new_contribs = self.extract_contributions(contribs)
contributions = []
for contrib in new_contribs:
atoms = self.split_contribution(contrib)
atoms = [self.extract_atom(x) for x in atoms]
atoms = [a for a in atoms if not a['name'] in fake_atom_names]
contributions += self.build_contributions(atoms)
if contributions:
r = create_rdc_restraint(seq_number, distances[0],
contributions)
restraints.append(r)
seq_number += 1
if restraints:
return restraints
if __name__ == '__main__':
noe = 'noe.tbl'
sequence = read_sequence_file('seq.dat', first_residue_number=1)
reader = TBLReader(sequence, ignore_warnings=True)
reader.read_distances(noe, key='test')
for line in fl:
tokens = line.split()
if not tokens[0].isdigit():
continue
resno = int(tokens[0]) + self.offset
check_residue(resno, tokens[1])
phi, psi, dphi, dpsi = map(lambda a: 2 * pi * float(a) / 360.0, tokens[2:6])
num = int(tokens[8])
if num == 0:
continue
self.add_mean_datum(resno, num, (phi, dphi), (psi, dpsi))
def read(self, fname):
"reads a TALOS file and returns data. See add_datum methods."
if self.detailed_input:
self._read_observations(fname)
else:
self._read_averages(fname)
def get_data(self):
return self.data
if __name__ == "__main__":
talos = "pred.tab"
sequence = read_sequence_file("seq.dat", sequence_match=(1, 5))
reader = TALOSReader(sequence)
reader.read(talos)
data = reader.get_data()
if not tokens[0].isdigit():
continue
resno = int(tokens[0]) + self.offset
check_residue(resno,tokens[1])
phi,psi,dphi,dpsi = map(lambda a: 2*pi*float(a)/360.,
tokens[2:6])
num=int(tokens[8])
if num == 0:
continue
self.add_mean_datum(resno, num, (phi, dphi), (psi, dpsi))
def read(self,fname):
"reads a TALOS file and returns data. See add_datum methods."
if self.detailed_input:
self._read_observations(fname)
else:
self._read_averages(fname)
def get_data(self):
return self.data
if __name__ == '__main__':
talos = 'pred.tab'
sequence = read_sequence_file('seq.dat', sequence_match=(1,5))
reader = TALOSReader(sequence)
reader.read(talos)
data=reader.get_data()
if not tokens[0].isdigit():
continue
resno = int(tokens[0]) + self.offset
check_residue(resno, tokens[1])
phi, psi, dphi, dpsi = [
2 * pi * float(a) / 360. for a in tokens[2:6]
]
num = int(tokens[8])
if num == 0:
continue
self.add_mean_datum(resno, num, (phi, dphi), (psi, dpsi))
def read(self, fname):
"reads a TALOS file and returns data. See add_datum methods."
if self.detailed_input:
self._read_observations(fname)
else:
self._read_averages(fname)
def get_data(self):
return self.data
if __name__ == '__main__':
talos = 'pred.tab'
sequence = read_sequence_file('seq.dat', sequence_match=(1, 5))
reader = TALOSReader(sequence)
reader.read(talos)
data = reader.get_data()
distances, volume = self.extract_target_values(contribs[0])
new_contribs = self.extract_contributions(contribs)
contributions = []
for contrib in new_contribs:
atoms = self.split_contribution(contrib)
atoms = [self.extract_atom(x) for x in atoms]
atoms = [a for a in atoms if not a["name"] in fake_atom_names]
contributions += self.build_contributions(atoms)
if contributions:
r = create_rdc_restraint(seq_number, distances[0], contributions)
restraints.append(r)
seq_number += 1
if restraints:
return restraints
if __name__ == "__main__":
noe = "noe.tbl"
sequence = read_sequence_file("seq.dat", first_residue_number=1)
reader = TBLReader(sequence, ignore_warnings=True)
reader.read_distances(noe, key="test")
contribs = [del_comment(x).strip() for x in line.split('or')]
distances, volume = self.extract_target_values(contribs[0])
new_contribs = self.extract_contributions(contribs)
contributions = []
for contrib in new_contribs:
atoms = self.split_contribution(contrib)
atoms = [self.extract_atom(x) for x in atoms]
atoms = [a for a in atoms if not a['name'] in fake_atom_names]
contributions += self.build_contributions(atoms)
if contributions:
r = create_rdc_restraint(seq_number, distances[0], contributions)
restraints.append(r)
seq_number += 1
if restraints:
return restraints
if __name__ == '__main__':
noe = 'noe.tbl'
sequence = read_sequence_file('seq.dat', first_residue_number=1)
reader = TBLReader(sequence, ignore_warnings=True)
reader.read_distances(noe, key='test')
