def test_noetools(self):
"""Self test for NMR.NOEtools.
Calculate and compare crosspeak peaklist files
Adapted from Doc/examples/nmr/simplepredict.py by Robert Bussell, Jr.
"""
self.xpk_i_file = os.path.join("NMR", "noed.xpk")
# out_example.xpk is created by running Doc/examples/nmr/simplepredict.py
# with noed.xpk as an input file.
self.xpk_expected = os.path.join("NMR", "out_example.xpk")
self.f_number, self.f_predicted = tempfile.mkstemp()
os.close(self.f_number)
# Calculate crosspeak from a peaklist input file
# and save to a temporal file for comparison.
try:
self.peaklist = xpktools.Peaklist(self.xpk_i_file)
self.res_dict = self.peaklist.residue_dict("H1")
max_res = self.res_dict["maxres"]
min_res = self.res_dict["minres"]
self.peaklist.write_header(self.f_predicted)
inc = 1 # The NOE increment (n where i->i+n and i->i-n are noes)
count = 0 # A counter that number the output data lines in order
res = min_res # minimum residue number in the set
out_list = [] # Holds the output data
while res <= max_res:
noe1 = NOEtools.predictNOE(self.peaklist, "15N2", "H1", res,
res + inc)
noe2 = NOEtools.predictNOE(self.peaklist, "15N2", "H1", res,
res - inc)
if noe1 != "":
noe1 = noe1 + "\012"
noe1 = xpktools.replace_entry(noe1, 1, count)
out_list.append(noe1)
count += 1
if noe2 != "":
noe2 = noe2 + "\012"
noe2 = xpktools.replace_entry(noe2, 1, count)
out_list.append(noe2)
count += 1
res += 1
# Open the output file and write the data
with open(self.f_predicted, "a") as outfile:
outfile.writelines(
out_list) # Write the output lines to the file
# Compare the content of the predicted output file with expected file
pre_content = open(self.f_predicted).read()
exp_content = open(self.xpk_expected).read()
self.assertEqual(pre_content, exp_content)
finally:
os.remove(self.f_predicted)
peaklist.write_header(outfn) # Write the header to the output file
# Predict the i->i+inc and i->i-inc noe positions if possible
# Write each one to the output file as they are calculated
count = 0 # A counter that number the output data lines in order
res = MINRES # minimum residue number in the set
outlist = [] # Holds the output data
while (res <= MAXRES):
# Predicting the NOE positions based on peak assignment data
# is done by supplying the peaklist to and specifying the label
# of the origin and detected atom in the NOE transfer as well as
# the residues between which the NOE transfer takes places.
noe1 = NOEtools.predictNOE(peaklist, "15N2", "H1", res, res + inc)
noe2 = NOEtools.predictNOE(peaklist, "15N2", "H1", res, res - inc)
# The output of predictNOE is in the form of an xpk entry line
# suitable for printing to an output file
# Additionally, it is possible to extract information easily from
# these output lines by using the xpktools.XpkEntry class
entry1 = xpktools.XpkEntry(noe1, peaklist.datalabels)
if noe1 != "":
# Here I'm using the XpkEntry class to gain access to
# specific fields in the that make the information
# more readable and suitable for creating data tables
# This output will be printed to the screen.