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))
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)
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))
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")
