# Make a GLG peptide object sequence = "GLG" 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)
# Make a GLG peptide object sequence = "GLG" 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)
# Loop over residue numbers for i in pdb.get_residue_numbers(): # Ignore first and last few residues as omega, # phi, or psi may be undefined. if (i < 3) or (i > n - 2): continue # Determine sequence of the three-residues # peptide model and make a Peptide object pep_seq = seq[i - 2:i + 1] pep = Peptide(pep_seq) print(i, pep_seq) # Loop over preceding, central, and following residue. for j in [-1, 0, 1]: # Read backbone and chi angles from pdb object bb = pdb.get_bb_angles(i + j) chi = pdb.get_chi_angles(i + j) # Set matching angles in the Peptide object pep.set_bb_angles(2 + j, bb) pep.set_chi_angles(2 + j, chi) # Short optimization and save xyz file pep.regularize() pep.write_xyz("pep_%04i.xyz" % (i))