Difference between revisions of "Import, export, and visualisation"

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(removed index entry for deleted function bloch_sph_plot.m (removed per IK instruction 2026-08-30))
 
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==Data import==
 
==Data import==
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[[b2spinach.m]] - Bruker NMR data import.
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[[c2spinach.m]] - Reads CASTEP .magres files.
 
[[c2spinach.m]] - Reads CASTEP .magres files.
  
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[[methyl_group.m]] - Coordinates for the four atoms of a methyl group.
 
[[methyl_group.m]] - Coordinates for the four atoms of a methyl group.
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[[merge_inp.m]] - Merges multiple sys and inter structures into one.
  
 
[[nuclacid.m]] - Nucleic acid data import from PDB and BMRB data.
 
[[nuclacid.m]] - Nucleic acid data import from PDB and BMRB data.
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[[protein.m]] - Protein data import from PDB and BMRB data.
 
[[protein.m]] - Protein data import from PDB and BMRB data.
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[[read_jeol_phase_cycle.m]] - Parses JEOL phase cycle specification.
 
  
 
[[read_pdb_nuc.m]] - Reads PDB data for nucleic acids.
 
[[read_pdb_nuc.m]] - Reads PDB data for nucleic acids.
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[[read_bmrb.m]] - Reads BMRB data for proteins.
 
[[read_bmrb.m]] - Reads BMRB data for proteins.
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[[s2spinach.m]] - Reads SIMPSON spin system specification and converts it into Spinach format.
 
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[[strychnine.m]] - Returns Spinach input structures for the spin system of strychnine.
 
  
 
[[v2spinach.m]] - Varian NMR data import.
 
[[v2spinach.m]] - Varian NMR data import.
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[[x2spinach.m]] - Reads SpinXML files and forms Spinach data structures.
 
[[x2spinach.m]] - Reads SpinXML files and forms Spinach data structures.
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==Standard spin systems==
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[[allyl_pyruvate.m]] - allyl pyruvate spin system.
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[[dac_reaction.m]] - Diels-Alder cycloaddition system.
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[[diamond_co.m]] - cobalt-related defect spin system for diamond.
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[[diamond_gev0.m]] - GeV0 spin system for diamond.
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[[diamond_n2vm.m]] - N2V- spin system for diamond.
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[[diamond_n_inter.m]] - nitrogen interstitial spin system for diamond.
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[[diamond_ni.m]] - nickel-related defect spin system for diamond.
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[[diamond_nv0_es.m]] - NV0 excited-state spin system for diamond.
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[[diamond_nvm_gs.m]] - NV centre ground state spin system for diamond.
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[[diamond_ov0.m]] - neutral oxygen-vacancy centre ground state spin system for diamond.
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[[diamond_p.m]] - phosphorus-related defect spin system for diamond.
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[[diamond_p1.m]] - P1 centre spin system for diamond.
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[[diamond_p1_13c.m]] - P1 centre spin system with 13C neighbours in diamond.
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[[diamond_r2.m]] - R2 self-interstitial spin system for diamond.
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[[diamond_siv0.m]] - SiV0 spin system for diamond.
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[[diamond_ti.m]] - titanium-related defect spin system for diamond.
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[[diamond_vacancy.m]] - vacancy-family defect spin systems for diamond.
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[[fatty_acid.m]] - a spin system approximating a fatty acid chain.
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[[lactate.m]] - 13C-labelled lactate spin system.
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[[strychnine.m]] - strychnine spin system.
  
 
==Data export and plotting==
 
==Data export and plotting==
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[[fid2ascii.m]] – writes out 1D, 2D and 3D free induction decays generated by Spinach as ASCII files.
 
[[fid2ascii.m]] – writes out 1D, 2D and 3D free induction decays generated by Spinach as ASCII files.
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[[fid2pipe.m]] – exports phase-sensitive 2D free induction decays into native NMRPipe time-domain files.
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[[fig2tiles.m]] - combines Matlab figure files into a single tiled figure.
  
 
[[int_2d.m]] – 2D spectral integration utility.
 
[[int_2d.m]] – 2D spectral integration utility.
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[[zoom_3d.m]] - zooming into 3D data cubes.
 
