pyNMR is a python module to import and analyze NMR data as generated by Bruker, TecMag, Magritek and Chemagnetics Consoles.
The module also provides basic processing routines.
offsetCorrection() - zeros the mean of the real and imaginary FID data
lineBroadening() - applies exponential linebroadening
fourierTransform() - complex fourier Transform
phase() - zero-order phase correction
autoPhase(0) - retunrs the zero-order phase that maximizes the real part of the spectrum in a specified frequency range
phaseFirstOrder() - first order phase correction
leftShift() - remove specified nubmer of points from beginning of the fid
zeroFilling() - fills the fid with zeros up to the specified number
getJoinedPartialSpectra() - concatenates spectral ranges from a 2D dataset (for plotting)
getPartialSpectrum() - returns part of the spectrum
integrateRealPart() - returns the integral of the real part over a specfied frequency range
integrateAllRealPart() - returns the integrals for all the spectra in a 2D dataset
getPeak() - get the maximum value of a spectrum
getCenterFrequency() - calculate the first moment of a spectrum in a specified range
getIndexFromFrequency() - get the index of a specified frequency from the frequency axis
getIndexFromPPM() - the same, but for a specified PPM value
getIndices() - get indices as above, but for an interval. scale may be specified as Hz or ppm
checkToPos() - internal function to create a position in .allFid
getPPMScale() - get PPM scale by specifying a reference frequeny and according shift value
export() - export ascii data
It provides a few basic routines for Fourier Transform. It is typically used in a IPython Notebook to interactively analyze NMR Data.
The data are stored in the allFid array. After import, the first FID of a 2D dataset (or the FID of a 1D dataset) is stored in nmrData.allFid
When processing nmrData, the new data maybe stored at a position incremented by 1, using the `fromPos` and `toPos` attributes of the various functions.
A typical set of processing commands is
import nmrDataMod as ndm data = ndm.nmrData(pathToData, "TopSpin") data.leftShift(0, 1, 70) data.lineBroadening(1, 2, 5) data.fourierTransform(2, 3) data.phase(3, 4, 45, degree = True)
Various functions exist to set a chemical shift scale or calculate integrals for all spectra in a 2D dataset.
The modules listed below provide some NMR related utiliy functions.
gammaList.py provides a table with the gamma values of the various nuclei.
fitMod.py may be used to fit nmr data interactively and includes simple models to fit data from a few very basic NMR experiments.
fwhm.py allows to calculate the full with at half maximum of a spectrum
polarization.py provides a routine to calculate thermal polarization as function of nucleus, field and temperature.
nutation.py implements a formula to estimate the π/2 pulse by specifying coil volume, circuit Q, Larmor frequency and RF power.