def pbassign_cli():
"""
PBassign command line.
"""
options, pdb_name_lst = user_inputs()
if options.p:
if pdb_name_lst:
print("{} PDB file(s) to process".format(len(pdb_name_lst)))
else:
print('Nothing to do. Good bye.')
return
# PB assignement of PDB structures
chains = PDB.chains_from_files(pdb_name_lst)
else:
# PB assignement of a Gromacs trajectory
chains = PDB.chains_from_trajectory(options.x, options.g)
all_comments = []
all_sequences = []
all_dihedrals = []
for comment, chain in chains:
dihedrals = chain.get_phi_psi_angles()
sequence = PB.assign(dihedrals)
all_comments.append(comment)
all_dihedrals.append(dihedrals)
all_sequences.append(sequence)
fasta_name = options.o + ".PB.fasta"
with open(fasta_name, 'w') as outfile:
PB.write_fasta(outfile, all_sequences, all_comments)
if options.flat:
flat_name = options.o + ".PB.flat"
with open(flat_name, 'w') as outfile:
PB.write_flat(outfile, all_sequences)
if options.phipsi:
phipsi_name = options.o + ".PB.phipsi"
with open(phipsi_name, 'w') as outfile:
PB.write_phipsi(outfile, all_dihedrals, all_comments)
print("wrote {0}".format(fasta_name))
if options.flat:
print("wrote {0}".format(flat_name))
if options.phipsi:
print("wrote {0}".format(phipsi_name))
def pbassign_cli():
"""
PBassign command line.
"""
options, pdb_name_lst = user_inputs()
if options.p:
if pdb_name_lst:
print("{} PDB file(s) to process".format(len(pdb_name_lst)))
else:
print('Nothing to do. Good bye.')
return
# PB assignement of PDB structures
chains = PDB.chains_from_files(pdb_name_lst)
else:
# PB assignement of a Gromacs trajectory
chains = PDB.chains_from_trajectory(options.x, options.g)
all_comments = []
all_sequences = []
all_dihedrals = []
for comment, chain in chains:
dihedrals = chain.get_phi_psi_angles()
sequence = PB.assign(dihedrals)
all_comments.append(comment)
all_dihedrals.append(dihedrals)
all_sequences.append(sequence)
fasta_name = options.o + ".PB.fasta"
with open(fasta_name, 'w') as outfile:
PB.write_fasta(outfile, all_sequences, all_comments)
if options.flat:
flat_name = options.o + ".PB.flat"
with open(flat_name, 'w') as outfile:
PB.write_flat(outfile, all_sequences)
if options.phipsi:
phipsi_name = options.o + ".PB.phipsi"
with open(phipsi_name, 'w') as outfile:
PB.write_phipsi(outfile, all_dihedrals, all_comments)
print("wrote {0}".format(fasta_name))
if options.flat:
print("wrote {0}".format(flat_name))
if options.phipsi:
print("wrote {0}".format(phipsi_name))
def test_get_dihedral(self):
"""
Test for get_dihedral()
"""
Result = collections.namedtuple("Result", ["A", "B", "C", "D", "torsion"])
results = (
Result(
(-7.28, -9.262, 5.077),
(-7.526, -10.643, 5.529),
(-6.221, -11.438, 5.555),
(-6.289, -12.685, 5.931),
-179.663656153,
),
Result(
(-1.373, -8.817, -4.389),
(-1.203, -8.335, -5.792),
(-1.891, -6.977, -5.927),
(-1.918, -6.429, -7.107),
-176.048770127,
),
Result(
(-0.533, -8.42, -3.47),
(-1.373, -8.817, -4.389),
(-1.203, -8.335, -5.792),
(-1.891, -6.977, -5.927),
-84.8356057692,
),
Result(
(-1.918, -6.429, -7.107),
(-2.609, -5.125, -7.305),
(-4.108, -5.392, -7.331),
(-4.469, -6.494, -7.911),
-36.8942888266,
),
Result(
(-11.285, 6.472, -7.44),
(-12.62, 5.829, -7.425),
(-13.585, 6.626, -6.544),
(-13.098, 7.621, -5.858),
-6.58786169376,
),
Result(
(-11.284, -0.971, -2.679),
(-12.65, -0.794, -3.226),
(-13.665, -1.664, -2.479),
(-13.262, -2.363, -1.452),
3.91626706556,
),
Result(
(-2.004, -10.892, -2.611),
(-1.87, -9.835, -1.853),
(-0.726, -8.877, -2.011),
(-0.533, -8.42, -3.47),
50.065196067,
),
Result(
(11.174, -6.725, 0.458),
(10.732, -7.258, -0.86),
(9.27, -6.869, -1.096),
(8.741, -7.185, -2.245),
175.872397707,
),
)
for res in results:
torsion = PDB.get_dihedral(res.A, res.B, res.C, res.D)
self.assertAlmostEqual(torsion, res.torsion)
