def load_data_J(self, filename, verbose=False):
"""Load in the experimental Jcoupling constant restraints from a .Jcoupling file format."""
# Read in the lines of the biceps data file
b = RestraintFile_J(filename=filename)
data = []
for line in b.lines:
data.append( b.parse_line_J(line) ) # [restraint_index, atom_index1, res1, atom_name1, atom_index2, res2, atom_name2, atom_index3, res3, atom_name3, atom_index4, res4, atom_name4, J_coupling(Hz)]
if verbose:
print 'Loaded from', filename, ':'
for entry in data:
print entry
### Jcoupling ###
# the equivalency indices for Jcoupling are in the first column of the *.Jcoupling file
equivalency_indices = [entry[0] for entry in data]
if verbose:
print 'distance equivalency_indices', equivalency_indices
# add the Jcoupling restraints
for entry in data:
restraint_index, i, j, k, l, exp_Jcoupling, karplus = entry[0], entry[1], entry[4], entry[7], entry[10], entry[13], entry[14]
self.add_dihedral_restraint(i, j, k, l, exp_Jcoupling, model_Jcoupling=None, equivalency_index=None, karplus_key=karplus)
# build groups of equivalency group indices, ambiguous group etc.
self.build_groups_J()
def load_expdata_J(self, filename, verbose=False):
"""Load in the experimental Jcoupling constant restraints from a .Jcoupling file format."""
# Read in the lines of the biceps data file
b = RestraintFile_J(filename=filename)
data = []
for line in b.lines:
data.append( b.parse_line_J(line) ) # [restraint_index, atom_index1, res1, atom_name1, atom_index2, res2, atom_name2, atom_index3, res3, atom_name3, atom_index4, res4, atom_name4, J_coupling(Hz)]
if verbose:
print 'Loaded from', filename, ':'
for entry in data:
print entry
### Jcoupling ###
# the equivalency indices for Jcoupling are in the first column of the *.Jcoupling file
equivalency_indices = [entry[0] for entry in data]
if verbose:
print 'distance 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 Jcoupling restraints
for entry in data:
restraint_index, i, j, k, l, exp_Jcoupling, karplus = entry[0], entry[1], entry[4], entry[7], entry[10], entry[13], entry[14]
self.add_dihedral_restraint(i, j, k, l, exp_Jcoupling, model_Jcoupling=None, equivalency_index=None, karplus_key=karplus)
# build groups of equivalency group indices, ambiguous group etc.
self.build_groups()
sys.exit(1)
pdbfile = 'albo_37.pdb'
# load in the pdbfile template
topology = md.load_pdb(pdbfile).topology
Karplusfilename = 'Karplus.txt'
filename=Karplusfilename
with open(filename) as f:
lines=f.readlines()
line=''.join(lines)
karplus = line.strip().split('\n')
r = RestraintFile_J()
all_atom_indices = [atom.index for atom in topology.atoms]
all_atom_residues = [atom.residue for atom in topology.atoms]
all_atom_names = [atom.name for atom in topology.atoms]
for i in range(Ind.shape[0]):
a1, a2, a3, a4 = int(Ind[i,0]), int(Ind[i,1]), int(Ind[i,2]), int(Ind[i,3])
restraint_index = restraint_data[i,0]
J_coupling = restraint_data[i,1]
r.add_line_J(restraint_index, a1, a2, a3, a4, topology, J_coupling, karplus)
print r
r.write('albo.Jcoupling')
