Chemical Section Searching

The chemical compounds can be searched by text (name, property etc.) and structure.

Text Searching

A default set of properties are presented in the lower half of the Search Chemicals screen. You can set your own layout and save this to your workspace if you wish.

Add a property to the search

To add a property click the Add Properties button in the left menu (desktop mode) or via the hamburger icon (mobile devices)

Select the property you wish to add and click Close.

Notes:

The new property is added to the end of the current list. If you wish to set a specific order so that you can link fields with Boolean operators you should add them in the order in which you wish to link them.
You can add a field more than once. This allows you to search for multiple terms in one field and link with Boolean operators

Delete a Property from the Search

Use the Delete button to the right of the screen to delete a property.

Note: empty property fields are ignored in the search so you do not need to delete fields you do not wish to use.

Search Terms

Text fields

In text fields you can use the wildcard * before and/or after your search term.

Numeric Fields

The majority of the fields are numeric properties (melting point etc.). These do not support the * wildcard but use the Comparison operators instead. Using these you can search for exact, greater than (or equal), less than (or equal) and ranges.

Browse indexes

Each searchable field has a browse index which you can use if you are not sure of the exact term you want to use. To open the browse index click [browse...] to the right of the input box for the field you wish to browse.

By default the index will open at the beginning of the index. You can paginate through the index using the navigation button.

Most indexes are quite large and so you can navigate closer to the term you wish to find by typing the first few characters into the search term box before clicking [browse...].

The index will open on the page on which that search term fragment exists. If the fragment does not exist in the index then it will open on the page where the first characters do exist. e.g. if you type rai into the Chemical Name search field, the browse index will open on the page containing the first instance of a name starting ra, since no names exist starting rai.

Clear Searchable Fields

To clear an individual searchable field click [clear] to the right (desktop mode) or below (mobile mode) of the input box.

To delete all fields click Clear Properties in the left menu (desktop mode) or via the hamburger menu (mobile mode).

Structure Searching

You can search for compounds by drawing a structure or substructure. Structure drawing is provided by the Marvin JS plug-in. Click here to go to the ChemAxon website for a comprehensive guide to using MarvinJS. A brief description of the major features is given by clicking here, but anyone with experience using chemical drawing software will be familiar with the basic concepts.

You can draw as much or little of the structure you wish if searching by substructure.

Use the templates in the bottom toolbar to draw common cyclic groups. You can search for many more using the Abbreviated Groups tool. Type the first few characters (e.g. pyrim) of the group.

Use the bond tool (single bond icon) in the left menu to switch from single to double bond etc.

Use the zigzag icon in the left menu to draw carbon chains.

Use the element icons in the right menu to change any carbon to that element. You can use this and the bond tool in conjunction with the zigzag and template tools to quickly draw more complex fragments.

Use the periodic table above the element icons for any other element.

Note: MarvinJS is a third party component and therefore contains many features that are not used by the Handbook web application.

For example, no stereochemistry should be included in structure searches since this information is not stored in Handbook searchable structures (these should not be confused with the display structures seen in chemical entries which are simple graphics and do contain stereochemistry).

Once you have drawn you structure or substructure, click the button at the bottom of the dialog '+ Click to add structure to search query'.

Select the type of structure search you wish to perform from the drop-down list above the structure window:

Select the Tautomers checkbox if you wish to include tautomers of the drawn structure in your search results.

You can search for structures and text at the same time. The Boolean operator to the left of the first text field that is used (empty text fields are ignored) describes the link between the structure and the text search.

Importing Structures

Structures can be imported into the structure drawing window. Click the Import button in the Structure Drawing dialog and either Select File, to open a structure file, or paste an InChI, SMILES or SMARTS string into the text box.

Supported file formats are: cdx, cdxml, cml, csmol, csrdf, csrgf, cssdf, cube, cxsmiles, inchi, mol, mol2, mrv, pdb, rdf, rgf, sdf, smarts, smiles, xyz

Customising the Search

The searchable fields you choose will be remembered between sessions provided you are signed in to your workspace (IP authenticated users) and will be used as your default. If you wish to revert to the system default search settings, select Customise Search Defaults

, then select Restore System Default.

Saving a Search

Searches can be saved so that you can return and re-run a search without having to re-enter all of the search terms and fields to the search screen.

In the Search Screen or Search Results page, click Save Search. Enter a name for the search then click the Save button

You can make changes to a saved search. The Save Search button appears red to indicate that there are unsaved changes

The Save Search dialog gives the option to update the current search or save as a new search:

Loading a Saved Search

Click the Saved Searches button in the left menu (desktop mode) or via the hamburger menu (mobile mode) to load a previously saved search.

Click the Select button next to the search you wish to load.

Click the delete button to delete a search.

Start a New Search

Clicking the Start a New Search button in the left menu (desktop mode) or via the hamburger menu (mobile mode) performs the following actions: