def spectrum_cb(self, name):
spectrum = sputil.name_to_spectrum(name, self.session)
if spectrum and spectrum.dimension == 2:
for a in range(2):
self.matrix_size.variables[a].set(spectrum.data_size[a])
self.save_path.set(spectrum.data_path + '.corma')
def spectrum_cb(self, name):
spectrum = sputil.name_to_spectrum(name, self.session)
if spectrum == None:
return
if spectrum.dimension == 3:
self.w3_range_widget.pack(side='left', anchor='w')
self.line_format = '%20s %5s %7s %s'
else:
self.w3_range_widget.pack_forget()
self.line_format = '%15s %5s %7s %s'
default_ppm_range = {'1H': .02, '13C': .2, '15N': .2}
for a in range(spectrum.dimension):
nucleus = spectrum.nuclei[a]
if default_ppm_range.has_key(nucleus):
ppm_range = default_ppm_range[nucleus]
else:
ppm_range = .02
self.ppm_range[a].set('%.2f' % ppm_range)
def spectrum_cb(self, name):
spectrum = sputil.name_to_spectrum(name, self.session)
if spectrum == None:
return
if spectrum.dimension == 3:
self.w3_range_widget.pack(side = 'left', anchor = 'w')
self.line_format = '%20s %s %7s %s'
else:
self.w3_range_widget.pack_forget()
self.line_format = '%15s %s %7s %s'
default_ppm_range = {'1H':.02, '13C':.2, '15N':.2}
for a in range(spectrum.dimension):
nucleus = spectrum.nuclei[a]
if default_ppm_range.has_key(nucleus):
ppm_range = default_ppm_range[nucleus]
else:
ppm_range = .02
self.ppm_range[a].set('%.2f' % ppm_range)
'15380') # this bmrb code is GB1 from Rienstra group
elif idx == 2: # SHIFTX
reference_shift = \
s.show_inputdialog('SHIFTX2',
'Paste SHIFTX2 CSV URL path or drop the file.',
'http://www.shiftx2.ca/wkdir/1611508737/2KQ4.cs')
# this shiftx2 url is my prediction with 2KQ4 PDB (also GB1)
else: # use pacsy chemical shift database prediction (default)
reference_shift = 'pacsy'
# use existing assignments
use_resonances = True
# spectrum to be simulated
from sputil import name_to_spectrum
spec = name_to_spectrum(spec_name, s)
if spec == None:
s.show_message('Error', 'Spectrum is not set properly.')
raise SystemExit
exp_list = ['2D-NCA', '2D-NCACB', '2D-NCO', '2D-CC', 'NCACB', 'NCACX',
'NCACO', 'NCOCA', 'NCOCACB', 'NCOCX', 'CANCO', 'CAN(CO)CX']
if spec.dimension == 2:
avail_exp_list = exp_list[0:4]
elif spec.dimension == 3:
avail_exp_list = exp_list[4:]
else:
s.show_message('Error', '4D spectrum is not set supported.')
raise SystemExit
idx = s.show_selectionexdialog('Experiment',
# To run this script:
# In Poky Notepad,
# File -> Run Python Module
#
#
import numpy as np
import nmrglue as ng
from skimage.restoration import denoise_tv_bregman
from sputil import name_to_spectrum
# POKY libraries
import __main__
s = __main__.main_session
specname = s.show_spectrumselectiondialog('Select a spectrum', 0)
sp = name_to_spectrum(specname, s)
if sp == None:
raise SystemError
import os.path
noisy_path = s.save_filedialog('Provide a name for saving the noisy spectrum',
'UCSF (*.ucsf);; Any (*)',
os.path.dirname(sp.data_path))
if noisy_path == '':
raise SystemError
denoise_path = s.save_filedialog(
'Provide a name for saving the de-noised spectrum',
'UCSF (*.ucsf);; Any (*)', os.path.dirname(sp.data_path))
return a * np.exp(-1 * x / b)
from sputil import name_to_spectrum, sort_peaks_by_assignment
import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from matplotlib import use as matplotlib_use
matplotlib_use('TkAgg')
# (time) parameters
xdataT1 = np.array(list(map(lambda sp: sp[1], T1_spec_list)))
xdataT2 = np.array(list(map(lambda sp: sp[1], T2_spec_list)))
# get spectrum instances first
spT1_list = list(map(lambda sp: name_to_spectrum(sp[0], s), T1_spec_list))
spT2_list = list(map(lambda sp: name_to_spectrum(sp[0], s), T2_spec_list))
if None in spT1_list:
none_name = T1_spec_list[spT1_list.index(None)][0]
print('T1 experiment (' + none_name +
') does not exist in your spectrum list.')
raise SystemExit
if None in spT2_list:
none_name = T2_spec_list[spT2_list.index(None)][0]
print('T2 experiment (' + none_name +
') does not exist in your spectrum list.')
raise SystemExit
# Exclude from cond_list using excl_cond_list
cond_list = [x for x in cond_list if x not in excl_cond_list]
# define function for making ROI list
# this can be replaced by custom definition like above
# we can use view name. we do not cluster by view names here
# however, it can be considered to make a rule to do that.
def make_ROIs(spec):
ROI_list = []
for view in s.project.view_list():
if view.spectrum == spec and view.name != spec.name:
ROI_list.append([view.name, view.name])
return ROI_list
# for unit conversion
ref_spec = name_to_spectrum(ref_specname, s)
ppm_per_pt = (ref_spec.spectrum_width[0] / (ref_spec.data_size[0] - 1),
ref_spec.spectrum_width[1] / (ref_spec.data_size[1] - 1))
# define function for boxing integration
# spec is a spectrum to analyze
from itertools import product
def box_sum(spec, region):
npoints = (int((region[1][0] - region[0][0]) / ppm_per_pt[0]),
int((region[1][1] - region[0][1]) / ppm_per_pt[1]))
it_list = list(product(range(npoints[0]), range(npoints[1])))
hts = []
for i in range(npoints[0]):
x = region[1][0] - ppm_per_pt[0] * i
for j in range(npoints[1]):
exp_func = t_exp_func
#exp_func = sea_exp_func # if sea-hsqc experiments
from sputil import name_to_spectrum
import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from matplotlib import use as matplotlib_use
matplotlib_use('TkAgg')
# (time) parameters
xdata = np.array(list(map(lambda sp: sp[1], spec_list)))
# get spectrum instances first
sp_list = list(map(lambda sp: name_to_spectrum(sp[0], s), spec_list))
if None in sp_list:
none_name = spec_list[sp_list.index(None)][0]
print(none_name + ' does not exist in your spectrum list.')
raise SystemExit
# collect reference peaks and positions from the first spectrum
# assignment needed!
ref_peaks = sp_list[0].peak_list()
# ref_peaks = sp_list[0].selected_peaks() # if only selected peaks preferred
# sort peaks by assignment
from sputil import sort_peaks_by_assignment
sorted_peaks = sort_peaks_by_assignment(ref_peaks, False)
outName = s.save_filedialog('Save your new restraint file as...',
'DIANA UPL file (*.upl);; XPLOR TBL file (*.tbl);; Any (*)', '')
# Processing start
from sputil import name_to_spectrum, sort_peaks_by_assignment, parse_assignment_entirely
import numpy as np
A_dict = {'C': 'CYS', 'D': 'ASP', 'S': 'SER', 'Q': 'GLN', 'K': 'LYS',
'I': 'ILE', 'P': 'PRO', 'T': 'THR', 'F': 'PHE', 'N': 'ASN',
'G': 'GLY', 'H': 'HIS', 'L': 'LEU', 'R': 'ARG', 'W': 'TRP',
'A': 'ALA', 'V':'VAL', 'E': 'GLU', 'Y': 'TYR', 'M': 'MET'}
import nomenclature
upl_list = []
for sp in spec_list:
spec = name_to_spectrum(sp, s)
if spec == None:
print('%s spectrum does not exist.' % (sp))
raise SystemError
dMin, dMax = 10**13, -10**13
peaks = spec.spectrum().peak_list()
if len(peaks) == 0: continue
peak_list = []
for peak in peaks:
nuc = spec.nuclei
freq = peak.frequency
if peak.is_assigned == 0 or peak.data_height == None: continue
if no_diagonal and abs(freq[0] - freq[1]) < res[nuc[0]]: continue
print('------------------------------------------------------')
import __main__
s = __main__.main_session
proj = s.project
# Parameters
ref_spec_name = s.show_spectrumselectiondialog('Reference spectrum', 0).strip()
noe_spec_name = s.show_spectrumselectiondialog('NOE spectrum', 0).strip()
only_selected = False # Use all assigned peaks if False
error_bar = True # Draw error bar if True
# Processing start
from sputil import name_to_spectrum, sort_peaks_by_assignment
ref_spec = name_to_spectrum(ref_spec_name, s)
noe_spec = name_to_spectrum(noe_spec_name, s)
if ref_spec == None:
print('Reference spectrum name %s is wrong.' % ref_spec_name)
raise SystemExit
if noe_spec == None:
print('NOE spectrum name %s is wrong.' % ref_spec_name)
raise SystemExit
# collect peaks and sort by number
temp_peaks = []
for p in ref_spec.peak_list():
if only_selected and p.selected == 0:
continue
if None not in p.resonances() and p.is_assigned == 1:
# To run this script:
# In Poky Notepad,
# File -> Run Python Module
#
#
import numpy as np
import nmrglue as ng
from sputil import name_to_spectrum
# POKY libraries
import __main__
s = __main__.main_session
specname = s.show_spectrumselectiondialog('Select spectrum one', 0)
sp = name_to_spectrum(specname, s)
if sp == None:
raise SystemError
specname2 = s.show_spectrumselectiondialog('Select spectrum two', 0)
sp2 = name_to_spectrum(specname2, s)
if sp2 == None:
raise SystemError
scale_offset = np.array(sp.scale_offset) - np.array(sp2.scale_offset)
import os.path
new_path = s.save_filedialog('New spectrum name', 'UCSF (*.ucsf);; Any (*)',
os.path.dirname(sp.data_path))
def spectrum(self):
return sputil.name_to_spectrum(self.get(), self.session)