Molecule Lists

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

You can view, create, and manage Molecule Lists in the Molecule List Manager, which can be access from the Analysis Configuration Exclude & Seek page by opening the dropdown menu for Predefined Lists of Molecules in either the Exclude or Seek section.

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.
• Drug Enforcement Administration, U.S. Department of Justice is a list of controlled substances and chemicals that may be used to manufacture controlled substances or illicit drugs. 
• 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.

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 tile,
• 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 tiles to show only the names.

• Click the ‘Collapse’ icon in the header,
  

• Click on any tile's ‘Expand’ icon to open its structure,
• Only one tile 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 tile.

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

• Alternatively, delete a series of molecules from a list by clicking on their tile 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.