Fragment Images

General Discussion
1

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?

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amide amide copy

  • No pictures, list of names is okay
  • 2D black-and-white “ChemDraw” style
  • 2D color “ChemDraw” style
  • 3D Balls-and-Sticks style
  • 3D Balls-and-Sticks style with atom labels
  • Something else (please comment below)

0 voters

2

Since I haven’t gotten many responses on here, I also created a Twitter poll:

3

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

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I have 113 fragments so far:

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

Here are a few 2D heterocycles:

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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).