Difference between revisions of "Import, export, and visualisation"
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;[[c2spinach.m]] | ;[[c2spinach.m]] | ||
:Reads CASTEP .magres files. | :Reads CASTEP .magres files. | ||
| − | |||
;[[cyprinol.m]] | ;[[cyprinol.m]] | ||
:Returns Spinach input structures for the spin system of cyprinol. | :Returns Spinach input structures for the spin system of cyprinol. | ||
| − | |||
;[[fatty_acid.m]] | ;[[fatty_acid.m]] | ||
:A reasonable approximation to a fatty acid spin system. | :A reasonable approximation to a fatty acid spin system. | ||
| − | |||
;[[gissmo2spinach.m]] | ;[[gissmo2spinach.m]] | ||
:Reads GISSMO XML files. | :Reads GISSMO XML files. | ||
| − | |||
;[[gparse.m]] | ;[[gparse.m]] | ||
:A parser for Gaussian03 and Gaussian09 calculation logs. | :A parser for Gaussian03 and Gaussian09 calculation logs. | ||
| − | |||
;[[g2spinach.m]] | ;[[g2spinach.m]] | ||
:Converts [[gparse.m]] output into ''Spinach'' input structures. | :Converts [[gparse.m]] output into ''Spinach'' input structures. | ||
| − | |||
;[[karplus_fit.m]] | ;[[karplus_fit.m]] | ||
:Performs Karplus coefficient estimation from a Gaussian J-coupling scan. | :Performs Karplus coefficient estimation from a Gaussian J-coupling scan. | ||
| − | |||
;[[killcross.m]] | ;[[killcross.m]] | ||
:Zeroes the specified rows and columns of a matrix. | :Zeroes the specified rows and columns of a matrix. | ||
| − | |||
;[[killdiag.m]] | ;[[killdiag.m]] | ||
:Zeroes out the diagonal of a 2D spectrum. | :Zeroes out the diagonal of a 2D spectrum. | ||
| − | |||
;[[methyl_group.m]] | ;[[methyl_group.m]] | ||
:Coordinates for the four atoms of a methyl group. | :Coordinates for the four atoms of a methyl group. | ||
| − | |||
;[[nuclacid.m]] | ;[[nuclacid.m]] | ||
:Nucleic acid data import from PDB and BMRB data. | :Nucleic acid data import from PDB and BMRB data. | ||
| − | |||
;[[oparse.m]] | ;[[oparse.m]] | ||
:A parser for ORCA logs. | :A parser for ORCA logs. | ||
| − | |||
;[[ocparse.m]] | ;[[ocparse.m]] | ||
:A parser for ORCA cubes. | :A parser for ORCA cubes. | ||
| − | |||
;[[parsexml.m]] | ;[[parsexml.m]] | ||
:Converts an XML file into a Matlab structure. | :Converts an XML file into a Matlab structure. | ||
| − | |||
;[[protein.m]] | ;[[protein.m]] | ||
:Protein data import from PDB and BMRB data. | :Protein data import from PDB and BMRB data. | ||
| − | |||
;[[read_jeol_phase_cycle.m]] | ;[[read_jeol_phase_cycle.m]] | ||
:Parses JEOL phase cycle specification. | :Parses JEOL phase cycle specification. | ||
| − | |||
;[[read_pdb_nuc.m]] | ;[[read_pdb_nuc.m]] | ||
:Reads PDB data for nucleic acids. | :Reads PDB data for nucleic acids. | ||
| − | |||
;[[read_pdb_pro.m]] | ;[[read_pdb_pro.m]] | ||
:Reads PDB data for proteins. | :Reads PDB data for proteins. | ||
| − | |||
;[[read_bmrb.m]] | ;[[read_bmrb.m]] | ||
:Reads BMRB data for proteins. | :Reads BMRB data for proteins. | ||
| − | |||
;[[s2spinach.m]] | ;[[s2spinach.m]] | ||
:Reads SIMPSON spin system specification and converts it into Spinach format. | :Reads SIMPSON spin system specification and converts it into Spinach format. | ||
| − | |||
;[[strychnine.m]] | ;[[strychnine.m]] | ||
:Returns Spinach input structures for the spin system of strychnine. | :Returns Spinach input structures for the spin system of strychnine. | ||
| − | |||
;[[v2spinach.m]] | ;[[v2spinach.m]] | ||
:Varian NMR data import. | :Varian NMR data import. | ||
| − | |||
;[[weblab2nqi.m]] | ;[[weblab2nqi.m]] | ||
:Converts the Weblab one-cone model parameters into NQI tensors used by Spinach. | :Converts the Weblab one-cone model parameters into NQI tensors used by Spinach. | ||
| − | |||
;[[x2spinach.m]] | ;[[x2spinach.m]] | ||
:Reads SpinXML files and forms Spinach data structures. | :Reads SpinXML files and forms Spinach data structures. | ||
Revision as of 15:54, 28 June 2021
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.
Contents
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.
- 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.
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
