def exercise_secondary_structure():
# what is tested here? Not a single assert or check.
pdb_in_p1 = """\
CRYST1 21.348 25.003 18.365 90.00 90.00 90.00 P 1
ATOM 1 N SER A 1 10.914 5.773 13.123 1.00 0.00
ATOM 2 CA SER A 1 12.373 5.809 13.123 1.00 0.00
ATOM 3 C SER A 1 12.880 7.231 13.123 1.00 0.00
ATOM 4 O SER A 1 12.115 8.196 13.123 1.00 0.00
ATOM 5 CB SER A 1 12.944 5.000 11.931 1.00 0.00
ATOM 6 N ASP A 2 14.192 7.378 13.123 1.00 0.00
ATOM 7 CA ASP A 2 14.822 8.695 13.123 1.00 0.00
ATOM 8 C ASP A 2 14.519 9.440 11.845 1.00 0.00
ATOM 9 O ASP A 2 14.263 10.684 11.836 1.00 0.00
ATOM 10 CB ASP A 2 16.348 8.559 13.365 1.00 0.00
ATOM 11 N PRO A 3 14.535 8.722 10.738 1.00 0.00
ATOM 12 CA PRO A 3 14.264 9.228 9.323 1.00 0.00
ATOM 13 C PRO A 3 12.793 9.507 9.027 1.00 0.00
ATOM 14 O PRO A 3 12.513 10.527 8.347 1.00 0.00
ATOM 15 CB PRO A 3 14.734 8.129 8.381 1.00 0.00
ATOM 16 N ALA A 4 11.844 8.703 9.470 1.00 0.00
ATOM 17 CA ALA A 4 10.431 8.949 9.199 1.00 0.00
ATOM 18 C ALA A 4 9.967 10.223 9.865 1.00 0.00
ATOM 19 O ALA A 4 9.185 11.004 9.310 1.00 0.00
ATOM 20 CB ALA A 4 9.645 7.712 9.664 1.00 0.00
ATOM 21 N ALA A 5 10.435 10.445 11.079 1.00 0.00
ATOM 22 CA ALA A 5 10.071 11.635 11.842 1.00 0.00
ATOM 23 C ALA A 5 10.591 12.886 11.175 1.00 0.00
ATOM 24 O ALA A 5 9.928 13.929 11.130 1.00 0.00
ATOM 25 CB ALA A 5 10.609 11.453 13.272 1.00 0.00
ATOM 26 N LEU A 6 11.801 12.803 10.654 1.00 0.00
ATOM 27 CA LEU A 6 12.432 13.934 9.979 1.00 0.00
ATOM 28 C LEU A 6 11.678 14.303 8.724 1.00 0.00
ATOM 29 O LEU A 6 11.492 15.483 8.391 1.00 0.00
ATOM 30 CB LEU A 6 13.921 13.618 9.660 1.00 0.00
ATOM 31 N LYS A 7 11.228 13.293 8.001 1.00 0.00
ATOM 32 CA LYS A 7 10.483 13.500 6.763 1.00 0.00
ATOM 33 C LYS A 7 9.162 14.181 7.033 1.00 0.00
ATOM 34 O LYS A 7 8.713 15.063 6.287 1.00 0.00
ATOM 35 CB LYS A 7 10.269 12.135 6.054 1.00 0.00
ATOM 36 N ARG A 8 8.515 13.780 8.112 1.00 0.00
ATOM 37 CA ARG A 8 7.227 14.350 8.498 1.00 0.00
ATOM 38 C ARG A 8 7.367 15.810 8.856 1.00 0.00
ATOM 39 O ARG A 8 6.516 16.641 8.545 1.00 0.00
ATOM 40 CB ARG A 8 6.648 13.528 9.682 1.00 0.00
ATOM 41 N ALA A 9 8.444 16.136 9.545 1.00 0.00
ATOM 42 CA ALA A 9 8.710 17.511 9.960 1.00 0.00
ATOM 43 C ALA A 9 8.937 18.403 8.764 1.00 0.00
ATOM 44 O ALA A 9 8.495 19.558 8.714 1.00 0.00
ATOM 45 CB ALA A 9 9.912 17.483 10.921 1.00 0.00
ATOM 46 N ARG A 10 9.646 17.883 7.780 1.00 0.00
ATOM 47 CA ARG A 10 9.944 18.630 6.562 1.00 0.00
ATOM 48 C ARG A 10 8.683 18.929 5.788 1.00 0.00
ATOM 49 O ARG A 10 8.510 20.003 5.215 1.00 0.00
ATOM 50 CB ARG A 10 10.955 17.817 5.707 1.00 0.00
ATOM 51 N ASN A 11 7.788 17.960 5.742 1.00 0.00
ATOM 52 CA ASN A 11 6.522 18.108 5.030 1.00 0.00
ATOM 53 C ASN A 11 5.662 19.170 5.672 1.00 0.00
ATOM 54 O ASN A 11 5.000 19.964 5.005 1.00 0.00
ATOM 55 CB ASN A 11 5.780 16.740 5.000 1.00 0.00
TER
END
"""
open("tst_geo_min_ss_phil.pdb", "w").write(pdb_in_p1)
