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Custom fragments in Avogadro


#1

Hi all,

I have defined a custom fragment in Avogadro 1.2.0. Could I also define the linking position? I explain myself. Let’s assume this custom fragment is acetic acid and I want to add it to a long hydrocarbon chain, like 1-dodecanol. When combining these two fragments I can get either dodecylacetate (linking atom oxygen of acetic acid) or 14-hydroxytetradecanoic acid (linking atom alpha-carbon of acetic acid).

Ideally, I would like to define two acetic fragments, one which links through the alpha-carbon and another, through the acid oxygen. Is that possible in Avogadro?

Thanks for your help!


#2

Currently, Avogadro v1.x uses the first atom in the file as the default linking atom. So if you change the atom order, you should be able to do this.

I’m dreaming up a better “template draw” tool for Avogadro v2 which should make this less critical.

Suggestions for how such an interface should work are most welcome. It’s clearly an important idea and I’d like to get the experience right. :slight_smile: