def test_make_extended_structure():
"""
Build a peptide containing all 20 amino acids in extended conformation.
The structure should be identical to `extended.pdb`
"""
structure = PeptideBuilder.make_extended_structure("ACDEFGHIKLMNPQRSTVWY")
assert compare_to_reference(structure, "extended.pdb")
# test unit tests by comparing structures that don't match
structure = PeptideBuilder.make_extended_structure("ACDEFGHIKLMNPQRSTVW")
assert not compare_to_reference(structure, "extended.pdb")
structure = PeptideBuilder.make_extended_structure("ACDEFGHIKLMNPQRSTVWW")
assert not compare_to_reference(structure, "extended.pdb")
print(outfile, Geometry.geometry(aa))
# Build a helix containing all 20 amino acids from list of geometries.
# The structure should be identical to test1.pdb
geos = []
for aa in "ACDEFGHIKLMNPQRSTVWY":
geos.append(Geometry.geometry(aa))
structure = PeptideBuilder.make_structure_from_geos(geos)
out.set_structure(structure)
out.save("test4.pdb")
# Build a peptide containing all 20 amino acids in extended conformation.
# The structure should be identical to test1.pdb
structure = PeptideBuilder.make_extended_structure("ACDEFGHIKLMNPQRSTVWY")
out.set_structure(structure)
out.save("test4.pdb")
# Build a peptide containing all 20 amino acids from list of geometries.
# The structure should be identical to test1.pdb
geos = []
for aa in "ACDEFGHIKLMNPQRSTVWY":
geos.append(Geometry.geometry(aa))
structure = PeptideBuilder.make_structure_from_geos(geos)
out.set_structure(structure)
out.save("test5.pdb")
# Build a helix containing all 20 amino acids, with slowly varying
def test_make_extended_structure():
structure = PeptideBuilder.make_extended_structure("ACDEFGHIKLMNPQRSTVWY")
assert compare_to_reference(structure, "extended.pdb")
