Import, export, and visualisation

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Spinach is not intended to be a data processing package. The functions listed below assist in importing simulation settings and exporting simulation results into formats that are readable to data processing software.

Tensor visualisation

cst_display.m – visualizes chemical shielding tensors and their eigensystems.

hfc_display.m – visualizes hyperfine coupling tensors and their eigensystems.

Data import

c2spinach.m - reads CASTEP .magres files.

cyprinol.m – returns Spinach input structures for the spin system of cyprinol.

fatty_acid.m - a reasonable approximation to a fatty acid spin system.

gissmo2spinach.m - reads GISSMO XML files.

gparse.m – a parser for Gaussian03 and Gaussian09 calculation logs.

g2spinach.m – converts gparse.m output into Spinach input structures.

karplus_fit.m – performs Karplus coefficient estimation from a Gaussian J-coupling scan.

killcross.m - zeroes the specified rows and columns of a matrix.

killdiag.m - zeroes out the diagonal of a 2D spectrum.

methyl_group.m - coordinates for the four atoms of a methyl group.

nuclacid.m - nucleic acid data import from PDB and BMRB data.

oparse.m - a parser for ORCA logs.

ocparse.m - a parser for ORCA cubes.

parsexml.m - converts an XML file into a Matlab structure.

protein.m – protein data import from PDB and BMRB data.

read_jeol_phase_cycle.m - parses JEOL phase cycle specification.

read_pdb_nuc.m - reads PDB data for nucleic acids.

read_pdb_pro.m - reads PDB data for proteins.

read_bmrb.m - reads BMRB data for proteins.

s2spinach.m – reads SIMPSON spin system specification and converts it into Spinach format.

strychnine.m – returns Spinach input structures for the spin system of strychnine.

v2spinach.m - Varian NMR data import.

x2spinach.m - reads SpinXML files and forms Spinach data structures.

Data export and plotting

axis_1d.m - axis ticks for plotting 1D spectra.

bwr_cmap.m - blue-white-red colour map with white at zero.

crop_2d.m - Crops 2D spectra to user-specified ranges.

cylgrid.m - cylindrical axis system.

fid2ascii.m – writes out 1D, 2D and 3D free induction decays generated by Spinach as ASCII files.

int_2d.m – 2D spectral integration utility.

molplot.m – stick plots of molecules.

mri_2d_plot.m - MRI image plotting with a black-and-white colour map.

plot_1d.m – 1D spectral plotting utility.

plot_2d.m – 2D spectral plotting utility.

plot_3d.m – 3D spectral plotting utility.

plot_uf.m - 2D ultrafast spectra plotting utility.

s2json.m - writes out JSON files that can be read by MestreNova.

scale_figure.m - Scales the current figure.

slice_2d.m – displays slices of 2D spectra.

volplot.m – volumetric ploting.

write_movie.m - rotation movies for 3D plots.

zoom_3d.m - zooming into 3D data cubes.

Pulse sequence import

jeol.m - parses and simulates 1D and 2D JEOL pulse sequences.

read_jeol_parameters.m - parameter import from JEOL pulse sequence files.

read_jeol_sequence.m - pulse sequence import from JEOL pulse sequence files.

translate_jeol_parameters.m - JEOL to Spinach parameter translation.

translate_jeol_phase_cycle.m - returns operators for a JEOL phase cycle.

translate_jeol_sequence.m - JEOL to Spinach pulse sequence translation.

Artefact removal

destreak.m – reduces streak artefacts in 2D and 3D NMR spectra.

External calls and interfaces

bootstrap.m - creates an empty spin_system structure that allows many Spinach functions to be used externally.

py_run.m - Bruker Xepr python script execution.

awg_interface.m - Bruker SpinJet AWG interface.

Version 2.5, authors: Ilya Kuprov