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ChemfilesViewer

Stable Dev Build Status Coverage Twitter

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

demo

Usage

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
viewer_id = get_current_chemviewer_id()
    
# change properties
d = generate_dict_molecule(mol)
d["atoms"][1]["color"] = "#f00000"
d["atoms"][1]["label"] = "Important atom"
d["atoms"][1]["radius"] = 1.0
render_dict_molecule(d, chemviewer_id=viewer_id)

# 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;"
    )
]
render_dict_molecule!(d, options=Dict("showLabels" => true))

# change view
set_camera_position!("x", "-")
set_options!(Dict("drawingType" => "wireframe"))
set_camera_position!("c", "+")
set_options!(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)
save_image_labels("test_labels.png")
# save the overlay of the render and the labels
save_overlay("test.png", "test_labels.png", "test_both.png")

# create a nice fadeout effect
save("test_fadeout.png", fadeout_img("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: Twitter