def load_data_cs_Ca(self, filename, verbose=False):
"""Load in the experimental chemical shift restraints from a .chemicalshift file format.
"""
# Read in the lines of the chemicalshift data file
b = RestraintFile_cs(filename=filename)
if verbose:
print b.lines
data = []
for line in b.lines:
data.append( b.parse_line_cs(line) ) # [restraint_index, atom_index1, res1, atom_name1, chemicalshift]
if verbose:
print 'Loaded from', filename, ':'
for entry in data:
print entry
### distances ###
# the equivalency indices for distances are in the first column of the *.biceps f
# equivalency_indices = [entry[0] for entry in data]
# add the chemical shift restraints
for entry in data:
restraint_index, i, exp_chemicalshift_Ca, model_chemicalshift_Ca = entry[0], entry[1], entry[4], entry[5]
self.add_chemicalshift_Ca_restraint(i, exp_chemicalshift_Ca, model_chemicalshift_Ca)
# build groups of equivalency group indices, ambiguous group etc.
self.compute_sse_chemicalshift_Ca()
def load_expdata_cs(self, filename, verbose=False):
"""Load in the experimental chemical shift restraints from a .chemicalshift file format.
"""
# Read in the lines of the chemicalshift data file
b = RestraintFile_cs(filename=filename)
if verbose:
print b.lines
data = []
for line in b.lines:
data.append( b.parse_line_cs(line) ) # [restraint_index, atom_index1, res1, atom_name1, chemicalshift]
if verbose:
print 'Loaded from', filename, ':'
for entry in data:
print entry
### distances ###
# the equivalency indices for distances are in the first column of the *.biceps file
equivalency_indices = [entry[0] for entry in data]
if verbose:
print 'chemicalshift equivalency_indices', equivalency_indices
# compile ambiguity indices for distances
""" ### not yet supported ###
for pair in data['NOE_Ambiguous']:
# NOTE a pair of multiple distance pairs
list1, list2 = pair[0], pair[1]
# find the indices of the distances pairs that are ambiguous
pair_indices1 = [ data['NOE_PairIndex'].index(p) for p in list1]
pair_indices2 = [ data['NOE_PairIndex'].index(p) for p in list2]
self.ambiguous_groups.append( [pair_indices1, pair_indices2] )
if verbose:
print 'distance ambiguous_groups', self.ambiguous_groups
except:
print 'Problem reading distance ambiguous_groups. Setting to default: no ambiguous groups.'
"""
# add the chemical shift restraints
for entry in data:
restraint_index, i, exp_chemicalshift = entry[0], entry[1], entry[4]
self.add_chemicalshift_restraint(i, exp_chemicalshift, model_chemicalshift=None, equivalency_index=restraint_index)
# build groups of equivalency group indices, ambiguous group etc.
self.build_groups()