[[zoom_3d.m]] - zooming into 3D data cubes.
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==Pulse sequence import==
 
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[[jeol.m]] - parses and simulates 1D and 2D JEOL pulse sequences.
 
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[[read_jeol_parameters.m]] - parameter import from JEOL pulse sequence files.
 
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[[read_jeol_sequence.m]] - pulse sequence import from JEOL pulse sequence files.
 
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[[translate_jeol_parameters.m]] - JEOL to Spinach parameter translation.
 
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[[translate_jeol_phase_cycle.m]] - returns operators for a JEOL phase cycle.
 
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[[translate_jeol_sequence.m]] - JEOL to Spinach pulse sequence translation.
 
  
 
==Microfluidic mesh import and plotting==
 
==Microfluidic mesh import and plotting==
 
[[comsol_conc.m]] - Imports ASCII 2D concentration files produced by COMSOL.
 
[[comsol_conc.m]] - Imports ASCII 2D concentration files produced by COMSOL.
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[[comsol_import.m]] - Imports COMSOL mesh and velocity data.
  
 
[[comsol_mesh.m]] - Imports ASCII 2D mesh files produced by COMSOL.
 
[[comsol_mesh.m]] - Imports ASCII 2D mesh files produced by COMSOL.
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[[mesh_plot.m]] - 2D microfluidic mesh plotting function.
 
[[mesh_plot.m]] - 2D microfluidic mesh plotting function.
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[[mesh_preplot.m]] - 2D microfluidic mesh preprocessing for drawing.
  
 
==Miscellaneous data processing==
 
==Miscellaneous data processing==
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[[autophase.m]] - Chebyshev autophasing of 1D NMR data
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[[destreak.m]] - reduces streak artefacts in 2D and 3D NMR spectra.
 
[[destreak.m]] - reduces streak artefacts in 2D and 3D NMR spectra.
  
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[[tikhonov.m]] - Tikhonov regularised positive solution to K*x=y
 
[[tikhonov.m]] - Tikhonov regularised positive solution to K*x=y
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[[tikhoind.m]] - Tikhonov regularised indeterminate solution to K*x=y
  
 
==External calls and interfaces==
 
==External calls and interfaces==
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[[py_run.m]] - Bruker Xepr python script execution.
 
[[py_run.m]] - Bruker Xepr python script execution.
  
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[[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.
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[[guess_j_pro.m]] - A reasonable attempt at a function that guesses and assigns all J-couplings in a protein.
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[[retrieve_file.m]] - Retrieves a file from an HTTPS link and stores it in a user-specified directory.
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[[spinach2hiper.m]] - Exports phase-modulated optimal control waveforms into the format expected by Graham Smith's HiPER instrument.
  
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''Version 2.8, authors: [[Ilya Kuprov]]''
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''Version 2.9, authors: [[Ilya Kuprov]]''

Latest revision as of 10:10, 30 August 2026

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

b2spinach.m - Bruker NMR 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_co.m - cobalt-related defect spin system for diamond.

diamond_gev0.m - GeV0 spin system for diamond.

diamond_n2vm.m - N2V- spin system for diamond.

diamond_n_inter.m - nitrogen interstitial spin system for diamond.

diamond_ni.m - nickel-related defect spin system for diamond.

diamond_nv0_es.m - NV0 excited-state spin system for diamond.

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

diamond_ov0.m - neutral oxygen-vacancy centre ground state spin system for diamond.

diamond_p.m - phosphorus-related defect spin system for diamond.

diamond_p1.m - P1 centre spin system for diamond.

diamond_p1_13c.m - P1 centre spin system with 13C neighbours in diamond.

diamond_r2.m - R2 self-interstitial spin system for diamond.

diamond_siv0.m - SiV0 spin system for diamond.

diamond_ti.m - titanium-related defect spin system for diamond.

diamond_vacancy.m - vacancy-family defect spin systems for diamond.

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

lactate.m - 13C-labelled lactate spin system.

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.

fid2pipe.m – exports phase-sensitive 2D free induction decays into native NMRPipe time-domain files.

fig2tiles.m - combines Matlab figure files into a single tiled figure.

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.

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

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