descending from the root compound enviPath recursively transforms its products until no further transformation is possible or the pathway prediction reaches one of the limits defined in the [[settings|settings]]. A pathway stores the biodegradation of compounds. A pathway can either be predicted or created manually by adding compounds and reactions. When predicting a pathway enviPath tries to apply a set of [[rules|transformation rules]] to the compound at hand, starting with the root compound, and will add the transformation product(s) to the pathway. If two different rules predict the same compound the pathway will only have one compound but there will be two connections from the educt to the product. Each connection represents a reaction. For every product a compound will be generated and added to package unless it is already present there. Descending from the root compound enviPath recursively transforms its products until no further transformation is possible or the pathway prediction reaches one of the limits defined in the [[settings|settings]].
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 +{{ :screenshot_2024-04-22_at_14.03.01.png?nolink |}}      
  ====== Create new pathway from scratch ======  ====== Create new pathway from scratch ======
    
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 There are three locations where a user can trigger the creation of a pathway. There are three locations where a user can trigger the creation of a pathway.
  
-1. By entering a smiles or drawing a structure on the [[https://envipath.org|homepage]].+1. By entering a smiles or drawing a structure as an input in the dialog box on the [[https://envipath.org|homepage]] of enviPath.
  
-2. By entering a smiles or drawing a structure on the [[https://envipath.org/pathway|pathway overview]] (package independent).+{{ :h16srng.png?nolink&600 |}}
  
-3. Inside a specific package by clicking on pathway.+2. On the [[https://envipath.org/pathway|Pathway]] page, click on “Actions” then “+ New Pathways”,and then enter a smiles or draw a structure as an input in the dialog box. Pathways created using this method are stored in the [[Packages#Default Package | default package]] of the user.
  
-When using the first option the currently associated [[settings|setting]] of the logged in user will be taken into account.+3. Inside a specific package by clicking on "Pathways" and following the same steps as Option 2.
  
 Options 2. and 3. are very much alike. But in option 2 the package is implicitly set to the default package of the user whereas in option 3 it is set to the selected pathway. Options 2. and 3. are very much alike. But in option 2 the package is implicitly set to the default package of the user whereas in option 3 it is set to the selected pathway.
pathways.1712830812.txt.gz · Last modified: 2024/04/11 10:20 by strich