Installation

Note

This is a package written in Julia. We invite you to experiment with the language, but if you want to just call this package from Python, read the From Python section of the manual. Understanding all the features of the package requires reading the manual as whole. The syntaxes of using this package from Julia or Python are almost identical, and the motivation for using Python should be mostly the familiarity with further analysis tools, as the plotting packages.

Install Julia

First you need to install the Julia language, version 1.9 or greater is required. Using the juliaup tool is a highly recommended way of installing and keeping Julia up to date.

Alternatively, you can install Julia by downloading the binaries directly from the Julia webpage.

Note

New to Julia? Julia is a modern high-level yet performant programming language. Some tips and a nice workflow for using it effectively can be found here.

For this specific package, following a the step-by-step examples provided here after installing Julia should be enough.

Install the packages

Within Julia, to install the packages required for running the examples here you need to do:

julia> import Pkg

julia> Pkg.add(["ComplexMixtures", "PBTools", "Plots", "EasyFit", "LaTeXStrings"])

Here, PDBTools.jl is an auxiliary package to read PDB files and select atoms within them. The Plots, EasyFit and LaTeXStrings packages will help producing nice looking plots.

Please read the recommended workflow below, for further information and to be sure to have a smoother experience.

Recommended workflow for reproducibility

Create an environment

Once Julia is installed, we recommend to create an environment that will contain all the packages you may use for your analyses, including ComplexMixtures, in such a way that your results can always be reproduced and you don't get any version incompatibility.

We illustrate this by creating the "MyNewPaper" environment, which will be hosted in a simple directory,

mkdir /home/user/Documents/MyNewPaper

Then, start Julia and activate the environment that will be hosted there:

julia> import Pkg; Pkg.activate("/home/user/Documents/MyNewPaper")
  Activating new project at `~/Documents/MyNewPaper`

and add to this environment the packages that your analyses will require:

julia> import Pkg; Pkg.add(["ComplexMixtures","PDBTools","Plots", "EasyFit", "LaTeXStrings"])

That's it. Close Julia. Note that this created the files Manifest.toml and Project.toml in the MyNewPaper directory, which contain the information of packages and exact package versions you are using now on in this environment. Saving these files may be relevant for the future exact reproduction of your analyses.

Run your analysis scripts in that environment

Now, your analysis scripts, described in the next section in details, will look like:

import Pkg; Pkg.activate("/home/user/Documents/MyNewPaper")

using ComplexMixtures
using PDBTools
using Plots
using EasyFit
using LaTeXStrings

# etc ...

And the script can be run with julia -t auto script.jl (where -t auto allows for multi-threading), or included in julia with julia> include("./scritp.jl"), as described in the next section.

Tip

By loading the package with

using ComplexMixtures

the most common functions of the package become readily available by their direct name, for example mddf(...).

If you don't want to bring the functions into the scope of your script, use

import ComplexMixtures

Then, the functions of the package are called, for example, using ComplexMixtures.mddf(...). To avoid having to write ComplexMixtures all the time, define an acronym. For example:

import ComplexMixtures as CM
CM.mddf(...)