def check_adp_set_b_iso(
cmd, xrsp_init, output, selection, selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance)
assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance)
assert approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance)
assert approx_equal(xrsp.u_iso_not_used, xrsp_init.u_iso_not_used,tolerance)
assert approx_equal(xrsp.u_cart_not_used,xrsp_init.u_cart_not_used,tolerance)
if(selection_str is None):
assert not_approx_equal(xrsp.u_iso_used, xrsp_init.u_iso_used,tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
else:
arg1 = xrsp.u_iso_used.select(selection.select(xrsp.use_u_iso))
arg2 = xrsp_init.u_iso_used.select(selection.select(xrsp_init.use_u_iso))
if(arg1.size() > 0): assert not_approx_equal(arg1, arg2,tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
def check_keep_selection(cmd,
xrsp_init,
output,
selection,
selection_str,
keep_selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
keep_selection = xrsp_init.selection(selection_strings=keep_selection_str)
assert approx_equal(xrsp.sites_cart,
xrsp_init.sites_cart.select(keep_selection), tolerance)
assert approx_equal(xrsp.occ, xrsp_init.occ.select(keep_selection),
tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso.select(keep_selection),
tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart.select(keep_selection),
tolerance)
sct1 = xrsp_init.xray_structure.scatterers().extract_scattering_types()
assert sct1.count("C") > 0 and sct1.size() > sct1.count("C")
sct2 = xrsp.xray_structure.scatterers().extract_scattering_types()
assert sct2.count("C") == sct2.size()
assert sct1.size() > keep_selection.count(True)
assert sct1.size() > sct2.size()
def check_adp_set_b_iso(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso, tolerance)
assert approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso, tolerance)
assert approx_equal(xrsp.u_iso_not_used, xrsp_init.u_iso_not_used,
tolerance)
assert approx_equal(xrsp.u_cart_not_used, xrsp_init.u_cart_not_used,
tolerance)
if (selection_str is None):
assert not_approx_equal(xrsp.u_iso_used, xrsp_init.u_iso_used,
tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
else:
arg1 = xrsp.u_iso_used.select(selection.select(xrsp.use_u_iso))
arg2 = xrsp_init.u_iso_used.select(
selection.select(xrsp_init.use_u_iso))
if (arg1.size() > 0): assert not_approx_equal(arg1, arg2, tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
def exercise_convert_met_to_semet():
pdb_str_met = """
ATOM 1 N MET B 37 7.525 5.296 6.399 1.00 10.00 N
ATOM 2 CA MET B 37 6.533 6.338 6.634 1.00 10.00 C
ATOM 3 C MET B 37 6.175 7.044 5.330 1.00 10.00 C
ATOM 4 O MET B 37 5.000 7.200 5.000 1.00 10.00 O
ATOM 5 CB MET B 37 7.051 7.351 7.655 1.00 10.00 C
ATOM 6 CG MET B 37 7.377 6.750 9.013 1.00 10.00 C
ATOM 7 SD MET B 37 8.647 5.473 8.922 1.00 10.00 S
ATOM 8 CE MET B 37 8.775 5.000 10.645 1.00 10.00 C
TER
END
"""
pi = iotbx.pdb.input(source_info=None, lines=pdb_str_met)
ph_met_in = pi.construct_hierarchy()
pi.write_pdb_file(file_name="exercise_convert_met_to_semet.pdb")
cmd = " ".join([
"phenix.pdbtools", "exercise_convert_met_to_semet.pdb",
"convert_met_to_semet=true"
])
run_command(command=cmd, verbose=False)
cmd = " ".join([
"phenix.pdbtools", "exercise_convert_met_to_semet.pdb_modified.pdb",
"convert_semet_to_met=true"
])
run_command(command=cmd, verbose=False)
pi_met_out = iotbx.pdb.input(
file_name="exercise_convert_met_to_semet.pdb_modified.pdb_modified.pdb"
).construct_hierarchy()
assert pi_met_out.is_similar_hierarchy(ph_met_in)
def exercise_normalize_occupancies():
pdb_in = """\
ATOM 16 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O
ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C
ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.41 12.23 C
ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 18 O AHOH B 3 1.132 5.963 7.065 0.80 15.00 O
ATOM 18 O BHOH B 3 1.132 5.963 7.065 0.50 15.00 O
ATOM 19 O AHOH B 4 4.132 9.963 7.800 0.50 15.00 O
ATOM 20 O BHOH B 4 4.132 9.963 7.800 0.40 15.00 O
ATOM 21 ZN ZN C 5 8.000 12.124 11.900 0.75 20.00 ZN
"""
open("tst_pdbtools_norm_occ.pdb", "w").write(pdb_in)
cmd = 'phenix.pdbtools tst_pdbtools_norm_occ.pdb occupancies.normalize=True modify.selection="not element ZN"'
run_command(command=cmd, verbose=False)
pdb_new = open("tst_pdbtools_norm_occ.pdb_modified.pdb").read()
assert (pdb_new == """\
ATOM 1 O AHOH A 2 5.131 5.251 5.823 1.00 10.00 O
ATOM 2 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 3 CB ALYS A 32 9.197 8.686 12.246 0.59 14.71 C
ATOM 4 CB BLYS A 32 9.193 8.732 12.170 0.41 12.23 C
ATOM 5 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 6 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
TER
ATOM 7 O AHOH B 3 1.132 5.963 7.065 0.50 15.00 O
ATOM 8 O BHOH B 3 1.132 5.963 7.065 0.50 15.00 O
ATOM 9 O AHOH B 4 4.132 9.963 7.800 0.60 15.00 O
ATOM 10 O BHOH B 4 4.132 9.963 7.800 0.40 15.00 O
TER
ATOM 11 ZN ZN C 5 8.000 12.124 11.900 0.75 20.00 Zn
TER
END
""")
def exercise_normalize_occupancies () :
pdb_in = """\
ATOM 16 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O
ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C
ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.41 12.23 C
ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 18 O AHOH B 3 1.132 5.963 7.065 0.80 15.00 O
ATOM 18 O BHOH B 3 1.132 5.963 7.065 0.50 15.00 O
ATOM 19 O AHOH B 4 4.132 9.963 7.800 0.50 15.00 O
ATOM 20 O BHOH B 4 4.132 9.963 7.800 0.40 15.00 O
ATOM 21 ZN ZN C 5 8.000 12.124 11.900 0.75 20.00 ZN
"""
open("tst_pdbtools_norm_occ.pdb", "w").write(pdb_in)
cmd = 'phenix.pdbtools tst_pdbtools_norm_occ.pdb occupancies.normalize=True modify.selection="not element ZN"'
run_command(command=cmd, verbose=False)
pdb_new = open("tst_pdbtools_norm_occ.pdb_modified.pdb").read()
assert (pdb_new == """\
ATOM 1 O AHOH A 2 5.131 5.251 5.823 1.00 10.00 O
ATOM 2 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 3 CB ALYS A 32 9.197 8.686 12.246 0.59 14.71 C
ATOM 4 CB BLYS A 32 9.193 8.732 12.170 0.41 12.23 C
ATOM 5 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 6 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
TER
ATOM 7 O AHOH B 3 1.132 5.963 7.065 0.50 15.00 O
ATOM 8 O BHOH B 3 1.132 5.963 7.065 0.50 15.00 O
ATOM 9 O AHOH B 4 4.132 9.963 7.800 0.60 15.00 O
ATOM 10 O BHOH B 4 4.132 9.963 7.800 0.40 15.00 O
TER
ATOM 11 ZN ZN C 5 8.000 12.124 11.900 0.75 20.00 Zn
TER
END
""")
def exercise_convert_met_to_semet():
pdb_str_met = """
ATOM 1 N MET B 37 7.525 5.296 6.399 1.00 10.00 N
ATOM 2 CA MET B 37 6.533 6.338 6.634 1.00 10.00 C
ATOM 3 C MET B 37 6.175 7.044 5.330 1.00 10.00 C
ATOM 4 O MET B 37 5.000 7.200 5.000 1.00 10.00 O
ATOM 5 CB MET B 37 7.051 7.351 7.655 1.00 10.00 C
ATOM 6 CG MET B 37 7.377 6.750 9.013 1.00 10.00 C
ATOM 7 SD MET B 37 8.647 5.473 8.922 1.00 10.00 S
ATOM 8 CE MET B 37 8.775 5.000 10.645 1.00 10.00 C
TER
END
"""
pi = iotbx.pdb.input(source_info=None, lines=pdb_str_met)
ph_met_in = pi.construct_hierarchy()
pi.write_pdb_file(file_name="exercise_convert_met_to_semet.pdb")
cmd = " ".join([
"phenix.pdbtools",
"exercise_convert_met_to_semet.pdb",
"convert_met_to_semet=true"])
run_command(command=cmd, verbose=False)
cmd = " ".join([
"phenix.pdbtools",
"exercise_convert_met_to_semet.pdb_modified.pdb",
"convert_semet_to_met=true"])
run_command(command=cmd, verbose=False)
pi_met_out = iotbx.pdb.input(
file_name="exercise_convert_met_to_semet.pdb_modified.pdb_modified.pdb"
).construct_hierarchy()
assert pi_met_out.is_similar_hierarchy(ph_met_in)
def exercise_move_waters():
pdb_in = """\
ATOM 16 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O
ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C
ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C
ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 18 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
ATOM 19 H1 HOH A 3 1.160 5.211 6.437 1.00 15.00 H
ATOM 20 H2 HOH A 3 1.122 5.579 7.967 1.00 15.00 H
HETATM 2397 P PO4 1 -7.520 25.376 38.369 1.00 39.37 P
HETATM 2398 O1 PO4 1 -6.610 24.262 38.967 1.00 40.00 O
HETATM 2399 O2 PO4 1 -6.901 25.919 37.049 1.00 41.07 O
HETATM 2400 O3 PO4 1 -8.894 24.741 38.097 1.00 45.09 O
HETATM 2401 O4 PO4 1 -7.722 26.556 39.350 1.00 42.48 O
ATOM 23 CL CL B 1 6.302 6.419 1.560 0.50 10.00 CL
HETATM 6362 O HOH B 2 47.616 10.724 150.212 1.00 46.48 B O
HETATM 6363 O AHOH B 3 46.408 16.672 146.066 0.50 12.81 B O
HETATM 6364 O HOH B 4 29.343 12.806 185.898 1.00 35.57 B O
HETATM 6365 O BHOH B 5 43.786 12.615 147.734 0.50 28.43 B O
HETATM 6366 O HOH B 6 35.068 19.167 155.349 1.00 15.97 B O
"""
pdb_out = """\
ATOM 1 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 2 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C
ATOM 3 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C
ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
TER
HETATM 6 O1 PO4 1 -6.610 24.262 38.967 1.00 40.00 O
HETATM 7 O2 PO4 1 -6.901 25.919 37.049 1.00 41.07 O
HETATM 8 O3 PO4 1 -8.894 24.741 38.097 1.00 45.09 O
HETATM 9 O4 PO4 1 -7.722 26.556 39.350 1.00 42.48 O
HETATM 10 P PO4 1 -7.520 25.376 38.369 1.00 39.37 P
TER
ATOM 11 CL CL B 1 6.302 6.419 1.560 0.50 10.00 Cl
TER
ATOM 12 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O
ATOM 13 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
ATOM 14 H1 HOH A 3 1.160 5.211 6.437 1.00 15.00 H
ATOM 15 H2 HOH A 3 1.122 5.579 7.967 1.00 15.00 H
TER
HETATM 16 O HOH B 2 47.616 10.724 150.212 1.00 46.48 B O
HETATM 17 O AHOH B 3 46.408 16.672 146.066 0.50 12.81 B O
HETATM 18 O HOH B 4 29.343 12.806 185.898 1.00 35.57 B O
HETATM 19 O BHOH B 5 43.786 12.615 147.734 0.50 28.43 B O
HETATM 20 O HOH B 6 35.068 19.167 155.349 1.00 15.97 B O
TER
END
"""
open("tst_pdbtools_move_waters.pdb", "w").write(pdb_in)
cmd = "phenix.pdbtools tst_pdbtools_move_waters.pdb move_waters_last=True"
run_command(command=cmd, verbose=False)
pdb_new = open("tst_pdbtools_move_waters.pdb_modified.pdb").read()
assert pdb_new == pdb_out, pdb_new
def exercise_move_waters () :
pdb_in = """\
ATOM 16 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O
ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C
ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C
ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 18 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
ATOM 19 H1 HOH A 3 1.160 5.211 6.437 1.00 15.00 H
ATOM 20 H2 HOH A 3 1.122 5.579 7.967 1.00 15.00 H
HETATM 2397 P PO4 1 -7.520 25.376 38.369 1.00 39.37 P
HETATM 2398 O1 PO4 1 -6.610 24.262 38.967 1.00 40.00 O
