def exercise_heavy () :
from mmtbx.regression import make_fake_anomalous_data
from mmtbx.command_line import validate_waters
import mmtbx.ions.utils
from iotbx.file_reader import any_file
file_base = "tst_validate_waters_1"
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(file_base=file_base)
mtz_file = make_fake_anomalous_data.generate_mtz_file(
file_base="tst_validate_waters_1",
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CD", fp=-0.29, fdp=2.676),
group_args(selection="element CL", fp=0.256, fdp=0.5),
])
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
hierarchy.write_pdb_file("%s_start.pdb" % file_base,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
args = ["tst_validate_waters_1_start.pdb", "tst_validate_waters_1.mtz",
"skip_twin_detection=True"]
results = validate_waters.run(args=args, out=null_out())
out = StringIO()
results.show(out=out)
s = easy_pickle.dumps(results)
r2 = easy_pickle.loads(s)
out2 = StringIO()
r2.show(out=out2)
assert not show_diff(out.getvalue(), out2.getvalue())
assert (results.n_bad >= 1) and (results.n_heavy == 2)
def exercise_heavy():
from mmtbx.regression import make_fake_anomalous_data
from mmtbx.command_line import validate_waters
import mmtbx.ions.utils
from iotbx.file_reader import any_file
file_base = "tst_validate_waters_1"
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base=file_base)
mtz_file = make_fake_anomalous_data.generate_mtz_file(
file_base="tst_validate_waters_1",
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CD", fp=-0.29, fdp=2.676),
group_args(selection="element CL", fp=0.256, fdp=0.5),
])
pdb_in = any_file(pdb_file)
hierarchy = pdb_in.file_object.hierarchy
hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
hierarchy.write_pdb_file(
"%s_start.pdb" % file_base,
crystal_symmetry=pdb_in.file_object.crystal_symmetry())
args = [
"tst_validate_waters_1_start.pdb", "tst_validate_waters_1.mtz",
"skip_twin_detection=True"
]
results = validate_waters.run(args=args, out=null_out())
out = StringIO()
results.show(out=out)
s = easy_pickle.dumps(results)
r2 = easy_pickle.loads(s)
out2 = StringIO()
r2.show(out=out2)
assert not show_diff(out.getvalue(), out2.getvalue())
assert (results.n_bad >= 1) and (results.n_heavy == 2)
def exercise():
from mmtbx.regression import make_fake_anomalous_data
import mmtbx.command_line.water_screen
import mmtbx.ions.utils
from iotbx.file_reader import any_file
pdb_in = """\
CRYST1 51.491 51.491 35.389 90.00 90.00 120.00 P 31 2 1
SCALE1 0.019421 0.011213 0.000000 0.00000
SCALE2 0.000000 0.022425 0.000000 0.00000
SCALE3 0.000000 0.000000 0.028257 0.00000
HETATM 32 CA CGU A 17 7.453 25.360 36.702 1.00 25.21 C
HETATM 33 C CGU A 17 6.252 24.666 36.060 1.00 24.08 C
HETATM 34 O CGU A 17 6.408 23.698 35.327 1.00 22.85 O
HETATM 35 CB CGU A 17 7.547 24.924 38.163 1.00 28.34 C
HETATM 36 CG CGU A 17 8.807 24.090 38.525 1.00 29.46 C
HETATM 37 CD1 CGU A 17 9.396 23.286 37.336 1.00 28.04 C
HETATM 38 CD2 CGU A 17 8.411 23.255 39.740 1.00 32.29 C
