Getting started
Installing NMRTools
Install NMRTools.jl through the Julia package manager:
using Pkg
Pkg.add("NMRTools")The examples in this tutorial also using the Plots package, which can be obtained similarly.
Plot a 1D spectrum
Let's load some example data. This can be a Bruker experiment directory, a specific pdata folder, or an NMRPipe-format file.
using NMRTools, Plots
spec = exampledata("1D_19F")┌ 5000-element NMRData{Float64, 1} ┐
├──────────────────────────────────┴───────────────────────────────────── dims ┐
↓ F1Dim Sampled{Float64} LinRange{Float64}(-119.5922, -124.16252020246354, 5000) ReverseOrdered Regular Points
├──────────────────────────────────────────────────────────────────── metadata ┤
Dict{Symbol, Any} with 18 entries:
:filename => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0…
:field => 11.7461
:label => "Example 19F 1D spectrum"
:ns => 64
:format => :pdata
:noise => 424.03
:solvent => "H2O+D2O"
:temperature => 318.151
:nuclei => Set(Nucleus[F19])
:experimentfolder => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0…
:pulseprogram => "zg"
:ndim => 1
:acqusfilename => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0…
:title => "Example 19F 1D spectrum\nSample details in second line\…
:topspin => v"3.2.0"
:date => DateTime("2017-08-07T07:08:12")
:acqus => Dict{Symbol, Any}(:fcuchan=>Dict(0=>0, 4=>0, 5=>0, 6=>0,…
:rg => 76.02
└──────────────────────────────────────────────────────────────────────────────┘
⋮ ⋱ NMRTools contains Plots recipes for common types of spectrum. To plot a 1D spectrum, use the plot command:
plot(spec)
We could zoom in on a particular region using the usual xlims arguments from Plots, but we can also select a chemical shift range from the data directly. To do this, we use square brackets [...] to access the data like an array, but use the .. selector to specify our chemical shift range:
plot(spec[-124.5 .. -123])
All plots can be saved as high quality vector graphics or png files, using the savefig command:
savefig("myspectrum.pdf")Plot a 2D spectrum
Two-dimensional spectra can be plotted in exactly the same way as for 1Ds.
spec = exampledata("2D_HN")
plot(spec)
Contour levels are set to five times the noise level. To adjust them, multiply or divide the spectrum by a scaling factor. You can also adjust the title — by default taken from the spectrum label — using the title keyword. Use an empty string (title="") to remove the title.
plot(spec / 2, title="spectrum divided by two")
Accessing your data
Spectrum data and associated axis information, metadata, etc, is encapsulated in an NMRData structure.
julia> spec = exampledata("1D_19F")┌ 5000-element NMRData{Float64, 1} ┐ ├──────────────────────────────────┴───────────────────────────────────── dims ┐ ↓ F1Dim Sampled{Float64} LinRange{Float64}(-119.5922, -124.16252020246354, 5000) ReverseOrdered Regular Points ├──────────────────────────────────────────────────────────────────── metadata ┤ Dict{Symbol, Any} with 18 entries: :filename => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :field => 11.7461 :label => "Example 19F 1D spectrum" :ns => 64 :format => :pdata :noise => 424.03 :solvent => "H2O+D2O" :temperature => 318.151 :nuclei => Set(Nucleus[F19]) :experimentfolder => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :pulseprogram => "zg" :ndim => 1 :acqusfilename => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :title => "Example 19F 1D spectrum\nSample details in second line\… :topspin => v"3.2.0" :date => DateTime("2017-08-07T07:08:12") :acqus => Dict{Symbol, Any}(:fcuchan=>Dict(0=>0, 4=>0, 5=>0, 6=>0,… :rg => 76.02 └──────────────────────────────────────────────────────────────────────────────┘ ⋮ ⋱
Data can be accessed with conventional array indexing, but also using the value-based selectors, Near and ..:
julia> spec[100:105]┌ 6-element NMRData{Float64, 1} ┐ ├───────────────────────────────┴──────────────────────────────────────── dims ┐ ↓ F1Dim Sampled{Float64} LinRange{Float64}(-119.68271044209722, -119.68728167654656, 6) ReverseOrdered Regular Points ├──────────────────────────────────────────────────────────────────── metadata ┤ Dict{Symbol, Any} with 18 entries: :filename => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :label => "Example 19F 1D spectrum" :ns => 64 :temperature => 318.151 :experimentfolder => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :pulseprogram => "zg" :ndim => 1 :acqusfilename => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :title => "Example 19F 1D spectrum\nSample details in second line\… :acqus => Dict{Symbol, Any}(:fcuchan=>Dict(0=>0, 4=>0, 5=>0, 6=>0,… :field => 11.7461 :format => :pdata :noise => 424.03 :solvent => "H2O+D2O" :nuclei => Set(Nucleus[F19]) :topspin => v"3.2.0" :date => DateTime("2017-08-07T07:08:12") :rg => 76.02 └──────────────────────────────────────────────────────────────────────────────┘ ⋮ ⋱julia> spec[Near(-124)]5808.748229980469julia> spec[-124 .. -123.5]┌ 547-element NMRData{Float64, 1} ┐ ├─────────────────────────────────┴────────────────────────────────────── dims ┐ ↓ F1Dim Sampled{Float64} LinRange{Float64}(-123.50060545419717, -123.99978425606656, 547) ReverseOrdered Regular Points ├──────────────────────────────────────────────────────────────────── metadata ┤ Dict{Symbol, Any} with 18 entries: :filename => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :label => "Example 19F 1D spectrum" :ns => 64 :temperature => 318.151 :experimentfolder => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :pulseprogram => "zg" :ndim => 1 :acqusfilename => "/home/runner/.julia/artifacts/8581f841a7ad0ab21edeb8fd0… :title => "Example 19F 1D spectrum\nSample details in second line\… :acqus => Dict{Symbol, Any}(:fcuchan=>Dict(0=>0, 4=>0, 5=>0, 6=>0,… :field => 11.7461 :format => :pdata :noise => 424.03 :solvent => "H2O+D2O" :nuclei => Set(Nucleus[F19]) :topspin => v"3.2.0" :date => DateTime("2017-08-07T07:08:12") :rg => 76.02 └──────────────────────────────────────────────────────────────────────────────┘ ⋮ ⋱
This also works for multidimensional data. For example:
julia> spec2d = exampledata("2D_HN")┌ 1216×512 NMRData{Float64, 2} ┐ ├──────────────────────────────┴───────────────────────────────────────── dims ┐ ↓ F1Dim Sampled{Float64} LinRange{Float64}(11.07119, 5.722488424064256, 1216) ReverseOrdered Regular Points, → F2Dim Sampled{Float64} LinRange{Float64}(128.9998, 107.04307400088886, 512) ReverseOrdered Regular Points ├──────────────────────────────────────────────────────────────────── metadata ┤ Dict{Symbol, Any} with 19 entries: :rg => 203 :filename => "/home/runner/.julia/artifacts/278430abd2b28a265273e7074… :field => 14.0967 :label => "13C,15N ubiquitin" :ns => 2 :format => :pdata :noise => 502.842 :solvent => "H2O+D2O" :temperature => 276.999 :nuclei => Set(Nucleus[H1, N15]) :experimentfolder => "/home/runner/.julia/artifacts/278430abd2b28a265273e7074… :pulseprogram => "sfhmqcf3gpph.cw" :ndim => 2 :acqusfilename => "/home/runner/.julia/artifacts/278430abd2b28a265273e7074… :title => "13C,15N ubiquitin\n500 uM in 10% D2O, 20 mM Pi pH 6.5, … :topspin => v"6.0.0" :acqu2s => Dict{Symbol, Any}(:origin=>nothing, :sw=>21.9971, :sw_h=… :acqus => Dict{Symbol, Any}(:fcuchan=>Dict(0=>0, 4=>0, 5=>0, 6=>0,… :date => DateTime("2019-11-20T19:41:09") └──────────────────────────────────────────────────────────────────────────────┘ ⋮ ⋱julia> spec2d[8.1 .. 8.3, Near(124)]┌ 45-element NMRData{Float64, 1} ┐ ├────────────────────────────────┴─────────────────────────────────────── dims ┐ ↓ F1Dim Sampled{Float64} LinRange{Float64}(8.297789182848133, 8.10409134799943, 45) ReverseOrdered Regular Points ├──────────────────────────────────────────────────────────────────── metadata ┤ Dict{Symbol, Any} with 19 entries: :filename => "/home/runner/.julia/artifacts/278430abd2b28a265273e7074… :label => "13C,15N ubiquitin" :ns => 2 :temperature => 276.999 :experimentfolder => "/home/runner/.julia/artifacts/278430abd2b28a265273e7074… :pulseprogram => "sfhmqcf3gpph.cw" :ndim => 2 :acqusfilename => "/home/runner/.julia/artifacts/278430abd2b28a265273e7074… :title => "13C,15N ubiquitin\n500 uM in 10% D2O, 20 mM Pi pH 6.5, … :acqus => Dict{Symbol, Any}(:fcuchan=>Dict(0=>0, 4=>0, 5=>0, 6=>0,… :field => 14.0967 :format => :pdata :noise => 502.842 :solvent => "H2O+D2O" :nuclei => Set(Nucleus[H1, N15]) :topspin => v"6.0.0" :acqu2s => Dict{Symbol, Any}(:origin=>nothing, :sw=>21.9971, :sw_h=… :date => DateTime("2019-11-20T19:41:09") :rg => 203 └──────────────────────────────────────────────────────────────────────────────┘ ⋮ ⋱
A plain array of data for the spectrum can be obtained from this using the data command:
julia> data(spec)5000-element Vector{Float64}: 4671.5184326171875 4675.192687988281 4679.9979248046875 4685.8551025390625 4692.506896972656 4699.526428222656 4706.362731933594 4712.417419433594 4717.134460449219 4720.0810546875 ⋮ 5900.0340576171875 5896.165588378906 5891.2984619140625 5885.714294433594 5879.7239990234375 5873.638427734375 5867.738952636719 5862.253173828125 5857.3370361328125
Similarly, a plain vector containing axis values can be obtained from this using the data command, passing an additional argument to specify the dimension. This can either be a number or the axis type, e.g. F1Dim:
julia> data(spec, 1)5000-element LinRange{Float64, Int64}: -119.592, -119.593, -119.594, -119.595, …, -124.161, -124.162, -124.163