HETATM 2399 O2 PO4 1 -6.901 25.919 37.049 1.00 41.07 O
HETATM 2400 O3 PO4 1 -8.894 24.741 38.097 1.00 45.09 O
HETATM 2401 O4 PO4 1 -7.722 26.556 39.350 1.00 42.48 O
ATOM 23 CL CL B 1 6.302 6.419 1.560 0.50 10.00 CL
HETATM 6362 O HOH B 2 47.616 10.724 150.212 1.00 46.48 B O
HETATM 6363 O AHOH B 3 46.408 16.672 146.066 0.50 12.81 B O
HETATM 6364 O HOH B 4 29.343 12.806 185.898 1.00 35.57 B O
HETATM 6365 O BHOH B 5 43.786 12.615 147.734 0.50 28.43 B O
HETATM 6366 O HOH B 6 35.068 19.167 155.349 1.00 15.97 B O
"""
pdb_out = """\
ATOM 1 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 2 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C
ATOM 3 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C
ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
TER
HETATM 6 O1 PO4 1 -6.610 24.262 38.967 1.00 40.00 O
HETATM 7 O2 PO4 1 -6.901 25.919 37.049 1.00 41.07 O
HETATM 8 O3 PO4 1 -8.894 24.741 38.097 1.00 45.09 O
HETATM 9 O4 PO4 1 -7.722 26.556 39.350 1.00 42.48 O
HETATM 10 P PO4 1 -7.520 25.376 38.369 1.00 39.37 P
TER
ATOM 11 CL CL B 1 6.302 6.419 1.560 0.50 10.00 Cl
TER
ATOM 12 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O
ATOM 13 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
ATOM 14 H1 HOH A 3 1.160 5.211 6.437 1.00 15.00 H
ATOM 15 H2 HOH A 3 1.122 5.579 7.967 1.00 15.00 H
TER
HETATM 16 O HOH B 2 47.616 10.724 150.212 1.00 46.48 B O
HETATM 17 O AHOH B 3 46.408 16.672 146.066 0.50 12.81 B O
HETATM 18 O HOH B 4 29.343 12.806 185.898 1.00 35.57 B O
HETATM 19 O BHOH B 5 43.786 12.615 147.734 0.50 28.43 B O
HETATM 20 O HOH B 6 35.068 19.167 155.349 1.00 15.97 B O
TER
END
"""
open("tst_pdbtools_move_waters.pdb", "w").write(pdb_in)
cmd = "phenix.pdbtools tst_pdbtools_move_waters.pdb move_waters_last=True"
run_command(command=cmd, verbose=False)
pdb_new = open("tst_pdbtools_move_waters.pdb_modified.pdb").read()
assert pdb_new == pdb_out, pdb_new
def test_quiet(file_name, verbose):
output_file_name = "shifted.pdb"
remove_files("log")
remove_files(output_file_name)
assert file_name.find('"') < 0
cmd= 'phenix.pdbtools "%s" output.file_name=%s shake=0.1 --quiet > log'%(
file_name, output_file_name)
run_command(command=cmd, verbose=verbose)
lines = open("log","r").readlines()
assert len(lines) == 0
def check_all_none(cmd, xrsp_init, output, verbose, tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso, tolerance)
assert approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso, tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso, tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart, tolerance)
def check_all_none(cmd, xrsp_init, output, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance) assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance) assert approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso,tolerance) assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance) assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance)
def test_quiet(file_name, verbose):
output_file_name = "shifted.pdb"
remove_files("log")
remove_files(output_file_name)
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" output.file_name=%s shake=0.1 --quiet > log' % (
file_name, output_file_name)
run_command(command=cmd, verbose=verbose)
lines = open("log", "r").readlines()
assert len(lines) == 0
def exercise_remove_first_n_atoms_fraction(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "enk_gbr.pdb")
n_atoms_start = iotbx.pdb.hierarchy.input(
file_name=file_name).xray_structure_simple().scatterers().size()
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" remove_first_n_atoms_fraction=0.6'%file_name
run_command(command=cmd, verbose=verbose)
pdb_inp = iotbx.pdb.hierarchy.input(file_name="enk_gbr.pdb_modified.pdb")
n_atoms_final = iotbx.pdb.hierarchy.input(
file_name="enk_gbr.pdb_modified.pdb").xray_structure_simple().scatterers().size()
assert n_atoms_final*1./n_atoms_start == 0.4
def exercise_truncate_to_polyala(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "enk_gbr.pdb")
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" truncate_to_polyala=true' % file_name
run_command(command=cmd, verbose=verbose)
ala_atom_names = [" N ", " CA ", " C ", " O ", " CB "]
pdb_inp = iotbx.pdb.hierarchy.input(file_name="enk_gbr.pdb_modified.pdb")
counter = 0
for a in pdb_inp.hierarchy.atoms_with_labels():
assert a.name in ala_atom_names
counter += 1
assert counter == 23
def exercise_remove_first_n_atoms_fraction(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "enk_gbr.pdb")
n_atoms_start = iotbx.pdb.hierarchy.input(
file_name=file_name).xray_structure_simple().scatterers().size()
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" remove_first_n_atoms_fraction=0.6' % file_name
run_command(command=cmd, verbose=verbose)
pdb_inp = iotbx.pdb.hierarchy.input(file_name="enk_gbr.pdb_modified.pdb")
n_atoms_final = iotbx.pdb.hierarchy.input(
file_name="enk_gbr.pdb_modified.pdb").xray_structure_simple(
).scatterers().size()
assert n_atoms_final * 1. / n_atoms_start == 0.4
def exercise_truncate_to_polyala(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "enk_gbr.pdb")
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" truncate_to_polyala=true'%file_name
