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 !"
from fragbuilder import Peptide
# Make a peptide object
sequence = "YDG"
pep = Peptide(sequence)
# Set some angles that will clash
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])
# Write an XYZ file
pep.write_xyz("clash.xyz")
# Remove clashes (keep dihedral angles)
pep.regularize()
# Write another XYZ file
pep.write_xyz("noclash.xyz")
# 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))