from mmtbx.command_line import secondary_structure_restraints
out = StringIO()
args = [
"tst_geo_min_ss_phil.pdb",
# "use_ksdssp=False",
]
secondary_structure_restraints.run(args, out=out, log=null_out())
# phenix.geometry_minimization
from mmtbx.command_line import geometry_minimization
open("tst_geo_min_ss_phil.phil", "w").write(out.getvalue())
args = [
"tst_geo_min_ss_phil.pdb",
"tst_geo_min_ss_phil.phil",
"secondary_structure.enabled=True",
]
geometry_minimization.run(args=args, log=null_out())
def exercise_metal_coordination():
pdb_in = """\
HETATM 6 PA ANP A 1 -2.347 2.100 -17.803 1.00 10.27 P
HETATM 7 PB ANP A 1 0.438 2.937 -18.222 1.00 10.85 P
HETATM 8 PG ANP A 1 1.125 2.500 -21.112 1.00 10.56 P
HETATM 9 C5' ANP A 1 -1.973 -0.334 -17.074 1.00 10.24 C
HETATM 10 O5' ANP A 1 -2.737 0.857 -16.887 1.00 9.76 O
HETATM 11 C4' ANP A 1 -2.889 -1.539 -17.210 1.00 10.40 C
HETATM 12 O4' ANP A 1 -3.627 -1.699 -15.990 1.00 10.47 O
HETATM 13 C3' ANP A 1 -3.936 -1.477 -18.319 1.00 9.24 C
HETATM 14 O3' ANP A 1 -3.371 -1.834 -19.590 1.00 10.01 O
HETATM 15 C2' ANP A 1 -4.953 -2.483 -17.795 1.00 9.88 C
HETATM 16 O2' ANP A 1 -4.490 -3.826 -17.960 1.00 11.25 O
HETATM 17 C1' ANP A 1 -4.915 -2.225 -16.303 1.00 11.21 C
HETATM 18 N1 ANP A 1 -9.509 -1.559 -14.126 1.00 11.19 N
HETATM 19 O1A ANP A 1 -3.108 3.253 -17.261 1.00 10.62 O
HETATM 20 O1B ANP A 1 0.034 4.332 -18.573 1.00 10.23 O
HETATM 21 O1G ANP A 1 2.434 1.809 -21.423 1.00 12.01 O
HETATM 22 C2 ANP A 1 -8.855 -2.697 -14.422 1.00 11.32 C
HETATM 23 O2A ANP A 1 -2.510 1.726 -19.235 1.00 9.76 O
HETATM 24 O2B ANP A 1 1.600 2.764 -17.285 1.00 12.69 O
HETATM 25 O2G ANP A 1 -0.014 2.061 -22.037 1.00 10.31 O
HETATM 26 N3 ANP A 1 -7.636 -2.728 -14.988 1.00 10.83 N
HETATM 27 N3B ANP A 1 0.614 2.050 -19.591 1.00 13.13 N
HETATM 28 O3A ANP A 1 -0.783 2.257 -17.423 1.00 11.18 O
HETATM 29 O3G ANP A 1 1.269 4.014 -21.065 1.00 10.83 O
HETATM 30 C4 ANP A 1 -7.053 -1.540 -15.290 1.00 10.41 C
HETATM 31 C5 ANP A 1 -7.703 -0.266 -15.019 1.00 10.36 C
HETATM 32 C6 ANP A 1 -9.013 -0.333 -14.380 1.00 10.39 C
HETATM 33 N6 ANP A 1 -9.709 0.784 -14.079 1.00 10.34 N
HETATM 34 N7 ANP A 1 -6.889 0.732 -15.437 1.00 10.05 N
HETATM 35 C8 ANP A 1 -5.791 0.126 -15.942 1.00 10.13 C
HETATM 36 N9 ANP A 1 -5.898 -1.223 -15.869 1.00 10.39 N
HETATM 37 MG MG A 2 -1.727 1.886 -21.040 1.00 8.15 MG
HETATM 38 MG MG A 3 -0.077 5.289 -20.356 1.00 9.42 MG
HETATM 1 O HOH A 4 -3.435 1.768 -22.164 1.00 8.59 O
HETATM 3 O HOH A 5 -2.158 5.884 -19.807 1.00 9.00 O
HETATM 4 O HOH A 6 -1.791 4.005 -20.881 1.00 7.86 O
HETATM 39 O HOH A 7 -1.518 -0.155 -21.151 1.00 13.31 O
HETATM 40 O HOH A 8 -0.256 6.271 -22.179 1.00 12.97 O
HETATM 41 O HOH A 9 0.913 6.863 -19.633 1.00 13.62 O """
open("tst_geo_min_metal_coord.pdb", "w").write(pdb_in)
params1 = """\
geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O2A and chain A and resname ANP and resseq 1
distance_ideal = 2.090000
sigma = 0.250