run_command(command=cmd, verbose=verbose)
ala_atom_names = [" N ", " CA ", " C ", " O ", " CB "]
pdb_inp = iotbx.pdb.hierarchy.input(file_name="enk_gbr.pdb_modified.pdb")
counter = 0
for a in pdb_inp.hierarchy.atoms_with_labels():
assert a.name in ala_atom_names
counter += 1
assert counter == 23
def exercise_show_number_of_removed(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "phe_h.pdb")
log = "exercise_show_number_of_removed.log"
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" remove="element H" > %s' % (file_name, log)
remove_files(log)
run_command(command=cmd, verbose=verbose)
assert os.path.isfile(log)
n_found = 0
for line in open(log).read().splitlines():
if (line == "Atoms to be kept: 13 of 24"):
n_found += 1
assert n_found == 1
def run_concoord(self, nstruct, prefix='prefix'):
env = libtbx.env_config.unpickle()
self.dist= env.find_dist_path('sastbx')+'/concoord/mydist.csh'
self.disco= env.find_dist_path('sastbx')+'/concoord/mydisco.csh'
# initialize distance constraints
op_file = prefix+".pdb"
og_file = prefix+".gro"
od_file = prefix+".dat"
run_command(self.dist+" -p %s -op %s -og %s -od %s >& %s.log0"%(self.pdb_file, op_file, og_file, od_file, prefix ) )
# run disco to generate nstruct conformations
#print "running:\n", self.disco+" -p %s -n %d -op %s>%s.log &"%(self.pdb_file,nstruct,prefix,prefix)
random_number = random.randint(1,741265)
run_command(self.disco+" -p %s -d %s -n %d -op %s -s %d >& %s.log &"%(op_file,od_file,nstruct,prefix,random_number,prefix) )
def exercise_show_number_of_removed(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "phe_h.pdb")
log = "exercise_show_number_of_removed.log"
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" remove="element H" > %s' % (file_name, log)
remove_files(log)
run_command(command=cmd, verbose=verbose)
assert os.path.isfile(log)
n_found = 0
for line in open(log).read().splitlines():
if (line == "Atoms to be kept: 13 of 24"):
n_found += 1
assert n_found == 1
def exercise_stop_for_unknowns () :
pdb_in = """\
HETATM 16 O UNK B 2 47.616 10.724 150.212 1.00 46.48 B O
HETATM 17 O UNK B 3 46.408 16.672 146.066 0.50 12.81 B O
HETATM 18 O UNK B 4 29.343 12.806 185.898 1.00 35.57 B O
HETATM 19 O UNK B 5 43.786 12.615 147.734 0.50 28.43 B O
HETATM 20 O UNK B 6 35.068 19.167 155.349 1.00 15.97 B O
"""
open("tst_pdbtools_unknown.pdb", "w").write(pdb_in)
cmd = "phenix.pdbtools tst_pdbtools_unknown.pdb set_b_iso=20"
run_command(command=cmd, sorry_expected=True)
cmd2 = cmd + " stop_for_unknowns=False"
run_command(command=cmd)
def check_adp_to_iso(
cmd, xrsp_init, output, selection, selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance)
assert not_approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance)
assert not_approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance)
assert xrsp.u_iso_not_used.size() == 0
assert xrsp_init.u_iso_not_used.size() > 0
assert xrsp.u_cart_used.size() == 0
assert xrsp_init.u_cart_used.size() > 0
def exercise_change_of_basis () :
open("tmp_pdbtools_cb_op.pdb", "w").write("""\
CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2
ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N
ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C
ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C
ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O """)
cmd = "phenix.pdbtools tmp_pdbtools_cb_op.pdb change_of_basis='a,c,b'"
run_command(command=cmd, verbose=False)
lines = open("tmp_pdbtools_cb_op.pdb_modified.pdb").readlines()
for line in lines :
if line.startswith("CRYST1") :
assert (line.strip() ==
"""CRYST1 21.937 23.477 4.866 90.00 90.00 107.08 P 1 1 21""")
break
def exercise_stop_for_unknowns():
pdb_in = """\
HETATM 16 O UNK B 2 47.616 10.724 150.212 1.00 46.48 B O
HETATM 17 O UNK B 3 46.408 16.672 146.066 0.50 12.81 B O
HETATM 18 O UNK B 4 29.343 12.806 185.898 1.00 35.57 B O
HETATM 19 O UNK B 5 43.786 12.615 147.734 0.50 28.43 B O
HETATM 20 O UNK B 6 35.068 19.167 155.349 1.00 15.97 B O
"""
open("tst_pdbtools_unknown.pdb", "w").write(pdb_in)
cmd = "phenix.pdbtools tst_pdbtools_unknown.pdb set_b_iso=20"
print cmd
run_command(command=cmd, sorry_expected=True)
cmd2 = cmd + " stop_for_unknowns=False"
print cmd2
run_command(command=cmd2)
def check_sites_rt(
cmd, xrsp_init, output, selection, selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance)
if(selection_str is None):
diff = xrsp.sites_cart - xrsp_init.sites_cart
assert math.sqrt(flex.mean(diff.dot())) > 1.0
else:
diff = xrsp.sites_cart - xrsp_init.sites_cart
assert math.sqrt(flex.mean(diff.select(selection).dot())) > 1.0
assert approx_equal(
math.sqrt(flex.mean(diff.select(~selection).dot())),0.,tolerance)
def exercise_change_of_basis():
open("tmp_pdbtools_cb_op.pdb", "w").write("""\
CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2
ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N
ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C
ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C
ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O """
)
cmd = "phenix.pdbtools tmp_pdbtools_cb_op.pdb change_of_basis='a,c,b'"
run_command(command=cmd, verbose=False)
lines = open("tmp_pdbtools_cb_op.pdb_modified.pdb").readlines()
for line in lines:
