The Chemical Compounds Module

The chemical compounds module allows for streamlined and enhanced management of all compounds' chemical properties and experimental data.

Eynav Haltzi avatar
Written by Eynav Haltzi
Updated over a week ago

The chemical compounds module gathers all compounds' information in one place and offers a seamless connection between compounds' chemical properties with experimental data.

Labguru is integrated with ChemAxon services, allowing chemists and scientists to register and manage chemical compounds, calculate and describe their chemical properties, and view structures along with other details.

Compounds can be added to Protocols and Experiments, directly linking chemical properties and experimental data.

Inventory compound collection:

The Compounds collection is where all the compounds' chemical properties and other information are documented. As in other collections, fields in the Compounds collection are customizable, and additional fields may be added to describe the compounds.

In addition, for each compound added to the collections, users may select chemical properties to be automatically calculated by the system on the customization page. This is available thanks to the integration with ChemAxon services.

How to populate the compound collection:

  1. Add a single compound by filling out a new compound form

    1. Go to the compound collection index page.

    2. Click on 'New compound' button at the top right corner to open a form showing the fields that were chosen to appear in that collection.

    3. Populated the fields with the required information and saved to create a new item.

    4. The compounds collection is integrated with ChemaAxon's Marvin Sketch editor which allows for chemical structure drawing or uploading existing structure file. Marvin Sketch allows for a wide variety of file types uploading, such as SMILES, InChI, MOL, CDX and more.

    5. Once saved the chemical properties (if enabled) of this specific compound are added automatically to the form.

  2. Bulk import

    Labguru compounds collection offers two main options to perform bulk compounds import - by using Excel template or SDF file upload.

    1. Excel template:

      Importing compounds using the Excel template allows users to create new compounds, update existing compounds as well as add stocks or update existing stocks, all at the same time.

      • Go to the compound collection index page.

      • Click on the 3 dots and select Import/Update.

      • On the New Import page, download Labguru’s import template (.xlsx format).

      • The compounds' structure may be described either by using SMILES (simplified molecular-input line-entry system) in the Structure (SMILES) header, or by using InChI (International Chemical Identifier) in the Structure (InChI) header.

        Please note that if both structure fields are populated (SMILES and InChI), the structure will be determined according to the InChI notation inserted.

      • Make sure to follow the general import instructions and upload the filled Excel file.

    2. SDF files upload:

      Importing compounds by uploading an SDF file allows users to create new compounds and generate a new stock for each imported compound. In case one of the imported compound's structure already exists in the collection, a stock will be generated for the original compound in the collection having this structure.

      The final number of imported compounds as well as the number of duplicates found will be listed in the SDF import summary.

      The generated stocks will be located in a temporary box named after the SDF file.

      To upload a SDF file:

      • Go to the compound collection index page.

      • Click on the 3 dots and select Import/Update.

      • Upload the designated SDF file in step 3 on the New Import page.

      • An SDF mapping wizard will open that will allow allocating the SDF attributes correctly to existing or new data fields in the compounds collection.

  3. Compounds can be added to the compounds collection via the Compound and Reaction elements in the ELN.
    Every compound added (drawn or uploaded via file) to the compound and/or reaction element will be added to the compound collection.
    To learn more about the compound and reaction element in experiments click here.

How to perform structure search in the compounds collection

Another added functionality in the compounds collection allows to search by structure.

  1. Go to the compound collection index page.

  2. Click on the magnifying glass button to open the Marvin Sketch editor.

  3. Add the required structure to search and click on sub or full structure search.

    1. Full structure search- finds molecules that are equal in size to the query structure.

    2. Sub-structure search- search whether a molecular structure contains a specific subgraph.

      Please note that if special molecular features are present on the query (e.g., stereochemistry, charge, etc.), only compounds containing the features will be presented in the search.

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