NMR Spectra generation through
the use of spin matrices.
- Clone repository
git clone https://github.com/PhiMykah/spingen- Install through pip
cd spingen
pip install -e .Spingen can be run in command-line mode or in scripts.
usage: spingen [-h] [-help] -in File Path [-fs Value (MHZ)] [-pts Value]
[-sw Value] [-obs Value] [-sc Values] [-d [{time,t,f,freq}]]
[-out File Path] [-fmt ] [-convert NMR File]
Insert description here
options:
-h, --help show this help message and exit
-help
-in File Path, --input File Path
Input XML file for spin matrix
-fs Value (MHZ), --field-strength Value (MHZ)
NMR instrument field strength for conversions
-pts Value, --points Value
NMR resolution by number of points
-sw Value, --spec-width Value
Spectral width of NMR data
-obs Value, --obs-freq Value
Observation fequency value
-sc Values, --sub-count Values
Number of independent subset spin matrices
-d [{time,t,f,freq}], --domain [{time,t,f,freq}]
Data output domain type
-out File Path, -output File Path
Designated output file location
-fmt [], -format [] Designated output file format
-convert NMR File NMRPipe format file to convert to ppm
import spingen as sg
synth_peaks = sg.get_peaksXML(input, system_count, field_strength, points, spec_width, obs_freq)
# ----------
# Or
# ----------
systems, line_widths = sg.loadSystems(xmlfile, system_count)
synth_peaks = sg.get_peaks(systems, line_widths, system_count, field_strength, points, spec_width, obs_freq)
real_peaks = sg.convert(nmr_file)loadSystems() returns a list of system objects which hold relevant data for generating a system.
"""
class system
============
system object with attributes describing spin matrix system
Parameters
----------
names : list[str]
list of proton names
cshifts : list[Hz]
list of chemical shifts per proton
cmat : ndarray
coupling matrix
center : ppm
center value for measurement
"""
newSystem = system(names, cshifts, cmat, center)
proton_names = system.names
chem_shifts = system.cshifts
coupling_matrix = system.cmat
center_value = system.centerget_peaksXML()
Obtain an x,y peaks array from an xml file with given parameters
Parameters
----------
input : str
imput xml file path as a string
system_count : int, optional
Number of submatrices in the system, by default 0
field_strength : Hz, optional
Field strength of measurement device, by default 500
points : int, optional
Number of points to sample, does not affect peaks but increases resolution, by default 1000
spec_width : float, optional
Spectral width of system, by default 50
obs_freq : float, optional
Observation frequency of measurement device, by default 50
Returns
-------
ndarray
2D array of peaks of shape (len(x),2)
get_peaks()
Obtain an x,y peaks array from a system set with given parameters
Parameters
----------
systems : list[system]
list of systems previously obtained from an xml file
line_widths : list[Hz]
list of line widths for each spin matrix
system_count : int, optional
Number of submatrices in the system, by default 0
field_strength : float, optional
Field strength of measurement device, by default 500
points : int, optional
Number of points to sample, does not affect peaks but increases resolution, by default 1000
spec_width : float, optional
Spectral width of system, by default 50
obs_freq : float, optional
Observation frequency of measurement device, by default 50
Returns
-------
ndarray
2D array of peaks of shape (len(x),2)
load_system()
Obtain information from a coupling matrix xml file system
Parameters
----------
xmlfile : str
File path for the xml file
system_count : int
Number of submatrices in system (0 | 1 if only one)
Returns
-------
tuple[list[system], list[Hz]]
- list of systems containing:
- hydrogen name labels
- chemical shift list
- coupling matrix
- center measurement in ppm
- list of linewidths for main system and sub matrices
nmrConvert()
convert NMR data into an (x,y) array in PPM
Parameters
----------
convert : str
converting file
Returns
-------
ndarray
2D array of peaks of shape (NDSIZE,2)
Raises
------
ValueError
Raises an error if the NMR data is multi-dimensional