if line.startswith("CRYST1"):
assert (
line.strip() ==
"""CRYST1 21.937 23.477 4.866 90.00 90.00 107.08 P 1 1 21"""
)
break
def check_keep_remove_conflict(cmd, output, verbose):
cmd += " keep=all remove=all "
cmd_result = run_command(command=cmd, verbose=verbose, sorry_expected=True)
sorry_lines = search_for(
pattern="Sorry: Ambiguous selection:"
" 'keep' and 'remove' keywords cannot be used simultaneously:",
mode="==",
lines=cmd_result.stdout_lines)
assert len(sorry_lines) == 1
def check_keep_remove_conflict(cmd, output, verbose):
cmd += " keep=all remove=all "
cmd_result = run_command(command=cmd, verbose=verbose, sorry_expected=True)
sorry_lines = search_for(
pattern="Sorry: Ambiguous selection:"
" 'keep' and 'remove' keywords cannot be used simultaneously:",
mode="==",
lines=cmd_result.stdout_lines)
assert len(sorry_lines) == 1
def check_adp_to_iso(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert not_approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso, tolerance)
assert not_approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso, tolerance)
assert xrsp.u_iso_not_used.size() == 0
assert xrsp_init.u_iso_not_used.size() > 0
assert xrsp.u_cart_used.size() == 0
assert xrsp_init.u_cart_used.size() > 0
def check_occ_randomize(
cmd, xrsp_init, output, selection,selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.sites_cart,xrsp_init.sites_cart,tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance)
if(selection_str is None):
diff = flex.abs(xrsp.occ - xrsp_init.occ)
assert flex.mean(diff) > 0.0
assert flex.max(diff) > 0.0
else:
diff = flex.abs(xrsp.occ - xrsp_init.occ)
assert flex.mean(diff) > 0.0
assert flex.max(diff) > 0.0
assert approx_equal(flex.mean(diff.select(~selection)),0.,tolerance)
def check_keep_selection(
cmd, xrsp_init, output, selection, selection_str,
keep_selection_str, verbose, tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
keep_selection = xrsp_init.selection(selection_strings = keep_selection_str)
assert approx_equal(xrsp.sites_cart,
xrsp_init.sites_cart.select(keep_selection),tolerance)
assert approx_equal(xrsp.occ, xrsp_init.occ.select(keep_selection),tolerance)
assert approx_equal(
xrsp.u_iso, xrsp_init.u_iso.select(keep_selection),tolerance)
assert approx_equal(
xrsp.u_cart, xrsp_init.u_cart.select(keep_selection),tolerance)
sct1 = xrsp_init.xray_structure.scatterers().extract_scattering_types()
assert sct1.count("C") > 0 and sct1.size() > sct1.count("C")
sct2 = xrsp.xray_structure.scatterers().extract_scattering_types()
assert sct2.count("C") == sct2.size()
assert sct1.size() > keep_selection.count(True)
assert sct1.size() > sct2.size()
def exercise_multiple(pdb_dir, verbose):
params = """\
modify{
adp {
atom_selection = chain A
randomize = True
}
adp {
atom_selection = chain B
shift_b_iso = 10
}
sites {
atom_selection = chain B
shake = 1.5
}
sites {
atom_selection = chain A or chain C
translate = 1 2 3
rotate = 4 5 6
}
occupancies
{
atom_selection = chain A
randomize = True
}
occupancies
{
atom_selection = chain C
set = 0.1
}
}
"""
open("params", "w").write(params)
file_name = os.path.join(pdb_dir, "phe_e.pdb")
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" modify.output.file_name=modified.pdb params' % (
file_name)
result = run_command(command=cmd, verbose=verbose)
lines = result.stdout_lines
for i, line in enumerate(lines):
if (line.find("Performing requested model manipulations") >= 0):
break
else:
raise RuntimeError("Expected output not found.")
assert lines[i + 1] == ""
assert lines[i + 8] == ""
assert not show_diff(
"\n".join(lines[i + 2:i + 8]), """\
Randomizing ADP: selected atoms: 12 of 36
Adding shift = 10.00 to all ADP: selected atoms: 12 of 36
Shaking sites (RMS = 1.500): selected atoms: 12 of 36
Rigid body shift: selected atoms: 24 of 36
Randomizing occupancies: selected atoms: 12 of 36
Setting occupancies to: 0.100: selected atoms: 12 of 36""")
def check_sites_rt(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso, tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart, tolerance)
if (selection_str is None):
diff = xrsp.sites_cart - xrsp_init.sites_cart
assert math.sqrt(flex.mean(diff.dot())) > 1.0
else:
diff = xrsp.sites_cart - xrsp_init.sites_cart
assert math.sqrt(flex.mean(diff.select(selection).dot())) > 1.0
assert approx_equal(
math.sqrt(flex.mean(diff.select(~selection).dot())), 0., tolerance)
def exercise_multiple(pdb_dir, verbose):
params = """\
modify{
adp {
atom_selection = chain A
randomize = True
}
adp {
atom_selection = chain B
shift_b_iso = 10
}
sites {
atom_selection = chain B
shake = 1.5
}
sites {
atom_selection = chain A or chain C
translate = 1 2 3
rotate = 4 5 6
}
occupancies
{
atom_selection = chain A
randomize = True
}
occupancies
{
atom_selection = chain C
set = 0.1
}
}
"""
open("params", "w").write(params)
file_name = os.path.join(pdb_dir, "phe_e.pdb")
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" modify.output.file_name=modified.pdb params' % (
file_name)
result = run_command(command=cmd, verbose=verbose)
lines = result.stdout_lines
for i,line in enumerate(lines):
if (line.find("Performing requested model manipulations") >= 0):
break
else:
raise RuntimeError("Expected output not found.")