HETATM 39 OE11 CGU A 17 10.339 23.775 36.690 1.00 31.46 O
HETATM 40 OE12 CGU A 17 8.917 22.160 37.075 1.00 26.97 O
HETATM 41 OE21 CGU A 17 7.958 23.926 40.668 1.00 35.00 O
HETATM 42 OE22 CGU A 17 8.527 22.036 39.780 1.00 33.69 O
ATOM 43 N PRO A 18 5.029 25.135 36.349 1.00 23.16 N
ATOM 62 CA ARG A 20 7.902 23.943 32.052 1.00 22.37 C
ATOM 63 C ARG A 20 7.515 22.468 32.019 1.00 24.90 C
ATOM 64 O ARG A 20 7.956 21.738 31.130 1.00 24.00 O
ATOM 65 CB ARG A 20 9.024 24.136 33.067 1.00 26.75 C
ATOM 67 CD ARG A 20 10.812 25.597 34.000 1.00 36.42 C
HETATM 72 N CGU A 21 6.701 22.022 32.980 1.00 24.22 N
HETATM 73 CA CGU A 21 6.293 20.612 33.012 1.00 23.24 C
HETATM 74 C CGU A 21 5.432 20.293 31.805 1.00 23.70 C
HETATM 75 O CGU A 21 5.561 19.221 31.216 1.00 20.30 O
HETATM 76 CB CGU A 21 5.506 20.267 34.289 1.00 24.58 C
HETATM 77 CG CGU A 21 6.392 20.445 35.528 1.00 26.52 C
HETATM 78 CD1 CGU A 21 7.353 19.249 35.754 1.00 27.96 C
HETATM 79 CD2 CGU A 21 5.507 20.718 36.738 1.00 29.78 C
HETATM 80 OE11 CGU A 21 8.366 19.406 36.482 1.00 27.23 O
HETATM 81 OE12 CGU A 21 7.056 18.159 35.217 1.00 25.25 O
HETATM 82 OE21 CGU A 21 4.695 21.625 36.586 1.00 36.91 O
HETATM 83 OE22 CGU A 21 5.664 20.139 37.797 1.00 32.02 O
ATOM 93 C CYS A 23 7.212 20.248 27.692 1.00 25.63 C
ATOM 94 O CYS A 23 7.306 19.599 26.656 1.00 22.02 O
HETATM 97 N CGU A 24 7.761 19.852 28.842 1.00 26.69 N
HETATM 98 CA CGU A 24 8.527 18.607 28.931 1.00 29.70 C
HETATM 99 C CGU A 24 7.665 17.456 28.476 1.00 31.08 C
HETATM 100 O CGU A 24 8.143 16.541 27.812 1.00 32.94 O
HETATM 101 CB CGU A 24 8.981 18.304 30.367 1.00 26.05 C
HETATM 102 CG CGU A 24 9.966 19.357 30.876 1.00 26.18 C
HETATM 103 CD1 CGU A 24 11.275 19.290 30.093 1.00 24.75 C
HETATM 104 CD2 CGU A 24 10.148 19.172 32.390 1.00 27.43 C
HETATM 105 OE11 CGU A 24 12.023 18.293 30.233 1.00 29.79 O
HETATM 106 OE12 CGU A 24 11.537 20.244 29.348 1.00 24.99 O
HETATM 107 OE21 CGU A 24 9.100 19.190 33.043 1.00 28.87 O
HETATM 108 OE22 CGU A 24 11.260 19.084 32.908 1.00 24.87 O
ATOM 143 O CYS A 29 10.353 21.841 23.789 1.00 30.74 O
ATOM 146 N ASP A 30 9.604 19.770 24.234 1.00 32.83 N
ATOM 147 CA ASP A 30 10.776 19.402 25.014 1.00 34.15 C
ATOM 148 C ASP A 30 12.026 19.580 24.177 1.00 36.29 C
ATOM 149 O ASP A 30 12.937 20.322 24.544 1.00 34.50 O
ATOM 150 CB ASP A 30 10.685 17.949 25.464 1.00 33.18 C
ATOM 151 CG ASP A 30 11.714 17.607 26.523 1.00 32.22 C
ATOM 152 OD1 ASP A 30 12.621 18.428 26.752 1.00 32.53 O
ATOM 153 OD2 ASP A 30 11.608 16.524 27.125 1.00 31.78 O
ATOM 154 N GLU A 31 12.056 18.885 23.045 1.00 39.34 N
ATOM 155 CA GLU A 31 13.186 18.954 22.135 1.00 40.16 C
ATOM 172 CA ALA A 33 13.225 23.877 24.346 1.00 39.26 C
ATOM 173 C ALA A 33 14.746 23.914 24.481 1.00 38.24 C
ATOM 175 CB ALA A 33 12.600 23.326 25.630 1.00 37.33 C
ATOM 176 N ASP A 34 15.400 22.799 24.170 1.00 39.56 N
ATOM 177 CA ASP A 34 16.857 22.723 24.258 1.00 40.96 C
ATOM 180 CB ASP A 34 17.352 21.300 23.976 1.00 40.20 C
ATOM 181 CG ASP A 34 17.006 20.327 25.083 1.00 38.93 C
