How to search for a chemical molecule by drawing its chemical structure

The molecule search allows users to search by text (name, CAS number) or to draw a molecule. Drawing the molecule can offer more customization possibilities to the search.

You can read the online Help Links for drawing (Marvin JS). For a start: Getting Started with Marvin JS

If you want to go further, you can find here a documentation about the sketcher options, and detailed information about drawing R-groups in Marvin JS.

If you are interested in the query features, which can be drawn in Marvin JS, a summary page is at your disposal.

To search by drawing the structure of a molecule, a sketcher is available.

Use the different icons representing the atoms / cycles / bonds to draw your molecule.  

A .mol file can also be imported directly into the sketcher:

To save time, instead of importing a file, the name of a structure (IUPAC, common, trade) can also be typed in the "auto-recognize" (import default menu) and the structure will be drawn instantaneously. The auto-recognize feature works with SMILES and CAS number as well. Modifications in order to extend the searched structures can now be drawn in the sketcher.

Differences between a structure with hydrogens drawn out and hydrogens implied in the sub-structure search:

• In the sub-structure search, if you do not actively draw out a hydrogen on a C, N, O, P, etc., it is considered by the system as a variation point in your sub-structure search. 
• If you purposely draw the hydrogen on the carbon you lock that position and force the system to search the structure with a hydrogen on that carbon.

Polymer search

Options legend:

• Green: add "any" (* symbol) to define the start and end of the polymer if unknown (H, cycles, etc.).
• Orange: to define the repeated motif with the square brackets.

• Blue, this is the way in which the repetition of the motif is organized (if the motif is symmetrical, then it's pointless):

  • ht: head-to-tail repeat pattern,

  • hh: head-to-head repeat pattern,

  • eu: either-unknown repeat pattern. Both repetitions are possible or the sequence is unknown.

• Red: number of repetitions, any (n), specific (like 8), range (5-8), or a combination (like 3, 5-8).