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))