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O2G and chain A and resname ANP and resseq 1
distance_ideal = 2.090000
sigma = 0.250
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O and chain A and resname HOH and resseq 4
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O and chain A and resname HOH and resseq 7
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O and chain A and resname HOH and resseq 6
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O3G and chain A and resname ANP and resseq 1
distance_ideal = 2.090000
sigma = 0.250
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O and chain A and resname HOH and resseq 9
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O1B and chain A and resname ANP and resseq 1
distance_ideal = 2.090000
sigma = 0.250
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O and chain A and resname HOH and resseq 8
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O and chain A and resname HOH and resseq 6
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O and chain A and resname HOH and resseq 5
distance_ideal = 2.070000
sigma = 0.050
}
}"""
params2 = "refinement {\n%s\n}" % params1
open("tst_geo_min_metal_coord_1.phil", "w").write(params1)
open("tst_geo_min_metal_coord_2.phil", "w").write(params2)
# phenix.geometry_minimization
from mmtbx.command_line import geometry_minimization
args = [
"file_name=tst_geo_min_metal_coord.pdb",
"output_file_name_prefix=tst_geo_min_metal_coord_1",
"write_geo_file=True",
"tst_geo_min_metal_coord_1.phil",
]
geometry_minimization.run(args=args, log=null_out())
geo_file_1 = open("tst_geo_min_metal_coord_1.geo").read()
args = [
"file_name=tst_geo_min_metal_coord.pdb",
"output_file_name_prefix=tst_geo_min_metal_coord_2",
"write_geo_file=True",
"tst_geo_min_metal_coord_2.phil",
]
geometry_minimization.run(args=args, log=null_out())
geo_file_2 = open("tst_geo_min_metal_coord_2.geo").read()
show_diff(geo_file_1, geo_file_2)
# phenix.pdbtools
from mmtbx import pdbtools
args = [
"tst_geo_min_metal_coord.pdb",
"tst_geo_min_metal_coord_1.phil",
"model_statistics=True",
]
out1 = StringIO()
pdbtools.run(args=args, out=out1, replace_stderr=False)
args = [
"tst_geo_min_metal_coord.pdb",
"tst_geo_min_metal_coord_2.phil",
"model_statistics=True",
]
out2 = StringIO()
pdbtools.run(args=args, out=out2, replace_stderr=False)
assert (""" atom 1: \"HETATM 37 MG MG A 2 .*. Mg \"""" in
out1.getvalue())
assert (""" atom 1: \"HETATM 37 MG MG A 2 .*. Mg \"""" in
out2.getvalue())
for line1, line2 in zip(out1.getvalue().splitlines(),
out2.getvalue().splitlines()):
line1 = line1.strip()
line2 = line2.strip()
if (line1.startswith("Date") or line1.startswith("PID") or
line1.startswith("Command line") or line1.startswith("Time")):
continue
else :
assert not show_diff(line1, line2)
def geo_opt(processed_pdb, log):
sites_cart = geometry_minimization.run(processed_pdb_file=processed_pdb,
