Skip to main content

graphics3d - Using ChemicalData to make molecule graphics


I would like to take the acetone ((CH3)2CO) and chloroform (HCCl3) molecules that Mathematica's chemical data provides, and plot them together. I want to show how chloroform can hydrogen bond to acetone. Right now I have them plotted on top of each other :/


Show[ChemicalData["Chloroform", "MoleculePlot"], 
ChemicalData["Acetone", "MoleculePlot"]]

acetone and chloroform




Answer



A quick way of showing how the two structures can be positioned relative to each other in a single Graphics3D is as follows:


With[{rMax = 500},
Manipulate[
Graphics3D[
{First@ChemicalData["Acetone", "MoleculePlot"],
GeometricTransformation[
First@ChemicalData["Chloroform", "MoleculePlot"],
Composition[
TranslationTransform[{displacementX, displacementY,

displacementZ}],
RotationTransform[
rotationAngle, {Cos[axisAzimuth] Sin[axisPolar],
Sin[axisAzimuth] Sin[axisPolar], Cos[axisPolar]}]]]},
PlotRange -> {{-rMax, rMax}, {-rMax, rMax}, {-rMax, rMax}}
],
{{displacementX, 0}, -rMax, rMax}, {{displacementY, 0}, -rMax,
rMax}, {{displacementZ, 0}, -rMax, rMax}, {rotationAngle, 0,
2 Pi},
{axisPolar, 0, 2 Pi}, {axisAzimuth, 0, 2 Pi}

]
]

manipulate


The Manipulate is just to let you do some manual re-positioning. You can eventually get better results by doing pre-calculated shifts and rotations based on the exact locations of the atoms. But I'm focusing here on the basic ingredients. For the display, this involves mainly the use of First to extract the contents of the Graphics3D of the molecule, then the translation and rotation using GeometricTransformation with a Composition of the former two operations.


The variable rMax sets the plot range and the maximum displacement of the chloroform molecule relative to the acetone.


Comments

Popular posts from this blog

functions - Get leading series expansion term?

Given a function f[x] , I would like to have a function leadingSeries that returns just the leading term in the series around x=0 . For example: leadingSeries[(1/x + 2)/(4 + 1/x^2 + x)] x and leadingSeries[(1/x + 2 + (1 - 1/x^3)/4)/(4 + x)] -(1/(16 x^3)) Is there such a function in Mathematica? Or maybe one can implement it efficiently? EDIT I finally went with the following implementation, based on Carl Woll 's answer: lds[ex_,x_]:=( (ex/.x->(x+O[x]^2))/.SeriesData[U_,Z_,L_List,Mi_,Ma_,De_]:>SeriesData[U,Z,{L[[1]]},Mi,Mi+1,De]//Quiet//Normal) The advantage is, that this one also properly works with functions whose leading term is a constant: lds[Exp[x],x] 1 Answer Update 1 Updated to eliminate SeriesData and to not return additional terms Perhaps you could use: leadingSeries[expr_, x_] := Normal[expr /. x->(x+O[x]^2) /. a_List :> Take[a, 1]] Then for your examples: leadingSeries[(1/x + 2)/(4 + 1/x^2 + x), x] leadingSeries[Exp[x], x] leadingSeries[(1/x + 2 + (1 - 1/x...

mathematical optimization - Minimizing using indices, error: Part::pkspec1: The expression cannot be used as a part specification

I want to use Minimize where the variables to minimize are indices pointing into an array. Here a MWE that hopefully shows what my problem is. vars = u@# & /@ Range[3]; cons = Flatten@ { Table[(u[j] != #) & /@ vars[[j + 1 ;; -1]], {j, 1, 3 - 1}], 1 vec1 = {1, 2, 3}; vec2 = {1, 2, 3}; Minimize[{Total@((vec1[[#]] - vec2[[u[#]]])^2 & /@ Range[1, 3]), cons}, vars, Integers] The error I get: Part::pkspec1: The expression u[1] cannot be used as a part specification. >> Answer Ok, it seems that one can get around Mathematica trying to evaluate vec2[[u[1]]] too early by using the function Indexed[vec2,u[1]] . The working MWE would then look like the following: vars = u@# & /@ Range[3]; cons = Flatten@{ Table[(u[j] != #) & /@ vars[[j + 1 ;; -1]], {j, 1, 3 - 1}], 1 vec1 = {1, 2, 3}; vec2 = {1, 2, 3}; NMinimize[ {Total@((vec1[[#]] - Indexed[vec2, u[#]])^2 & /@ R...

plotting - Plot 4D data with color as 4th dimension

I have a list of 4D data (x position, y position, amplitude, wavelength). I want to plot x, y, and amplitude on a 3D plot and have the color of the points correspond to the wavelength. I have seen many examples using functions to define color but my wavelength cannot be expressed by an analytic function. Is there a simple way to do this? Answer Here a another possible way to visualize 4D data: data = Flatten[Table[{x, y, x^2 + y^2, Sin[x - y]}, {x, -Pi, Pi,Pi/10}, {y,-Pi,Pi, Pi/10}], 1]; You can use the function Point along with VertexColors . Now the points are places using the first three elements and the color is determined by the fourth. In this case I used Hue, but you can use whatever you prefer. Graphics3D[ Point[data[[All, 1 ;; 3]], VertexColors -> Hue /@ data[[All, 4]]], Axes -> True, BoxRatios -> {1, 1, 1/GoldenRatio}]