def structure_gen(self, pep_seq): if not os.path.exists("strs"): os.makedirs("strs") print "Structure being Generated !" b = len(pep_seq) bar = Bar('Processing PEPTIDES', fill='>', max=b) for seq in pep_seq: try: pep = Peptide(seq, nterm="charged", cterm="neutral") pep.regularize() pep.write_pdb(os.path.join("./strs", seq + ".pdb")) bar.next() obConversion = openbabel.OBConversion() obConversion.SetInAndOutFormats("pdb", "sdf") mol = openbabel.OBMol() obConversion.ReadFile(mol, os.path.join("./strs", seq + ".pdb")) mol.AddHydrogens() obConversion.WriteFile(mol, os.path.join("./strs", seq + ".sdf")) except: pass bar.finish() print "Structure Generation Finished !"
def generate_peptide(sequence, sample, output, seed, number): start = time.time() set_seed(seed) for i in range(number): pept = Peptide(sequence.upper(), nterm="neutral", cterm="neutral") pept.sample_bb_angles(sample) if sequence[sample] != "P": pept.sample_chi_angles(sample) if output is None: name = sequence + '_{:06d}.pdb'.format(i) else: name = output + '_{:06d}.pdb'.format(i) pept.write_pdb(str(name)) bb = pept.get_bb_angles(2) print(bb) # print("TE : {:12.4f}".format(time.time() - start)) return True
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)