def test_add_terminal_OXT():
"""
Build a peptide with terminal OXT
"""
structure = PeptideBuilder.initialize_res("A")
for aa in "CDEFGHIKLMNPQRSTVWY":
PeptideBuilder.add_residue(structure, aa)
PeptideBuilder.add_terminal_OXT(structure)
assert compare_to_reference(structure, "extended_OXT.pdb")
# check that presence of OXT is tested
assert not compare_to_reference(structure, "extended.pdb")
"""
Simple example script demonstrating how to use the PeptideBuilder library.
The script generates a peptide consisting of six arginines in alpha-helix
conformation, and it stores the peptide under the name "example.pdb".
"""
from PeptideBuilder import Geometry
import PeptideBuilder
# create a peptide consisting of 6 glycines
geo = Geometry.geometry("G")
geo.phi = -60
geo.psi_im1 = -40
structure = PeptideBuilder.initialize_res(geo)
for i in range(5):
PeptideBuilder.add_residue(structure, geo)
# add terminal oxygen (OXT) to the final glycine
PeptideBuilder.add_terminal_OXT(structure)
import Bio.PDB
out = Bio.PDB.PDBIO()
out.set_structure(structure)
out.save("example.pdb")