assert lines[i+1] == ""
assert lines[i+8] == ""
assert not show_diff("\n".join(lines[i+2:i+8]), """\
Randomizing ADP: selected atoms: 12 of 36
Adding shift = 10.00 to all ADP: selected atoms: 12 of 36
Shaking sites (RMS = 1.500): selected atoms: 12 of 36
Rigid body shift: selected atoms: 24 of 36
Randomizing occupancies: selected atoms: 12 of 36
Setting occupancies to: 0.100: selected atoms: 12 of 36""")
def exercise_remove_alt_confs () :
pdb_in = """\
ATOM 16 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O
ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C
ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C
ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 18 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
ATOM 19 O BHOH A 4 4.132 9.963 7.800 0.50 15.00 O
"""
open("tst_pdbtools_alt_confs.pdb", "w").write(pdb_in)
cmd = "phenix.pdbtools tst_pdbtools_alt_confs.pdb remove_alt_confs=True"
run_command(command=cmd, verbose=False)
pdb_new = open("tst_pdbtools_alt_confs.pdb_modified.pdb").read()
assert (pdb_new == """\
ATOM 1 O HOH A 2 5.131 5.251 5.823 1.00 10.00 O
ATOM 2 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 3 CB LYS A 32 9.197 8.686 12.246 1.00 14.71 C
ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 6 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
TER
END
""")
cmd = "phenix.pdbtools tst_pdbtools_alt_confs.pdb remove_alt_confs=True " +\
"always_keep_one_conformer=True"
run_command(command=cmd, verbose=False)
pdb_new = open("tst_pdbtools_alt_confs.pdb_modified.pdb").read()
assert (pdb_new == """\
ATOM 1 O HOH A 2 5.131 5.251 5.823 1.00 10.00 O
ATOM 2 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 3 CB LYS A 32 9.193 8.732 12.170 1.00 12.23 C
ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 6 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
ATOM 7 O HOH A 4 4.132 9.963 7.800 1.00 15.00 O
TER
END
""")
def exercise_remove_alt_confs():
pdb_in = """\
ATOM 16 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O
ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C
ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C
ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 18 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
ATOM 19 O BHOH A 4 4.132 9.963 7.800 0.50 15.00 O
"""
open("tst_pdbtools_alt_confs.pdb", "w").write(pdb_in)
cmd = "phenix.pdbtools tst_pdbtools_alt_confs.pdb remove_alt_confs=True"
run_command(command=cmd, verbose=False)
pdb_new = open("tst_pdbtools_alt_confs.pdb_modified.pdb").read()
assert (pdb_new == """\
ATOM 1 O HOH A 2 5.131 5.251 5.823 1.00 10.00 O
ATOM 2 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 3 CB LYS A 32 9.197 8.686 12.246 1.00 14.71 C
ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 6 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
TER
END
""")
cmd = "phenix.pdbtools tst_pdbtools_alt_confs.pdb remove_alt_confs=True " +\
"always_keep_one_conformer=True"
run_command(command=cmd, verbose=False)
pdb_new = open("tst_pdbtools_alt_confs.pdb_modified.pdb").read()
assert (pdb_new == """\
ATOM 1 O HOH A 2 5.131 5.251 5.823 1.00 10.00 O
ATOM 2 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C
ATOM 3 CB LYS A 32 9.193 8.732 12.170 1.00 12.23 C
ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C
ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C
ATOM 6 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O
ATOM 7 O HOH A 4 4.132 9.963 7.800 1.00 15.00 O
TER
END
""")
def check_occ_randomize(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert approx_equal(xrsp.u_iso, xrsp_init.u_iso, tolerance)
assert approx_equal(xrsp.u_cart, xrsp_init.u_cart, tolerance)
if (selection_str is None):
diff = flex.abs(xrsp.occ - xrsp_init.occ)
assert flex.mean(diff) > 0.0
assert flex.max(diff) > 0.0
else:
diff = flex.abs(xrsp.occ - xrsp_init.occ)
assert flex.mean(diff) > 0.0
assert flex.max(diff) > 0.0
assert approx_equal(flex.mean(diff.select(~selection)), 0., tolerance)
def exercise_no_cryst1(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "t.pdb")
output = "modified.pdb"
assert file_name.find('"') < 0
base = 'phenix.pdbtools "%s" modify.output.file_name=%s '%(file_name, output)
cmd = base+'sites.rotate="0 0 0" sites.translate="0 0 0"'
run_command(command=cmd, verbose=verbose)
lines1 = []
for line in open(file_name,"r").readlines():
line = line.strip()
assert line.count("CRYST1") == 0
if(line.startswith("ATOM") or line.startswith("HETATM")):
lines1.append(line)
lines2 = []
for line in open(output,"r").readlines():
line = line.strip()
assert line.count("CRYST1") == 0
if(line.startswith("ATOM") or line.startswith("HETATM")):
lines2.append(line)
assert len(lines1) == len(lines2)
for l1,l2 in zip(lines1, lines2):
