View source for 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_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.

[[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.

==Standard spin systems==

[[allyl_pyruvate.m]] - allyl pyruvate spin system.

[[dac_reaction.m]] - Diels-Alder cycloaddition system.

[[diamond_nvm_gs.m]] - NV centre ground state spin system for diamond.

[[diamond_p1.m]] - P1 centre spin system for diamond.

[[fatty_acid.m]] - a spin system approximating a fatty acid chain.

[[strychnine.m]] - strychnine spin system.

==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.

[[bloch_sph_plot.m]] - Bloch sphere plot of a 3D trajectory with linear interpolation between points.

==Microfluidic mesh import and plotting==
[[comsol_conc.m]] - Imports ASCII 2D concentration files produced by COMSOL.

[[comsol_import.m]] - Imports COMSOL mesh and velocity data.

[[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==
[[autophase.m]] - Chebyshev autophasing of 1D NMR data

[[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

[[tikhoind.m]] - Tikhonov regularised indeterminate 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.

[[guess_csa_pro.m]] - Guesses reasonable amide bond nitrogen and carbon CSA tensors (anisotropic parts only), given the local protein geometry.

[[guess_j_nuc.m]] - Assigns J-couplings in nucleic acids from atomic coordinates using semi-empirical estimates.

[[guess_j_pro.m]] - A reasonable attempt at a function that guesses and assigns all J-couplings in a protein.

[[retrieve_file.m]] - Retrieves a file from an HTTPS link and stores it in a user-specified directory.

[[spinach2hiper.m]] - Exports phase-modulated optimal control waveforms into the format expected by Graham Smith's HiPER instrument.

''Version 2.9, authors: [[Ilya Kuprov]]''