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_residue(residue, output, seed, number, cterm, nterm):
set_seed(seed)
for i in range(number):
pept = Peptide(residue.upper(), nterm=nterm, cterm=cterm)
pept.sample_bb_angles(1)
if residue != "P":
pept.sample_chi_angles(1)
if output is None:
name = 'c{:s}c'.format(residue) + '_{:06d}.mol2'.format(i)
else:
name = output + '_{:06d}.mol2'.format(i)
pept.write_file('mol2', str(name))
bb = pept.get_bb_angles(1)
print(bb)
return True
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
from fragbuilder import Peptide
from fragbuilder import G09_opt
from fragbuilder import G09_energy
from fragbuilder import G09_NMR
sequence = "GLG"
pep = Peptide(sequence, nterm="methyl", cterm="methyl")
print "Charge:", pep.get_charge()
for i in pep.get_residue_numbers():
pep.sample_bb_angles(i)
pep.sample_chi_angles(i)
pep.optimize()
opt = G09_opt(pep)
opt.set_method("B3LYP/6-31G(d)")
opt.write_com("g09_opt_%s.com" % (sequence))
opt.write_com("g09_opt_%s_constraint.com" % (sequence), constraint_dihedrals=True)
energy = G09_energy(pep)
energy.set_method("PM3")
energy.write_com("g09_energy_%s.com" % (sequence))
nmr = G09_NMR(pep)
nmr.set_method("B3LYP/6-31+G(d,p)")
nmr.write_com("g09_nmr_%s.com" % (sequence))
from fragbuilder import Peptide
# Create a peptide object with the sequence
# glycine-leucine-glycine.
sequence = "GLG"
pep = Peptide(sequence)
# Define a list of angles.
angles = range(-180, 180, 60)
# Double loop over phi/psi angles in the desired range.
for psi in angles:
for phi in angles:
# Set the second (leucine) residue to (phi, psi).
pep.set_bb_angles(2, [phi, psi])
# Save each conformation.
pep.write_xyz("pep_%04i_%04i.xyz" % (phi, psi))
from __future__ import print_function
from fragbuilder import Peptide
# 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")
from __future__ import print_function
from fragbuilder import Peptide
from fragbuilder import G09_opt
from fragbuilder import G09_energy
from fragbuilder import G09_NMR
sequence = "GLG"
pep = Peptide(sequence, nterm="methyl", cterm="methyl")
print("Charge:", pep.get_charge())
for i in pep.get_residue_numbers():
pep.sample_bb_angles(i)
pep.sample_chi_angles(i)
pep.optimize()
opt = G09_opt(pep)
opt.set_method("B3LYP/6-31G(d)")
opt.write_com("g09_opt_%s.com" % (sequence))
opt.write_com("g09_opt_%s_constraint.com" % (sequence),
constraint_dihedrals=True)
energy = G09_energy(pep)
energy.set_method("PM3")
energy.write_com("g09_energy_%s.com" % (sequence))
nmr = G09_NMR(pep)
nmr.set_method("B3LYP/6-31+G(d,p)")
nmr.write_com("g09_nmr_%s.com" % (sequence))
from fragbuilder import Peptide
# 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)
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")
# Extract length and sequence
n = pdb.get_length()
seq = pdb.get_sequence()
# 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
from fragbuilder import Peptide
aas = "FYWDENQHKRGASTCVLIMP"
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)
from fragbuilder import Peptide
# Make a GLAG peptide object
sequence = "GLAG"
pep = Peptide(sequence)
# Loop over residues:
for i in pep.get_residue_numbers():
pep.sample_bb_angles(i)
pep.sample_chi_angles(i)
# Regularize to remove any steric clashes
pep.regularize()
# Write files
pep.write_xyz("pep.xyz")
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")