ATOM 182 OD1 ASP A 34 16.981 20.742 26.262 1.00 41.79 O
ATOM 183 OD2 ASP A 34 16.777 19.140 24.778 1.00 37.45 O
TER
HETATM 316 CA CA A 71 13.077 17.433 32.271 1.00 22.23 CA
HETATM 317 CA CA A 72 13.835 18.867 28.887 1.00 30.50 CA
HETATM 318 CA CA A 73 10.897 18.813 35.385 1.00 50.79 CA
HETATM 320 O HOH A 75 13.387 22.461 33.530 1.00 24.93 O
HETATM 323 O HOH A 78 10.578 15.304 29.567 1.00 23.15 O
HETATM 324 O HOH A 79 5.020 20.563 40.636 1.00 44.02 O
HETATM 325 O HOH A 80 2.823 22.144 38.546 1.00 36.74 O
HETATM 326 O HOH A 81 10.434 22.631 29.604 1.00 25.89 O
HETATM 327 O HOH A 82 6.522 15.691 36.473 1.00 27.82 O
HETATM 332 O HOH A 87 11.624 15.358 31.822 1.00 24.92 O
HETATM 333 O HOH A 88 13.763 16.798 28.667 1.00 29.47 O
HETATM 334 O HOH A 89 6.350 16.973 32.340 1.00 37.83 O
HETATM 338 O HOH A 93 10.474 21.054 34.739 1.00 25.48 O
HETATM 342 O HOH A 97 16.203 18.688 27.720 1.00 28.10 O
HETATM 343 O HOH A 98 8.186 14.327 30.477 1.00 49.44 O
HETATM 344 O HOH A 99 8.625 16.477 33.868 1.00 48.13 O
HETATM 347 O HOH A 102 15.462 16.714 24.789 1.00 42.90 O
HETATM 356 O HOH A 111 4.757 17.423 38.879 1.00 34.26 O
HETATM 358 O HOH A 113 10.313 14.495 25.452 1.00 40.66 O
HETATM 359 O HOH A 114 1.979 18.616 37.760 1.00 34.25 O
HETATM 363 O HOH A 118 13.926 20.627 27.271 1.00 29.62 O
HETATM 365 O HOH A 120 16.240 23.471 27.700 1.00 48.79 O
HETATM 370 O HOH A 125 2.747 18.823 35.170 1.00 50.30 O
HETATM 372 O HOH A 127 5.228 23.553 41.559 1.00 42.02 O
HETATM 373 O HOH A 128 5.298 21.833 43.473 1.00 41.96 O
HETATM 377 O HOH A 132 13.181 22.613 29.210 1.00 35.43 O
TER
"""
file_base = "tst_symmetry_axis"
with open(file_base + ".pdb", "w") as f:
f.write(pdb_in)
f = any_file(file_base + ".pdb")
hierarchy = f.file_object.hierarchy
xrs = f.file_object.xray_structure_simple()
hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
assert (n == 3)
with open(file_base + "_in.pdb", "w") as f:
f.write(hierarchy.as_pdb_string(crystal_symmetry=xrs))
mtz_file = make_fake_anomalous_data.generate_mtz_file(
file_base=file_base,
d_min=1.5,
anomalous_scatterers=[
group_args(selection="element CA", fp=0.0, fdp=0.4)
])
args = [
file_base + "_in.pdb",
file_base + ".mtz",
"wavelength=0.9792",
"use_phaser=False",
"nproc=1",
"skip_twin_test=True",
"elements=CA",
]
out = StringIO()
mmtbx.command_line.water_screen.run(args=args, out=out)
assert "Valence sum: 1.916" in out.getvalue()
assert out.getvalue().count("Probable cation: CA+2") >= 1
os.remove(file_base + ".pdb")
os.remove(file_base + "_in.pdb")
os.remove(file_base + ".mtz")
os.remove(file_base + "_fmodel.eff")
def exercise () :
from mmtbx.regression import make_fake_anomalous_data
import mmtbx.command_line.water_screen
import mmtbx.ions.utils
from iotbx.file_reader import any_file
pdb_in = """\
CRYST1 51.491 51.491 35.389 90.00 90.00 120.00 P 31 2 1
SCALE1 0.019421 0.011213 0.000000 0.00000
SCALE2 0.000000 0.022425 0.000000 0.00000
SCALE3 0.000000 0.000000 0.028257 0.00000
