Molecule Lists

‘Molecule Lists’ allow you to quickly build and save a collection of molecules that you want to avoid or favor in your results (see “Exclude & Seek” to learn how to use them in your analysis settings).

You can view, create, and manage ‘Molecule Lists’ by selecting this option from the ‘Lists’ drop-down menu in the SYNTHIA™ header.

Regulated Lists

SYNTHIA™ provides several default lists of regulated substances from different governmental agencies.

• Australia group is a list of controlled chemical weapons precursors
• Department of Homeland Security is a list of chemicals of interest monitored by the DHS for counter-terrorism purposes
• Environmental Protection Agency is a list regulated substances that may cause serious adverse effects to human health or the environment if accidentally released
• Environmental Protection Agency List of Lists is a consolidated list of hazardous chemicals subject to reporting requirements

Click on one of the lists to see the structures of the substances it contains. 

Note: Default ‘Regulated Lists’ provided by SYNTHIA™ cannot be modified or deleted.

Create a Custom Molecule List

You can create your own molecule list by following the steps below:

• Click on ‘New Molecule List’
• Type a new name in the text box, or leave the default one
• Press ‘Enter’, or click on the ‘Save’ icon

• Your new list will be displayed under ‘My Molecule Lists’

Add Molecules to a Custom Molecule List

You can add molecules to a custom molecule list using any of the methods listed below:

• Draw structures in the molecule editor
• Upload a file (supported formats: sdf and mol files)
• Search for compounds by name in our databases of commercial and published compounds
• Copy or move molecules from existing molecule lists

Draw

• Click on ‘Draw’ to open the molecule editor
  
• Draw a structure in the editor
• Click ‘Add to List’ 
• Draw more structures if needed

• Click on any SMILES string to see its structure in the editor
• Click ‘Save and Close’ to go back to the main page

Upload

•  Click on ‘Upload’ 
• Select your file and click ‘Open’
• Supported formats: sdf and mol files
• The structures in the file are then loaded into SYNTHIA™

Search

• Click on ‘Search’ 
• Type a compound’s partial or full name in the text box, and press ‘Enter’, or click on ‘Search’
• Select the desired compound from the list

• Click ‘Close’ to go back to the main page

Copy or move

• Open a molecule list
• Select the molecules you wish to copy by clicking on their card
• Click on ‘Copy to’, and select the destination list in the menu

• Alternatively, if the original molecule list is a custom list, you may also move the selected molecules from one list to another by clicking ‘Move to’, and selecting from the destination list in the menu

Filter

You can filter the list by name or or partial name to find a molecule more easily.

•  Click on the ‘Filter’ icon

• Type a compound’s partial or full name in the text box

Note: If you close the filter without clearing the content of the text box, the filtered results are still displayed, and the filter will be also applied to any other list you open.

Collapse

For a quick glance of a list’s content, you can collapse all the molecule cards to show only the names.

• Click the ‘Collapse’ icon in the header
  

• Click on any card’s ‘Expand’ icon to open its structure
• Only one card can be expanded at a time

• Click on the ‘Expand’ icon in the header to display all the structures again

Manage Custom Molecule Lists

• Rename or delete a custom molecule list by clicking on the corresponding icon next to the list name

• Edit a molecule structure by clicking on the ‘Edit Molecule’ icon in the molecule card

• Copy a molecule’s SMILES string by clicking on the ‘Copy’ icon in the molecule card
• Remove a molecule from a list by clicking on the ‘Delete’ icon in the molecule card

• Alternatively, delete a series of molecules from a list by clicking on their card to select them, and clicking on the ‘Delete’ icon in the header

• Select and unselect all the molecules in a list by clicking on the ‘Select’ and ‘Unselect’ icons in the header