assert l1[11:70].strip() == l2[11:70].strip()
def exercise_no_cryst1(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "t.pdb")
output = "modified.pdb"
assert file_name.find('"') < 0
base = 'phenix.pdbtools "%s" modify.output.file_name=%s ' % (file_name,
output)
cmd = base + 'sites.rotate="0 0 0" sites.translate="0 0 0"'
run_command(command=cmd, verbose=verbose)
lines1 = []
for line in open(file_name, "r").readlines():
line = line.strip()
assert line.count("CRYST1") == 0
if (line.startswith("ATOM") or line.startswith("HETATM")):
lines1.append(line)
lines2 = []
for line in open(output, "r").readlines():
line = line.strip()
assert line.count("CRYST1") == 0
if (line.startswith("ATOM") or line.startswith("HETATM")):
lines2.append(line)
assert len(lines1) == len(lines2)
for l1, l2 in zip(lines1, lines2):
assert l1[11:70].strip() == l2[11:70].strip()
def exercise_convert_semet_to_met () :
open("tmp_semet.pdb", "w").write("""\
HETATM 507 N MSE A 106 53.211 45.681 34.889 1.00 1.05 N
HETATM 508 CA MSE A 106 51.827 45.381 35.207 1.00 1.35 C
HETATM 509 C MSE A 106 50.937 45.462 33.968 1.00 3.57 C
HETATM 510 O MSE A 106 49.956 44.737 33.860 1.00 4.67 O
HETATM 511 CB MSE A 106 51.318 46.310 36.304 1.00 1.07 C
HETATM 512 CG MSE A 106 49.833 46.180 36.603 1.00 1.06 C
HETATM 513 SE MSE A 106 49.249 47.284 38.129 0.82 10.02 Se
HETATM 514 CE MSE A 106 50.851 47.140 39.206 1.00 1.19 C
""")
cmd = "phenix.pdbtools tmp_semet.pdb convert_semet_to_met=True"
run_command(command=cmd, verbose=False)
assert (not "HETATM" in open("tmp_semet.pdb_modified.pdb").read())
pdb_inp = iotbx.pdb.hierarchy.input(file_name="tmp_semet.pdb_modified.pdb")
found_sd = False
for atom in pdb_inp.hierarchy.atoms() :
labels = atom.fetch_labels()
assert (labels.resname == "MET")
if (atom.name == " SD ") :
found_sd = True
assert (atom.element == ' S')
break
assert (found_sd)
def exercise_convert_semet_to_met():
open("tmp_semet.pdb", "w").write("""\
HETATM 507 N MSE A 106 53.211 45.681 34.889 1.00 1.05 N
HETATM 508 CA MSE A 106 51.827 45.381 35.207 1.00 1.35 C
HETATM 509 C MSE A 106 50.937 45.462 33.968 1.00 3.57 C
HETATM 510 O MSE A 106 49.956 44.737 33.860 1.00 4.67 O
HETATM 511 CB MSE A 106 51.318 46.310 36.304 1.00 1.07 C
HETATM 512 CG MSE A 106 49.833 46.180 36.603 1.00 1.06 C
HETATM 513 SE MSE A 106 49.249 47.284 38.129 0.82 10.02 Se
HETATM 514 CE MSE A 106 50.851 47.140 39.206 1.00 1.19 C
""")
cmd = "phenix.pdbtools tmp_semet.pdb convert_semet_to_met=True"
run_command(command=cmd, verbose=False)
assert (not "HETATM" in open("tmp_semet.pdb_modified.pdb").read())
pdb_inp = iotbx.pdb.hierarchy.input(file_name="tmp_semet.pdb_modified.pdb")
found_sd = False
for atom in pdb_inp.hierarchy.atoms():
labels = atom.fetch_labels()
assert (labels.resname == "MET")
if (atom.name == " SD "):
found_sd = True
assert (atom.element == ' S')
break
assert (found_sd)
def exercise_show_geometry_statistics(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "phe_e.pdb")
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" --show-geometry-statistics' % file_name
run_command(command=cmd, verbose=verbose)
def iterate(self):
self.n1 = self.nmodes
if (self.Niter > 0): # need to build PDB object from the last PDB file
iter_name = self.root + str(self.Niter) + ".pdb"
self.pdb = PDB(iter_name, method=self.method)
self.pdb.Hessian(self.cutoff, self.nmode_init, self.scale_factor)
# Generate random normal modes
self.modes = flex.int(range(self.nmodes - 1)) + 7
self.modes.append(
int(random.random() * (self.nmode_init - self.nmodes)) + 7 +
self.nmodes)
self.scale = 0
candidates = []
score = []
for kk in range(self.topn * 10):
if (kk == 0):
vec = flex.random_double(self.nmodes) * 0
else:
vec = (flex.random_double(self.nmodes) -
0.5) * 2 * self.step_size
result = self.target(vec)
insert = 0
for ii in range(len(score)):
if (score[ii] > result):
score.insert(ii, result)
candidates.insert(ii, vec)
insert = 1
break
if (insert == 0):
score.append(result)
candidates.append(vec)
for kk in range(self.topn):
self.starting_simplex = []
cand = candidates[kk]
for ii in range(self.n1):
self.starting_simplex.append(
flex.double(self.orth(ii, self.n1)) * self.step_size +
cand)
self.starting_simplex.append(cand)
self.optimizer = simplex.simplex_opt(dimension=self.n1,
matrix=self.starting_simplex,
evaluator=self,
monitor_cycle=5,
tolerance=1e-2)
self.x = self.optimizer.get_solution()
candidates[kk] = self.x.deep_copy()
score[kk] = self.optimizer.get_score()
minscore = min(score[0:self.topn])
print self.Niter, minscore, self.counter
print >> self.chi, self.Niter, minscore
if ((self.Niter % self.optNum) > 1):
self.stopCheck(minscore)
self.updateScore(minscore)
minvec = candidates[score.index(minscore)]
