should organic molecule be divided into fragments?

[Serious-Huang]

Hi, I am impressed by your research ideas and achievements. I am a beginner and I have some questions: 1）how to divide fragments for organic molecules, such as heterocyclic compounds? According to the files in folder test/CF3, it seems the molecule is divided into atoms.

2）have any papers been published about this method? Although the tutorial has detailed steps, I have not fully understood the principles.

Thanks.

P.S. 1) some errors in FAMO/parsegjf.py:

from chemistry.atom import Atom
from chemistry.molecule import Molecule

should be

from atom import Atom
from molecule import Molecule

[jxzhangcc]

Thanks for your comments, especially for the bug report. Concerning your molecule of interest, the key point would be why you wanna apply FAMO (or whatever method) to your system, or what information you wanna learn from bonding analysis. For example, if you want to compute the pi-orbitals of the right-hand-side ring with heteroatoms, you can can align the whole molecule to the left part only (so the left part will be "aligned away"). If you wanna compute how the S=O group interacts with the rest part, you can divide the molecule into a S=O group (it its triplet state, but there would be a rotational symmetry issue here, which may require some tricks) and the C8H6 fragment (also in its triplet state).

[jxzhangcc]

In any case, I'd say organic molecules (which have rather traditional bonding patterns) are not the best case to apply FAMO analysis. I'm still exploring its scope but for now I think it's most suitable for cluster compounds and metalloaromatic systems.

[Serious-Huang]

I see. Thank you for your detailed response!👍