ChemfilesViewer

A julia library to visualize chemical molecules and other structures in the Chemfiles format.

The structures can be rendered in Jupyter or in an external window (via Blink). Pluto should work if WebIO support is implemented.

Demo

Usage

```julia using ChemfilesViewer

read molecule

mol = load_moelcule("mol.sdf")

render molecule

render_molecule(mol)

render another molecule in the same window

render_molecule!(mol)

save reference to last used output

viewerid = getcurrentchemviewerid()

change properties

d = generatedictmolecule(mol) d["atoms"][1]["color"] = "#f00000" d["atoms"][1]["label"] = "Important atom" d["atoms"][1]["radius"] = 1.0 renderdictmolecule(d, chemviewerid=viewerid)

add labels

d["labels"] = [ Dict( "label" => "porphyrin", "location" => [0,0,2], "color" => "#600000" ), Dict( "label" => "pyrrole", "location" => [-0.6, 3.2, 0], "style" => "font-size:80%;opacity:0.5;" ) ] renderdictmolecule!(d, options=Dict("showLabels" => true))

change view

setcameraposition!("x", "-") setoptions!(Dict("drawingType" => "wireframe")) setcameraposition!("c", "+") setoptions!(Dict("drawingType" => "ball and stick"))

change style

set_options!(Dict("styles" => Dict( "H" => Dict("color" => "#c0c0c0", "radius" => 0.4), "N" => Dict("color" => "#241571"), "bond" => Dict("color" => "#ffffff", "radius" => 0.3) )))

clar labels (atom-labels are kept, though)

clear_labels!()

add label

add_label!(Dict( "label" => "some other text", "location" => [2,5,5], "style" => "font-weight:bold;color:blue;font-size:3em;" ))

save image

save_image("test.png")

save labels (this is somewhat experimental)

saveimagelabels("test_labels.png")

save the overlay of the render and the labels

saveoverlay("test.png", "testlabels.png", "test_both.png")

create a nice fadeout effect

save("testfadeout.png", fadeoutimg("test_both.png")) ```

Use mouse to rotate, zoom and pan. Keyboard shortcuts x, y, z set the view along the x, y and z axis. Analogously, a, b, c set the view along the unit cell vectors. Uppercase letters (X, Y, Z, A, B, C) set the opposite view direction.

Notes

The javascript rendering is based on Patrick Fuller's imolecule.

Get in touch

Please post issues, suggestions, and pull requests on github. Follow me on twitter for updates and more information about this project: