chemical terms and standardization
I have a question about the properties calculations. I import some molecules with a custom standardization file, mainly aromatization and removal of salts. I assume that the similarity search works the same way as in the jsp examples of JChemBase, i.e. with the standardized structures, although the input structures are displayed. Is this the same with calculations like LogP?
Yes, that is essentially correct. The standardized form is used for searchcing and property calculation.
In IJC you can choose to display the standardized form of the structure if you wish. You do this in the display settings of the grid view or the settings of the structure widget in the form view. In the form view you can display the stucture in both forms by adding 2 structure widgets to the form.
Thank you Tim!
It works indeed - I thought it did not because my standardization file upon import did not do the job (some mistake I made), with regeneration everything was OK
Great tip for the widget, although it could be nice (and that is actually true for all widgets) to be able to customize the name display of the widget to differentiate or be clearer for the user, instead of the column definition.
The name can be customised. Open the widget settings editor and change the 'Title name' property.
well, I tried to find this but with no success - I have the dev version 200610171010...
Whoops, that's in the development version, not the released version. Sorry!
We should have a new release next week that will contain this.