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All Projects → fogleman → Mol

fogleman / Mol

Licence: mit
Render ball-and-stick models of molecules.

Programming Languages

go
31211 projects - #10 most used programming language

mol The Molecule Renderer

Examples

Installation

go get github.com/fogleman/mol

Usage

The program parses MDL Molfiles or SDF files and generates PNGs.

mol input.sdf
mol examples/*

There are no other command line options as of yet, though one can imagine several possibilities. Output resolution, output format (SVG), camera position, animations, etc. Quality pull requests are welcome. Also, I know very little about chemistry, so if something doesn't look right, let me know!

Input Files

You can search for molecules here:

https://www.ncbi.nlm.nih.gov/pccompound/?term=benzene

Select a result and click Download > 3D Conformer > SDF.

There are also several examples in the examples folder.

How it Works

mol uses another library I created called ln. ln is a 3D vector renderer that works somewhat like a ray tracer. mol simply constructs spheres and cylinders in the right places and uses ln to render.

https://github.com/fogleman/ln

Camera Placement

The program automatically positions the camera to maximize visibility of all atoms in the molecule.

Example

The two molecules shown above are the same (testosterone). One is shown from the most optimal point of view while the other is shown from the least optimal point of view. See camera.go to see how this works. It's pretty straightforward.

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