Import, export, and visualisation

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.

Interaction visualisation

cst_display.m – chemical shielding tensors and their eigensystems.

efg_display.m - electric field gradient tensors and their eigensystems.

hfc_display.m – 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.

weblab2nqi.m

Converts the Weblab one-cone model parameters into NQI tensors used by Spinach.

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.

Microfluidic mesh import and plotting

mesh_vorn.m - Voronoi tessellation of a microfluidic mesh.

mesh_plot.m - 2D microfluidic mesh plotting function.

Miscellaneous data processing

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

lpredict.m - forward linear prediction.

External calls and interfaces

awg_interface.m - Bruker SpinJet AWG interface.

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

gslice.m - Gaussian geometry scan log slicing

py_run.m - Bruker Xepr python script execution.

Version 2.5, authors: Ilya Kuprov