def exercise_presence_of_h():
tst_pdb_1 = """\
HELIX 2 2 GLY A 100 TRP A 101 1 2
ATOM 866 N GLY A 100 -128.903-139.939-104.460 1.00 27.58 N
ATOM 867 CA GLY A 100 -128.223-140.890-103.603 1.00 27.58 C
ATOM 868 C GLY A 100 -128.381-142.356-103.959 1.00 27.58 C
ATOM 869 O GLY A 100 -129.283-142.755-104.686 1.00 27.58 O
ATOM 870 H GLY A 100 -129.862-139.777-104.337 1.00 36.09 H
ATOM 871 N TRP A 101 -127.491-143.163-103.397 1.00 25.83 N
ATOM 872 CA TRP A 101 -127.455-144.601-103.619 1.00 25.83 C
ATOM 873 C TRP A 101 -128.824-145.274-103.752 1.00 25.83 C
ATOM 874 O TRP A 101 -129.091-145.962-104.734 1.00 25.83 O
ATOM 875 CB TRP A 101 -126.659-145.240-102.480 1.00 42.04 C
ATOM 876 CG TRP A 101 -126.207-146.635-102.729 1.00 42.04 C
ATOM 877 CD1 TRP A 101 -126.180-147.300-103.922 1.00 42.04 C
ATOM 878 CD2 TRP A 101 -125.677-147.528-101.760 1.00 42.04 C
ATOM 879 NE1 TRP A 101 -125.663-148.557-103.751 1.00 42.04 N
ATOM 880 CE2 TRP A 101 -125.347-148.723-102.429 1.00 42.04 C
ATOM 881 CE3 TRP A 101 -125.446-147.437-100.384 1.00 42.04 C
ATOM 882 CZ2 TRP A 101 -124.799-149.820-101.767 1.00 42.04 C
ATOM 883 CZ3 TRP A 101 -124.899-148.528 -99.725 1.00 42.04 C
ATOM 884 CH2 TRP A 101 -124.581-149.703-100.415 1.00 42.04 C
ATOM 885 H TRP A 101 -126.863-142.797-102.745 1.00 42.04 H
"""
pdb_inp = iotbx.pdb.input(source_info=None, lines=tst_pdb_1)
ann = pdb_inp.extract_secondary_structure()
model = mmtbx.model.manager(
model_input = pdb_inp,
build_grm = True)
model.set_ss_annotation(ann)
rm = ssb.substitute_ss(
model,
)
def exercise_some_atoms_are_absent():
""" CD1, CD2 from 101 residue are absent"""
tst_pdb_2 = """\
HELIX 2 2 GLY A 100 TRP A 101 1 2
ATOM 866 N GLY A 100 -128.903-139.939-104.460 1.00 27.58 N
ATOM 867 CA GLY A 100 -128.223-140.890-103.603 1.00 27.58 C
ATOM 868 C GLY A 100 -128.381-142.356-103.959 1.00 27.58 C
ATOM 869 O GLY A 100 -129.283-142.755-104.686 1.00 27.58 O
ATOM 871 N TRP A 101 -127.491-143.163-103.397 1.00 25.83 N
ATOM 872 CA TRP A 101 -127.455-144.601-103.619 1.00 25.83 C
ATOM 873 C TRP A 101 -128.824-145.274-103.752 1.00 25.83 C
ATOM 874 O TRP A 101 -129.091-145.962-104.734 1.00 25.83 O
ATOM 875 CB TRP A 101 -126.659-145.240-102.480 1.00 42.04 C
ATOM 876 CG TRP A 101 -126.207-146.635-102.729 1.00 42.04 C
ATOM 879 NE1 TRP A 101 -125.663-148.557-103.751 1.00 42.04 N
ATOM 880 CE2 TRP A 101 -125.347-148.723-102.429 1.00 42.04 C
ATOM 881 CE3 TRP A 101 -125.446-147.437-100.384 1.00 42.04 C
"""
pdb_inp = iotbx.pdb.input(source_info=None, lines=tst_pdb_2)
ann = pdb_inp.extract_secondary_structure()
model = mmtbx.model.manager(
model_input = pdb_inp,
build_grm = True)
model.set_ss_annotation(ann)
rm = ssb.substitute_ss(
model)
rm.run()
def exercise_ca_absent():
# should raise Sorry
""" CA from 101 residue are absent. We don't handle it at the moment."""
tst_pdb_1 = """\
HELIX 2 2 GLY A 100 TRP A 101 1 2
ATOM 866 N GLY A 100 -128.903-139.939-104.460 1.00 27.58 N
ATOM 867 CA GLY A 100 -128.223-140.890-103.603 1.00 27.58 C
ATOM 868 C GLY A 100 -128.381-142.356-103.959 1.00 27.58 C
ATOM 869 O GLY A 100 -129.283-142.755-104.686 1.00 27.58 O
ATOM 870 H GLY A 100 -129.862-139.777-104.337 1.00 36.09 H
ATOM 871 N TRP A 101 -127.491-143.163-103.397 1.00 25.83 N
ATOM 873 C TRP A 101 -128.824-145.274-103.752 1.00 25.83 C
ATOM 874 O TRP A 101 -129.091-145.962-104.734 1.00 25.83 O
ATOM 875 CB TRP A 101 -126.659-145.240-102.480 1.00 42.04 C
ATOM 876 CG TRP A 101 -126.207-146.635-102.729 1.00 42.04 C
ATOM 877 CD1 TRP A 101 -126.180-147.300-103.922 1.00 42.04 C
ATOM 878 CD2 TRP A 101 -125.677-147.528-101.760 1.00 42.04 C
ATOM 879 NE1 TRP A 101 -125.663-148.557-103.751 1.00 42.04 N
ATOM 880 CE2 TRP A 101 -125.347-148.723-102.429 1.00 42.04 C
ATOM 881 CE3 TRP A 101 -125.446-147.437-100.384 1.00 42.04 C
ATOM 882 CZ2 TRP A 101 -124.799-149.820-101.767 1.00 42.04 C
ATOM 883 CZ3 TRP A 101 -124.899-148.528 -99.725 1.00 42.04 C
ATOM 884 CH2 TRP A 101 -124.581-149.703-100.415 1.00 42.04 C
ATOM 885 H TRP A 101 -126.863-142.797-102.745 1.00 42.04 H
"""
pdb_inp = iotbx.pdb.input(source_info=None, lines=tst_pdb_1)
ann = pdb_inp.extract_secondary_structure()
model = mmtbx.model.manager(
model_input = pdb_inp,
build_grm = True)
model.set_ss_annotation(ann)
try:
rm = ssb.substitute_ss(
model)
rm.run()
except Sorry as e:
assert e.args[0].startswith("C, CA or N")
except Exception:
assert 0, "Error: This test failed"
else:
assert 0, "Error: This test failed"