pep = Peptide(sequence, nterm="neutral", cterm="charged")
print "SMILES: ", pep.get_smiles()
print "Charge: ", pep.get_charge()
print "Length: ", pep.get_length()
print "Sequence:", pep.get_sequence()
# Set [PHI, PSI] angles for residues 1, 2 and 3
pep.set_bb_angles(1, [ -156.3, 142.3])
pep.set_bb_angles(2, [ 48.8, 42.3])
pep.set_bb_angles(3, [ 81.3, 0.2])
# Set and read chi angles for residue 2
pep.set_chi_angles(2, [ -50.6, -75.1])
print pep.get_bb_angles(2)
# Sample (and set) backbone angles for residue 2
print pep.sample_bb_angles(2)
print pep.get_bb_angles(2)
# Sample (and set) chi angles for residue 2
print pep.sample_chi_angles(2)
print pep.get_chi_angles(2)
# Write files
pep.write_xyz("pep.xyz")
pep.write_pdb("pep.pdb", QUIET=False)
pep = Peptide(sequence, nterm="neutral", cterm="charged")
print("SMILES: ", pep.get_smiles())
print("Charge: ", pep.get_charge())
print("Length: ", pep.get_length())
print("Sequence:", pep.get_sequence())
# Set [PHI, PSI] angles for residues 1, 2 and 3
pep.set_bb_angles(1, [ -156.3, 142.3])
pep.set_bb_angles(2, [ 48.8, 42.3])
pep.set_bb_angles(3, [ 81.3, 0.2])
# Set and read chi angles for residue 2
pep.set_chi_angles(2, [ -50.6, -75.1])
print(pep.get_bb_angles(2))
# Sample (and set) backbone angles for residue 2
print(pep.sample_bb_angles(2))
print(pep.get_bb_angles(2))
# Sample (and set) chi angles for residue 2
print(pep.sample_chi_angles(2))
print(pep.get_chi_angles(2))
# Write files
pep.write_xyz("pep.xyz")
pep.write_pdb("pep.pdb", QUIET=False)
for l1 in aas:
# Define sequence
seq = "A" + l1 * 10 + "A"
print seq
# Create peptide
pep = Peptide(seq, nterm="charged", cterm="charged")
# Sample (and set) backbone angles for residue 2
for i in range(10):
pep.sample_bb_angles(2 + i)
print pep.get_bb_angles(2 + i)
# Sample (and set) chi angles for residue 2
try:
pep.sample_chi_angles(2 + i)
print pep.get_chi_angles(2 + i)
except:
pass
# MMFF94 optimization
pep.optimize()
# Write files
filename = seq + ".pdb"
pep.write_pdb(filename, QUIET=False)