new_coord = self.pdb.NMPerturb(self.modes, minvec)
print list(minvec)
self.Niter = self.Niter + 1
iter_base = self.root + str(self.Niter)
iter_name = iter_base + ".pdb"
self.pdb.writePDB(new_coord, iter_name)
if (self.Niter % self.optNum == 0):
print self.pulchra
run_command(command=self.pulchra + ' ' + iter_name)
run_command(command='mv ' + iter_base + '.rebuilt.pdb ' +
iter_name)
#processed_pdb, pdb_inp = self.pdb_processor.process_pdb_files( pdb_file_names=[iter_name] )
#new_coord = geo_opt(processed_pdb, self.log)
#self.pdb.writePDB(new_coord,iter_name)
# if(not self.stop):
if (self.Niter < 40):
self.iterate()
def exercise_mmcif_support():
from libtbx.test_utils import open_tmp_file
f = open_tmp_file(suffix="pdbtools.cif")
f.write("""\
data_phenix
_space_group.name_H-M_alt 'C 1 2 1'
_space_group.name_Hall ' C 2y'
_cell.length_a 46.053
_cell.length_b 9.561
_cell.length_c 20.871
_cell.angle_alpha 90.0
_cell.angle_beta 97.43
_cell.angle_gamma 90.0
_cell.volume 9112.60599144
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_model_num
ATOM 2 CA . LYS A 1 ? 7.49733 -0.62028 4.35289 1.000 10.25989 C ? A ? 1 1
ATOM 11 CA . LEU A 2 ? 3.72032 -0.19320 3.89326 1.000 7.80433 C ? A ? 2 1
ATOM 19 CA . VAL A 3 ? 0.78668 -0.39555 6.35234 1.000 5.03864 C ? A ? 3 1
ATOM 26 CA . PHE A 4 ? -2.75438 -0.21383 5.02429 1.000 8.93080 C ? A ? 4 1
ATOM 37 CA . PHE A 5 ? -6.05155 -0.46197 6.85390 1.000 9.57417 C ? A ? 5 1
ATOM 48 CA . ALA A 6 ? -9.57646 -0.10942 5.55847 1.000 17.73488 C ? A ? 6 1
ATOM 54 CA . LYS B 1 ? -8.86604 -5.20044 5.46515 1.000 16.15297 C ? B ? 7 1
""")
f.close()
cmd = " ".join([
"phenix.pdbtools",
"\"%s\"" % f.name, "rename_chain_id.old_id=A",
"rename_chain_id.new_id=C"
])
run_command(command=cmd, verbose=False)
assert os.path.isfile(f.name + "_modified.pdb")
pdb_inp = iotbx.pdb.input(file_name=f.name + "_modified.pdb")
assert pdb_inp.file_type() == "pdb"
hierarchy = pdb_inp.construct_hierarchy()
assert [chain.id for chain in hierarchy.chains()] == ['C', 'B']
cmd = " ".join([
"phenix.pdbtools",
"\"%s\"" % f.name, "adp.convert_to_anisotropic=True",
"output.format=mmcif"
])
run_command(command=cmd, verbose=False)
assert os.path.isfile(f.name + "_modified.cif")
pdb_inp = iotbx.pdb.input(file_name=f.name + "_modified.cif")
assert pdb_inp.file_type() == "mmcif"
xs = pdb_inp.xray_structure_simple()
assert xs.use_u_aniso().all_eq(True)
def run_pulchra(input, output):
cmd = 'pulchra %s' % (input)
run_command(command=cmd)
def exercise_mmcif_support():
from libtbx.test_utils import open_tmp_file
f = open_tmp_file(suffix="pdbtools.cif")
f.write("""\
data_phenix
_space_group.name_H-M_alt 'C 1 2 1'
_space_group.name_Hall ' C 2y'
_cell.length_a 46.053
_cell.length_b 9.561
_cell.length_c 20.871
_cell.angle_alpha 90.0
_cell.angle_beta 97.43
_cell.angle_gamma 90.0
_cell.volume 9112.60599144
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.type_symbol
_atom_site.pdbx_formal_charge
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_model_num
ATOM 2 CA . LYS A 1 ? 7.49733 -0.62028 4.35289 1.000 10.25989 C ? A ? 1 1
ATOM 11 CA . LEU A 2 ? 3.72032 -0.19320 3.89326 1.000 7.80433 C ? A ? 2 1
ATOM 19 CA . VAL A 3 ? 0.78668 -0.39555 6.35234 1.000 5.03864 C ? A ? 3 1
ATOM 26 CA . PHE A 4 ? -2.75438 -0.21383 5.02429 1.000 8.93080 C ? A ? 4 1
ATOM 37 CA . PHE A 5 ? -6.05155 -0.46197 6.85390 1.000 9.57417 C ? A ? 5 1
ATOM 48 CA . ALA A 6 ? -9.57646 -0.10942 5.55847 1.000 17.73488 C ? A ? 6 1
ATOM 54 CA . LYS B 1 ? -8.86604 -5.20044 5.46515 1.000 16.15297 C ? B ? 7 1
""")
f.close()
cmd = " ".join(["phenix.pdbtools", "\"%s\"" % f.name,
"rename_chain_id.old_id=A",
"rename_chain_id.new_id=C"])
run_command(command=cmd, verbose=False)
assert os.path.isfile(f.name+"_modified.pdb")
pdb_inp = iotbx.pdb.input(file_name=f.name+"_modified.pdb")
assert pdb_inp.file_type() == "pdb"
hierarchy = pdb_inp.construct_hierarchy()
assert [chain.id for chain in hierarchy.chains()] == ['C', 'B']
cmd = " ".join(["phenix.pdbtools", "\"%s\"" % f.name,
"adp.convert_to_anisotropic=True",
"output.format=mmcif"])
run_command(command=cmd, verbose=False)
assert os.path.isfile(f.name+"_modified.cif")
pdb_inp = iotbx.pdb.input(file_name=f.name+"_modified.cif")
assert pdb_inp.file_type() == "mmcif"
xs = pdb_inp.xray_structure_simple()
assert xs.use_u_aniso().all_eq(True)
def geo_opt(input, output):
log = "tmp.log"
cmd = 'phenix.pdbtools %s --geometry-regularization modify.output.file_name=%s > %s' % (
input, output, log)
run_command(command=cmd)
def exercise_show_geometry_statistics(pdb_dir, verbose):
file_name = os.path.join(pdb_dir, "phe_e.pdb")
assert file_name.find('"') < 0
cmd = 'phenix.pdbtools "%s" --show-geometry-statistics'%file_name
run_command(command=cmd, verbose=verbose)
