Rendering the chemical structures
In the previous tutorial we built the FileMaker database, imported the
structures as SMILES strings and then built the substructure searching script.
Whilst SMILES strings are a brilliant way to store chemical structures in a
database in a very compact form, they leave a little to be desired when it comes
to actually working out what structure the SMILES encodes.
A D V E R T I S E M E N T
To add a depiction of the structure we first add a container field to the
database, this will hold the rendered structure.
We now need to generate the structures, whilst it would be possible to draw
all the structures by hand by using a mixture of FileMaker scripting and
Applescript with ChemDraw it is possible to automate the structure generation.
First we need to build the FileMaker scripts, within FileMaker open ScriptMaker
from the Scripts menu and create a new script called "Chemdraw_from_SMILES" as
shown in the image below. The first step checks we are in Browse mode and then
at the first record. We then loop through each of the records, first copying the
SMILES string and then using Applescript to get ChemDraw to generate the
When you add the "Perform Applescript" FileMaker script step a window will
open onto which you can paste the following Applescript. First using the "Paste
Special" menu to convert the SMILES to a rendered structure, then selecting it
and copying it to the clipboard.
if enabled of menu item "Select All" then
tell application "CS Chemdraw Ultra"
if enabled of menu item "Paste" then do menu item "SMILES" of menu "Paste
Special" of menu "Edit"
do menu item "Select All"
do menu item "Cut"
tell window "SMILES_Database" of application "Filemaker Pro"
do script "Paste_CD"
The Paste_CD script now pastes the contents of the clipboard into the container
If you now run the "Chemdraw_from_SMILES" script it should loop through all
the records in the current found set, use ChemDraw to generate the structure and
copy it into the Structure container field.