# Fragment Images

**URL:** <https://discuss.avogadro.cc/t/fragment-images/3639>\
**Category:** General Discussion\
**Created:** [September 20, 2021, 12:19am UTC](https://discuss.avogadro.cc/t/fragment-images/3639 "2021-09-20T00:19:16Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [September 20, 2021, 12:19am UTC](https://discuss.avogadro.cc/t/fragment-images/3639/1 "2021-09-20T00:19:16Z")

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Okay, I’ve been working on a “build by fragment” tool, that will also eventually support attaching bidentate and tridentate ligands, π-conjugated ligands like Cp rings, etc.

I started with a list of ligands in a pop-up menu, but it seemed like images would be good.

My thought is that you’d pick a ligand and have a preview on the right side, but I’m curious whether it’s better to have a 2D depiction or a 3D depiction.

Thoughts? Feedback?

 ![Screen Shot 2021-09-19 at 8.10.08 PM](https://discuss.avogadro.cc/uploads/default/original/1X/44ba0556b56d1c4d3fa990224f0e37ff311c7b85.png) ![amide](https://discuss.avogadro.cc/uploads/default/original/1X/52f0c3e21a706df35d577432099c881df37ec73b.png) ![amide copy](https://discuss.avogadro.cc/uploads/default/original/1X/18f493282b4ec05f5cd8be7f9e8a199465531b8f.png)

_Poll ([view on site](https://discuss.avogadro.cc/t/fragment-images/3639/1))_

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<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [September 20, 2021, 6:07pm UTC](https://discuss.avogadro.cc/t/fragment-images/3639/2 "2021-09-20T18:07:32Z")

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Since I haven’t gotten many responses on here, I also created a Twitter poll:  
[https://twitter.com/ghutchis/status/1439995620400537609](https://twitter.com/ghutchis/status/1439995620400537609)

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<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [September 22, 2021, 12:04am UTC](https://discuss.avogadro.cc/t/fragment-images/3639/3 "2021-09-22T00:04:43Z")

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Twitter seems strongly in favor of color 2D diagrams, so I coded up preview images in RDKit today.

 ![Screen Shot 2021-09-21 at 7.58.31 PM](https://discuss.avogadro.cc/uploads/default/original/1X/aa69fdb1f925ded3d6728dab639cc73d7777b06a.png)

I have 113 fragments so far:

- alkanes
- aromatics
- cyclic alkanes
- bicyclic
- heteroaromatics
- boron
- oxygen
- sulfur
- nitrogen
- phosphorus

Here are a few 2D heterocycles:

 ![Screen Shot 2021-09-21 at 8.01.32 PM](https://discuss.avogadro.cc/uploads/default/original/1X/15c7494b96a0f91937934706a2b25409139fea63.png)

The code generates all the fragments from SMILES, so it should be pretty easy to add / tweak them over time.

I’ll also generate 3D preview images with atom labels, but that needs some separate work (e.g. adding support to tell Avogadro to save an image to a particular filename).