HETATM 32 CA CGU A 17 7.453 25.360 36.702 1.00 25.21 C
HETATM 33 C CGU A 17 6.252 24.666 36.060 1.00 24.08 C
HETATM 34 O CGU A 17 6.408 23.698 35.327 1.00 22.85 O
HETATM 35 CB CGU A 17 7.547 24.924 38.163 1.00 28.34 C
HETATM 36 CG CGU A 17 8.807 24.090 38.525 1.00 29.46 C
HETATM 37 CD1 CGU A 17 9.396 23.286 37.336 1.00 28.04 C
HETATM 38 CD2 CGU A 17 8.411 23.255 39.740 1.00 32.29 C
HETATM 39 OE11 CGU A 17 10.339 23.775 36.690 1.00 31.46 O
HETATM 40 OE12 CGU A 17 8.917 22.160 37.075 1.00 26.97 O
HETATM 41 OE21 CGU A 17 7.958 23.926 40.668 1.00 35.00 O
HETATM 42 OE22 CGU A 17 8.527 22.036 39.780 1.00 33.69 O
ATOM 43 N PRO A 18 5.029 25.135 36.349 1.00 23.16 N
ATOM 62 CA ARG A 20 7.902 23.943 32.052 1.00 22.37 C
ATOM 63 C ARG A 20 7.515 22.468 32.019 1.00 24.90 C
ATOM 64 O ARG A 20 7.956 21.738 31.130 1.00 24.00 O
ATOM 65 CB ARG A 20 9.024 24.136 33.067 1.00 26.75 C
ATOM 67 CD ARG A 20 10.812 25.597 34.000 1.00 36.42 C
HETATM 72 N CGU A 21 6.701 22.022 32.980 1.00 24.22 N
HETATM 73 CA CGU A 21 6.293 20.612 33.012 1.00 23.24 C
HETATM 74 C CGU A 21 5.432 20.293 31.805 1.00 23.70 C
HETATM 75 O CGU A 21 5.561 19.221 31.216 1.00 20.30 O
HETATM 76 CB CGU A 21 5.506 20.267 34.289 1.00 24.58 C
HETATM 77 CG CGU A 21 6.392 20.445 35.528 1.00 26.52 C
HETATM 78 CD1 CGU A 21 7.353 19.249 35.754 1.00 27.96 C
HETATM 79 CD2 CGU A 21 5.507 20.718 36.738 1.00 29.78 C
HETATM 80 OE11 CGU A 21 8.366 19.406 36.482 1.00 27.23 O
HETATM 81 OE12 CGU A 21 7.056 18.159 35.217 1.00 25.25 O
HETATM 82 OE21 CGU A 21 4.695 21.625 36.586 1.00 36.91 O
HETATM 83 OE22 CGU A 21 5.664 20.139 37.797 1.00 32.02 O
ATOM 93 C CYS A 23 7.212 20.248 27.692 1.00 25.63 C
ATOM 94 O CYS A 23 7.306 19.599 26.656 1.00 22.02 O
HETATM 97 N CGU A 24 7.761 19.852 28.842 1.00 26.69 N
HETATM 98 CA CGU A 24 8.527 18.607 28.931 1.00 29.70 C
HETATM 99 C CGU A 24 7.665 17.456 28.476 1.00 31.08 C
HETATM 100 O CGU A 24 8.143 16.541 27.812 1.00 32.94 O
HETATM 101 CB CGU A 24 8.981 18.304 30.367 1.00 26.05 C
HETATM 102 CG CGU A 24 9.966 19.357 30.876 1.00 26.18 C
HETATM 103 CD1 CGU A 24 11.275 19.290 30.093 1.00 24.75 C
HETATM 104 CD2 CGU A 24 10.148 19.172 32.390 1.00 27.43 C
HETATM 105 OE11 CGU A 24 12.023 18.293 30.233 1.00 29.79 O
HETATM 106 OE12 CGU A 24 11.537 20.244 29.348 1.00 24.99 O
HETATM 107 OE21 CGU A 24 9.100 19.190 33.043 1.00 28.87 O
HETATM 108 OE22 CGU A 24 11.260 19.084 32.908 1.00 24.87 O
ATOM 143 O CYS A 29 10.353 21.841 23.789 1.00 30.74 O
ATOM 146 N ASP A 30 9.604 19.770 24.234 1.00 32.83 N
ATOM 147 CA ASP A 30 10.776 19.402 25.014 1.00 34.15 C
ATOM 148 C ASP A 30 12.026 19.580 24.177 1.00 36.29 C
ATOM 149 O ASP A 30 12.937 20.322 24.544 1.00 34.50 O
ATOM 150 CB ASP A 30 10.685 17.949 25.464 1.00 33.18 C
ATOM 151 CG ASP A 30 11.714 17.607 26.523 1.00 32.22 C
ATOM 152 OD1 ASP A 30 12.621 18.428 26.752 1.00 32.53 O
ATOM 153 OD2 ASP A 30 11.608 16.524 27.125 1.00 31.78 O
ATOM 154 N GLU A 31 12.056 18.885 23.045 1.00 39.34 N
ATOM 155 CA GLU A 31 13.186 18.954 22.135 1.00 40.16 C