log=log)
return sites_cart
def run(args):
#log = StringIO()
if len(args) != 3:
raise Usage("mmtbx.nqh_minimize input.pdb output.pdb temp_dir_path")
filename = args[0]
outfile = args[1]
temp_dir = args[2]
basename = os.path.basename(filename)
flipped_residues = parse_user_mods(filename=filename)
selection = "selection = (not (name ' CA ' or name ' N ' or name ' C ' " +\
"or name ' O ' or name ' HA ' or name ' H ' " +\
"or name ' OXT')) and ("
restrain = "pdb_interpretation.reference_coordinate_restraints.selection = " +\
"(not (name ' CA ' or name ' N ' or name ' C ' " +\
"or name ' O ' or name ' HA ' or name ' H ' " +\
"or name ' OXT')) and ("
is_first = True
for flip in flipped_residues:
if not is_first:
selection += " or"
restrain += " or"
else:
is_first = False
chain_id = flip[0:2]
if (len(flip) == 10): #not an altloc
if chain_id == ' ':
selection += " (resseq %s and resname %s)" % \
(flip[2:6].strip(), flip[7:])
restrain += " (resseq %s and resname %s)" % \
(flip[2:6].strip(), flip[7:])
else:
selection += " (chain '%s' and resseq %s and resname %s)" % \
(flip[0:2], flip[2:6].strip(), flip[7:])
restrain += " (chain '%s' and resseq %s and resname %s)" % \
(flip[0:2], flip[2:6].strip(), flip[7:])
else: #is an alternate
if chain_id == ' ':
selection += \
" (resseq %s and resname %s and altid '%s')" % \
(flip[2:6].strip(), flip[7:10], flip[-1:])
restrain += \
" (resseq %s and resname %s and altid '%s')" % \
(flip[2:6].strip(), flip[7:10], flip[-1:])
else:
selection += \
" (chain '%s' and resseq %s and resname %s and altid '%s')" % \
(flip[0:2], flip[2:6].strip(), flip[7:10], flip[-1:])
restrain += \
" (chain '%s' and resseq %s and resname %s and altid '%s')" % \
(flip[0:2], flip[2:6].strip(), flip[7:10], flip[-1:])
selection += " )"
restrain += " )"
sigma = "pdb_interpretation.reference_coordinate_restraints.sigma=0.05"
directory = "directory=" + temp_dir
params = os.path.join(temp_dir, "nqh.params")
p = open(params, 'w')
print(selection, file=p)
print(restrain, file=p)
print(sigma, file=p)
print("pdb_interpretation.reference_coordinate_restraints.enabled=True",
file=p)
print(directory, file=p)
print("stop_for_unknowns=False", file=p)
print("pdb_interpretation.clash_guard.nonbonded_distance_threshold=None",
file=p)
p.close()
temp_pdb = os.path.join(temp_dir, "nqh_flips.pdb")
out = open(temp_pdb, 'w')
f = open(filename, 'rb')
for line in f.readlines():
if line.startswith("ATOM "):
id_str = line[16:26]
key = id_str[4:6] + id_str[6:] + ' ' + id_str[1:4]
if id_str[0] != ' ':
key = key + " %s" % id_str[0]
if key in flipped_residues:
print(line.strip(), file=out)
out.close()
f.close()
min_args = []
min_args.append(filename)
min_args.append(params)
log_file = os.path.join(temp_dir, "nqh.log")
log = open(log_file, 'w')
o = geometry_minimization.run(min_args, log=log)
updated_coords = {}
ind = max(0, basename.rfind("."))
