def test_hewl():
mtz = gemmi.read_mtz_file(data_path("hewl_data.mtz"))
fsigf = DataItem(mtz, "F_New,SIGF_New")
fphi = DataItem(mtz, "FWT,PHWT")
comit = Comit(fsigf, fphi)
assert comit.abcd.nreflections == mtz.nreflections
assert comit.fphi.nreflections == mtz.nreflections
def test_combine_data_items():
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
fsigf = DataItem(mtz, "FP,SIGFP")
freer = DataItem(mtz, "FREE")
combined = _combine_data_items([fsigf, freer])
assert combined.column_labels() == ["H", "K", "L", "FP", "SIGFP", "FREE"]
assert mtz.nreflections == combined.nreflections
def test_1kv9():
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
fsigf = DataItem(mtz, "FP,SIGFP")
freer = DataItem(mtz, "FREE")
structure = read_structure(data_path("1kv9_model.pdb"))
sheetbend = Sheetbend(fsigf, freer, structure)
assert ModelStats(structure) == ModelStats(sheetbend.structure)
def test_1kv9():
contents = AsuContents(data_path("1kv9_sequence.fasta"))
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
fsigf = DataItem(mtz, "FP,SIGFP")
freer = DataItem(mtz, "FREE")
phases = DataItem(mtz, "HL")
parrot = Parrot(contents, fsigf, freer, phases)
assert parrot.abcd.nreflections == mtz.nreflections
assert parrot.fphi.nreflections == mtz.nreflections
def test_1kv9_prune():
structure = read_structure(data_path("1kv9_model.pdb"))
stats_in = ModelStats(structure)
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
fsigf = DataItem(mtz, "FP,SIGFP")
freer = DataItem(mtz, "FREE")
refmac = Refmac(structure, fsigf, freer, cycles=1)
prune = Prune(structure, refmac.fphi_best, refmac.fphi_diff)
stats_out = ModelStats(prune.structure)
assert stats_out.residues < stats_in.residues
def test_1kv9_fix_side_chains():
structure = read_structure(data_path("1kv9_model.pdb"))
stats_in = ModelStats(structure)
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
fsigf = DataItem(mtz, "FP,SIGFP")
freer = DataItem(mtz, "FREE")
refmac = Refmac(structure, fsigf, freer, cycles=1)
sidechains = FixSideChains(structure, refmac.fphi_best, refmac.fphi_diff)
stats_out = ModelStats(sidechains.structure)
assert stats_out.residues == stats_in.residues
def test_1kv9():
structure = read_structure(data_path("1kv9_model.pdb"))
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
fsigf = DataItem(mtz, "FP,SIGFP")
freer = DataItem(mtz, "FREE")
refmac = Refmac(structure, fsigf, freer, cycles=1)
assert refmac.fsigf.nreflections == mtz.nreflections
assert refmac.abcd.nreflections == mtz.nreflections
assert refmac.fphi_best.nreflections == mtz.nreflections
assert refmac.fphi_diff.nreflections == mtz.nreflections
assert refmac.fphi_calc.nreflections == mtz.nreflections
assert refmac.rwork_change < 0
def test_1kv9_dataitem_init_types():
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
item = DataItem(mtz, "FP,SIGFP") # str
assert item.label() == "FP,SIGFP"
item = DataItem(mtz, mtz.columns[4:6]) # gemmi.MtzColumns
assert item.label() == "FP,SIGFP"
item = DataItem(mtz,
[mtz.columns[4], mtz.columns[5]]) # List[gemmi.Mtz.Column]
assert item.label() == "FP,SIGFP"
def test_1kv9():
contents = AsuContents(data_path("1kv9_sequence.fasta"))
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
fsigf = DataItem(mtz, "FP,SIGFP")
freer = DataItem(mtz, "FREE")
phases = DataItem(mtz, "HL")
buccaneer = Buccaneer(contents=contents,
fsigf=fsigf,
freer=freer,
phases=phases,
cycles=1)
stats = ModelStats(buccaneer.structure)
assert stats.residues > 0
def test_invalid_columns_for_mtz_with_multiple_datasets(columns):
mtz = gemmi.read_mtz_file(data_path("hewl_data.mtz"))
mtz.add_dataset("Old")
mtz.add_column("HLA", "A")
mtz.add_column("HLB", "A")
mtz.add_column("HLC", "A")
mtz.add_column("HLD", "A")
with pytest.raises(ValueError):
DataItem(mtz, columns)
def test_1kv9():
structure = read_structure(data_path("1kv9_model.pdb"))
stats_in = ModelStats(structure)
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
fsigf = DataItem(mtz, "FP,SIGFP")
freer = DataItem(mtz, "FREE")
refmac = Refmac(structure, fsigf, freer, cycles=1)
findwaters = FindWaters(structure, refmac.fphi_best)
stats_out = ModelStats(findwaters.structure)
assert stats_out.residues == stats_in.residues
assert stats_out.waters > stats_in.waters
assert stats_out.dummy_atoms == stats_in.dummy_atoms
findwaters = FindWaters(structure, refmac.fphi_best, dummy=True)
stats_out = ModelStats(findwaters.structure)
assert stats_out.residues == stats_in.residues
assert stats_out.waters == stats_in.waters
assert stats_out.dummy_atoms > stats_in.dummy_atoms
def test_valid_columns_for_mtz_with_multiple_datasets(columns):
mtz = gemmi.read_mtz_file(data_path("hewl_data.mtz"))
mtz.add_dataset("Old")
mtz.add_column("HLA", "A")
mtz.add_column("HLB", "A")
mtz.add_column("HLC", "A")
mtz.add_column("HLD", "A")
abcd = DataItem(mtz, columns)
assert abcd.types == "AAAA"
assert len(abcd.columns) == 7
def test_valid_1kv9_free_columns(columns: str):
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
free = DataItem(mtz, columns)
assert len(free.columns) == 4
def test_1kv9_item_search(types: str, expected_labels: List[str]):
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
labels = [item.label() for item in DataItem.search(mtz, types)]
assert labels == expected_labels
def test_1kv9_resolution():
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
item = DataItem(mtz, "FP,SIGFP")
assert item.resolution == pytest.approx(1.8, abs=0.001)
def test_invalid_1kv9_columns(columns: str):
mtz = gemmi.read_mtz_file(data_path("1kv9_data.mtz"))
with pytest.raises(ValueError):
DataItem(mtz, columns)
def test_hewl_item_search(types, expected_labels):
mtz = gemmi.read_mtz_file(data_path("hewl_data.mtz"))
labels = [item.label() for item in DataItem.search(mtz, types)]
assert labels == expected_labels
def test_hewl_abcd_columns(columns: str):
mtz = gemmi.read_mtz_file(data_path("hewl_data.mtz"))
abcd = DataItem(mtz, columns)
assert abcd.types == "AAAA"
assert len(abcd.columns) == 7