Differences

This shows you the differences between two versions of the page.

--- searching_function [2024/03/19 09:38] – created shankar
+++ searching_function [2025/02/10 08:18] (current) – shankar
@@ Line 1: / Line 1: @@
 ====== Searching Function ======
-On the Search page, the default searching packages will be EAWAG-BBD, EAWAG-SOIL, and EAWAG-SLUDGE. It is allowed to select/unselect certain packages to include/exclude them for searching.
-{{ :searching_function.png?nolink&800 |}}
+The Search page enables quick and efficient data retrieval across enviPath. By default, the search is configured to include the EAWAG-BBD, EAWAG-SOIL, and EAWAG-SLUDGE packages.
+{{ :search.png |}}
+You can customize the selection by expanding or narrowing the set of packages using the dropdown menu. Multiple search methods are available to suit your needs:
+  - **Text**: Your input text will be searched across all the names and descriptions of all the objects (Compounds, Reactions, Rules, Pathways, …) for the selected packages.
+  - **SMILES**: Your text will be assumed to be expressed in a valid SMILES format and compared with all the compounds in the selected packages. When SMILES search is selected search modes must be provided:
+    -**Default**: The stereochemistry and charge of the molecule will be ignored for this type of search. This means that inputs that differ on only on stereochemistry and/or charge will be returned for this search. For example, assuming you created a package containing (E)-1-Propenol (C/C=C/O), (Z)-1-Propenol (C\C=C/O) and (E)-prop-1-en-1-olate (C/C=C/[O-]), using this method search and using “C/C=C/O”, would return all these compounds.
+    -**Canonical**: The stereochemistry of the input molecule will be ignored for this search. The canonicalization method used for this search is provided by CDK’s “unique” flavour of SmilesGenerator. Using the above example and same input, the result of this search would only return the E and Z enantiomers of 1-Propenol.
+    -**Exact**: Both stereochemistry and charge of the SMILES will be preserved. The provided input will be processed by CDK’s “absolute” flavour of SmilesGenerator to ensure that stereochemistry is preserved and that different atom orderings of SMILES that represent the same molecule (e.g., acetone can be represented as CC(=O)C and as CC(C)=O) are mapped to a common SMILES. Using the same example and input as above the output will be (E)-1-Propenol independently of the atom ordering (i.e., using “C(/C)=C/C” as input will also return only (E)-1-Propenol).
+  - **InChIKey**: The option of searching by InChIKey is also provided. For this method, it is permitted to use the entire InChIKey as well as parts of it, and it will be used to match with the compounds in the provided packages.