ATOM 172 CA ALA A 33 13.225 23.877 24.346 1.00 39.26 C
ATOM 173 C ALA A 33 14.746 23.914 24.481 1.00 38.24 C
ATOM 175 CB ALA A 33 12.600 23.326 25.630 1.00 37.33 C
ATOM 176 N ASP A 34 15.400 22.799 24.170 1.00 39.56 N
ATOM 177 CA ASP A 34 16.857 22.723 24.258 1.00 40.96 C
ATOM 180 CB ASP A 34 17.352 21.300 23.976 1.00 40.20 C
ATOM 181 CG ASP A 34 17.006 20.327 25.083 1.00 38.93 C
ATOM 182 OD1 ASP A 34 16.981 20.742 26.262 1.00 41.79 O
ATOM 183 OD2 ASP A 34 16.777 19.140 24.778 1.00 37.45 O
TER
HETATM 316 CA CA A 71 13.077 17.433 32.271 1.00 22.23 CA
HETATM 317 CA CA A 72 13.835 18.867 28.887 1.00 30.50 CA
HETATM 318 CA CA A 73 10.897 18.813 35.385 1.00 50.79 CA
HETATM 320 O HOH A 75 13.387 22.461 33.530 1.00 24.93 O
HETATM 323 O HOH A 78 10.578 15.304 29.567 1.00 23.15 O
HETATM 324 O HOH A 79 5.020 20.563 40.636 1.00 44.02 O
HETATM 325 O HOH A 80 2.823 22.144 38.546 1.00 36.74 O
HETATM 326 O HOH A 81 10.434 22.631 29.604 1.00 25.89 O
HETATM 327 O HOH A 82 6.522 15.691 36.473 1.00 27.82 O
HETATM 332 O HOH A 87 11.624 15.358 31.822 1.00 24.92 O
HETATM 333 O HOH A 88 13.763 16.798 28.667 1.00 29.47 O
HETATM 334 O HOH A 89 6.350 16.973 32.340 1.00 37.83 O
HETATM 338 O HOH A 93 10.474 21.054 34.739 1.00 25.48 O
HETATM 342 O HOH A 97 16.203 18.688 27.720 1.00 28.10 O
HETATM 343 O HOH A 98 8.186 14.327 30.477 1.00 49.44 O
HETATM 344 O HOH A 99 8.625 16.477 33.868 1.00 48.13 O
HETATM 347 O HOH A 102 15.462 16.714 24.789 1.00 42.90 O
HETATM 356 O HOH A 111 4.757 17.423 38.879 1.00 34.26 O
HETATM 358 O HOH A 113 10.313 14.495 25.452 1.00 40.66 O
HETATM 359 O HOH A 114 1.979 18.616 37.760 1.00 34.25 O
HETATM 363 O HOH A 118 13.926 20.627 27.271 1.00 29.62 O
HETATM 365 O HOH A 120 16.240 23.471 27.700 1.00 48.79 O
HETATM 370 O HOH A 125 2.747 18.823 35.170 1.00 50.30 O
HETATM 372 O HOH A 127 5.228 23.553 41.559 1.00 42.02 O
HETATM 373 O HOH A 128 5.298 21.833 43.473 1.00 41.96 O
HETATM 377 O HOH A 132 13.181 22.613 29.210 1.00 35.43 O
TER
"""
file_base = "tst_symmetry_axis"
with open(file_base + ".pdb", "w") as f:
f.write(pdb_in)
f = any_file(file_base + ".pdb")
hierarchy = f.file_object.hierarchy
xrs = f.file_object.xray_structure_simple()
hierarchy, n = mmtbx.ions.utils.anonymize_ions(hierarchy, log=null_out())
assert (n == 3)
with open(file_base + "_in.pdb", "w") as f:
f.write(hierarchy.as_pdb_string(crystal_symmetry=xrs))
mtz_file = make_fake_anomalous_data.generate_mtz_file(
file_base=file_base,
d_min=1.5,
anomalous_scatterers=[group_args(
selection="element CA",
fp=0.0,
fdp=0.4)])
args = [
file_base + "_in.pdb",
file_base + ".mtz",
"wavelength=0.9792",
"use_phaser=False",
"nproc=1",
"skip_twin_test=True",
"elements=CA",
]
out = StringIO()
mmtbx.command_line.water_screen.run(args=args, out=out)
assert "Valence sum: 1.916" in out.getvalue()
assert out.getvalue().count("Probable cation: CA+2") >= 1
os.remove(file_base + ".pdb")
os.remove(file_base + "_in.pdb")
os.remove(file_base + ".mtz")
os.remove(file_base + "_fmodel.eff")
