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.

merge_inp.m - Merges multiple sys and inter structures into one.

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.

stack_2d.m - Stack plotting utility for 2D NMR 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

comsol_conc.m - Imports ASCII 2D concentration files produced by COMSOL.

comsol_mesh.m - Imports ASCII 2D mesh files produced by COMSOL.

comsol_velo.m - Imports ASCII 2D flow velocity files produced by COMSOL.

conc_plot.m - 2D microfluidic concentration plotting function.

mesh_crop.m - 2D microfluidic mesh cropping.

mesh_inact.m - Marks 2D microfluidic mesh vertices as inactive.

mesh_vorn.m - Voronoi tessellation of a microfluidic mesh.

mesh_plot.m - 2D microfluidic mesh plotting function.

mesh_preplot.m - 2D microfluidic mesh preprocessing for drawing.

Miscellaneous data processing

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

lpredict.m - forward linear prediction.

tikhonov.m - Tikhonov regularised positive solution to K*x=y

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 2.8, authors: Ilya Kuprov