This is an R package that provides support for 3Dmol.js
as a htmlwidgets.
Important: This package is still very early in its development stages. Please give the repository a star on Github if you find the package is useful. In addition, we need your feedback to improve the package, feel free to create an issue if you have any question or feature requirement. You are more than welcome to submit a PR to make any feasible improvements.
# install.packages("devtools")
devtools::install_github("swsoyee/r3dmol")
library(r3dmol)
# Set up the initial viewer
r3dmol(
viewer_spec = m_viewer_spec(
cartoonQuality = 10,
lowerZoomLimit = 50,
upperZoomLimit = 350
),
id = "demo",
elementId = "demo"
) %>%
# Add model to scene
m_add_model(data = pdb_6zsl, format = "pdb") %>%
# Zoom to encompass the whole scene
m_zoom_to() %>%
# Set style of structures
m_set_style(style = m_style_cartoon(color = "#00cc96")) %>%
# Set style of specific selection (selecting by secondary)
m_set_style(
sel = m_sel(ss = "s"),
style = m_style_cartoon(color = "#636efa", arrows = TRUE)
) %>%
# Style the alpha helix
m_set_style(
sel = m_sel(ss = "h"), # Style alpha helix
style = m_style_cartoon(color = "#ff7f0e")
) %>%
# Rotate the scene by given angle on given axis
m_rotate(angle = 90, axis = "y") %>%
# Animate the scene by spinning it
m_spin()
xyz <- "4
* (null), Energy -1000.0000000
N 0.000005 0.019779 -0.000003 -0.157114 0.000052 -0.012746
H 0.931955 -0.364989 0.000003 1.507100 -0.601158 -0.004108
H -0.465975 -0.364992 0.807088 0.283368 0.257996 -0.583024
H -0.465979 -0.364991 -0.807088 0.392764 0.342436 0.764260
"
r3dmol(
width = 400,
height = 400,
backgroundColor = "0xeeeeee",
id = "demo_xyz",
elementId = "demo_xyz"
) %>%
m_add_model(
data = xyz,
format = "xyz",
options = list(vibrate = list(frames = 10, amplitude = 1))
) %>%
m_set_style(style = m_style_stick()) %>%
m_animate(list(loop = "backAndForth")) %>%
m_zoom_to()
benz <- "
RDKit 3D
6 6 0 0 0 0 0 0 0 0999 V2000
-0.9517 0.7811 -0.6622 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2847 1.3329 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2365 0.5518 0.3512 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9517 -0.7811 0.6644 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2847 -1.3329 0.3144 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2365 -0.5518 -0.3489 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
M END
$$$$"
r3dmol(id = "demo_sdf", elementId = "demo_sdf") %>%
m_add_model(data = benz, format = "sdf") %>%
m_set_style(style = m_style_stick()) %>%
m_set_style(
sel = m_sel(model = 0),
style = m_style_stick(colorScheme = "cyanCarbon")
) %>%
m_zoom_to()If you know some JavaScript, then you are able to write a function to
set dynamic styles. The following code shows how to color atoms based on
their positions. You can also use m_png() to convert the
widget to a png image.
r3dmol() %>%
m_add_model(data = pdb_1j72) %>%
m_set_style(style = m_style_cartoon(
colorfunc = "
function(atom) {
return atom.resi % 2 == 0 ? 'white' : 'green';
}"
)) %>%
m_zoom_to() %>%
m_png()
m1 <- r3dmol() %>%
m_add_model(data = pdb_6zsl, format = "pdb") %>%
m_zoom_to()
m2 <- m1 %>%
m_set_style(style = m_style_cartoon(color = "spectrum"))
m3 <- r3dmol() %>%
m_add_model(data = pdb_1j72, format = "pdb") %>%
m_set_style(style = m_style_stick()) %>%
m_zoom_to()
m4 <- m3 %>%
m_set_style(style = m_style_sphere())
m_grid(
viewer = list(m1, m2, m3, m4),
rows = 2,
cols = 2,
control_all = TRUE,
viewer_config = m_viewer_spec(
backgroundColor = "lightblue"
)
)3Dmol.js
Nicholas Rego, David Koes, 3Dmol.js: molecular visualization with WebGL, Bioinformatics, Volume 31, Issue 8, 15 April 2015, Pages 1322–1324,