Converting structures from 3D to 2D in Excel

User 1ea534ed04

01-12-2009 00:54:17


I am trying to convert the structures imported as an sdf (more than a 1000 structures). I know I can do it one at a time by clicking on the image; however, I would appreciate it if you tell me how to clean all structures and make them 2D at the same time.


Your help would be most appreciated.

Thanks !


ChemAxon bd13b5bd77

01-12-2009 09:28:10

Dear Hamed!

After the import of an SD file you can insert columns keeping the original structure column (e.g. [A]) and

add JC2D and JC3DCleanStructure function there, use them normally like Excel functions to browse the source parameter of the routine by clicking on the cell (e.g. A2) and press Enter or OK at the end.

When the structure 2D and 3d clean works you can extend the calculated function along with the 1000 rows down.


User 1ea534ed04

01-12-2009 13:55:26

Thanks for the help. The function works; however, is there any function that allow me to remove explicit hydrogen atoms in order for my molecules to look less complicated? I still need the terminal hydrogens though.


Thank you so much!


ChemAxon 0e37943a96

01-12-2009 16:38:05


you can actually do both in one step:

=JCStandardizeStructure(<cell address>,"clean:full..removeexplicitH") or only one

=JCStandardizeStructure(<cell address>,"removeexplicitH")

for the possible list of action strings that can be passed to JCStandardizeStructure, see: