I have two dataframes, shown below, which represent a molecule. I want to produce a plot of this molecule with plot_ly.
One dataframe, df, contains coordinates and element type.
The other dataframe, conn, contains connection structure between the atoms, and the number of bonds, (1, 2, or 3), which connect two atoms.
For example, from row two of conn, atom 55 connects to atom 54 with a double bond.
head(df)
atomId element xCord yCord zCord
1 54 C -16.47474 -14.96508 8.332247
2 55 C -15.43503 -14.37500 7.599300
3 56 C -15.03843 -13.23943 8.285489
4 57 C -15.82452 -13.17686 9.413819
5 58 N -16.68804 -14.21907 9.439404
6 59 H -17.41647 -14.37430 10.166242
head(conn)
atom1 atom2 order
135 58 54 1
136 55 54 2
137 71 55 1
138 70 56 1
139 55 56 1
140 58 57 1
df <- structure(list(atomId = c("54", "55", "56", "57", "58", "59",
"69", "70", "71"), element = c("C", "C", "C", "C", "N", "H",
"H", "H", "H"), xCord = c(-16.474736, -15.43503, -15.038428,
-15.82452, -16.68804, -17.416475, -15.788173, -14.29002, -15.038094
), yCord = c(-14.965081, -14.375, -13.239429, -13.176858, -14.219065,
-14.374302, -12.380838, -12.509718, -14.671816), zCord = c(8.332247,
7.5993, 8.285489, 9.413819, 9.439404, 10.166242, 10.151304, 7.979794,
6.636516)), class = "data.frame", row.names = c(NA, -9L))
conn <- structure(list(atom1 = c(58, 55, 71, 70, 55, 58, 56, 69, 59),
atom2 = c(54, 54, 55, 56, 56, 57, 57, 57, 58), order = c(1,
2, 1, 1, 1, 1, 2, 1, 1)), row.names = 135:143, class = "data.frame")
I want to plot this molecule in R. I was able to make a 3D scatter plot, but I am having a hard time plotting the bonds.
plot_ly(x = df$xCord, y = df$yCord, z = df$zCord, type="scatter3d",
mode="markers", color = df$element, hoverinfo = "text",
text = paste('AtomId: ', df$atomId, "\nElement: ", df$element)
I really like this plot because it is interactive, and I can annotate the points. However, I would like to draw lines between the connections. I would like to show bond lines, such as in this image, however, I actually prefer the dots in plotly instead of giant ugly 3D spheres, as in the second picture.
Can anyone help me represent the bond lines in Plotly, or some other comparable package? Worst case I understand if they have to be color coded, or encoded with dashed/solid lines, ect. Id prefer to see double lines for a double bond, but will take what I can get.
Thanks!