ofn = \
basename+"_minimized.pdb" if ind==0 else basename[:ind]+"_minimized.pdb"
min_file = open(os.path.join(temp_dir, ofn), 'rb')
for line in min_file.readlines():
if line.startswith("ATOM "):
id_str = line[16:26]
check_key = id_str[4:6] + id_str[6:] + ' ' + id_str[1:4]
if id_str[0] != ' ':
check_key = check_key + " %s" % id_str[0]
if check_key in flipped_residues:
key = line[12:26]
coords = line[30:54]
updated_coords[key] = coords
min_file.close()
finalize_coords(filename=filename,
outfile=outfile,
updated_coords=updated_coords)
def exercise_metal_coordination () :
pdb_in = """\
HETATM 6 PA ANP A 1 -2.347 2.100 -17.803 1.00 10.27 P
HETATM 7 PB ANP A 1 0.438 2.937 -18.222 1.00 10.85 P
HETATM 8 PG ANP A 1 1.125 2.500 -21.112 1.00 10.56 P
HETATM 9 C5' ANP A 1 -1.973 -0.334 -17.074 1.00 10.24 C
HETATM 10 O5' ANP A 1 -2.737 0.857 -16.887 1.00 9.76 O
HETATM 11 C4' ANP A 1 -2.889 -1.539 -17.210 1.00 10.40 C
HETATM 12 O4' ANP A 1 -3.627 -1.699 -15.990 1.00 10.47 O
HETATM 13 C3' ANP A 1 -3.936 -1.477 -18.319 1.00 9.24 C
HETATM 14 O3' ANP A 1 -3.371 -1.834 -19.590 1.00 10.01 O
HETATM 15 C2' ANP A 1 -4.953 -2.483 -17.795 1.00 9.88 C
HETATM 16 O2' ANP A 1 -4.490 -3.826 -17.960 1.00 11.25 O
HETATM 17 C1' ANP A 1 -4.915 -2.225 -16.303 1.00 11.21 C
HETATM 18 N1 ANP A 1 -9.509 -1.559 -14.126 1.00 11.19 N
HETATM 19 O1A ANP A 1 -3.108 3.253 -17.261 1.00 10.62 O
HETATM 20 O1B ANP A 1 0.034 4.332 -18.573 1.00 10.23 O
HETATM 21 O1G ANP A 1 2.434 1.809 -21.423 1.00 12.01 O
HETATM 22 C2 ANP A 1 -8.855 -2.697 -14.422 1.00 11.32 C
HETATM 23 O2A ANP A 1 -2.510 1.726 -19.235 1.00 9.76 O
HETATM 24 O2B ANP A 1 1.600 2.764 -17.285 1.00 12.69 O
HETATM 25 O2G ANP A 1 -0.014 2.061 -22.037 1.00 10.31 O
HETATM 26 N3 ANP A 1 -7.636 -2.728 -14.988 1.00 10.83 N
HETATM 27 N3B ANP A 1 0.614 2.050 -19.591 1.00 13.13 N
HETATM 28 O3A ANP A 1 -0.783 2.257 -17.423 1.00 11.18 O
HETATM 29 O3G ANP A 1 1.269 4.014 -21.065 1.00 10.83 O
HETATM 30 C4 ANP A 1 -7.053 -1.540 -15.290 1.00 10.41 C
HETATM 31 C5 ANP A 1 -7.703 -0.266 -15.019 1.00 10.36 C
HETATM 32 C6 ANP A 1 -9.013 -0.333 -14.380 1.00 10.39 C
HETATM 33 N6 ANP A 1 -9.709 0.784 -14.079 1.00 10.34 N
HETATM 34 N7 ANP A 1 -6.889 0.732 -15.437 1.00 10.05 N
HETATM 35 C8 ANP A 1 -5.791 0.126 -15.942 1.00 10.13 C
HETATM 36 N9 ANP A 1 -5.898 -1.223 -15.869 1.00 10.39 N
HETATM 37 MG MG A 2 -1.727 1.886 -21.040 1.00 8.15 MG
HETATM 38 MG MG A 3 -0.077 5.289 -20.356 1.00 9.42 MG
HETATM 1 O HOH A 4 -3.435 1.768 -22.164 1.00 8.59 O
HETATM 3 O HOH A 5 -2.158 5.884 -19.807 1.00 9.00 O
HETATM 4 O HOH A 6 -1.791 4.005 -20.881 1.00 7.86 O
HETATM 39 O HOH A 7 -1.518 -0.155 -21.151 1.00 13.31 O
HETATM 40 O HOH A 8 -0.256 6.271 -22.179 1.00 12.97 O
HETATM 41 O HOH A 9 0.913 6.863 -19.633 1.00 13.62 O """
open("tst_geo_min_metal_coord.pdb", "w").write(pdb_in)
params1 = """\
geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O2A and chain A and resname ANP and resseq 1
distance_ideal = 2.090000
sigma = 0.250
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O2G and chain A and resname ANP and resseq 1
distance_ideal = 2.090000
sigma = 0.250
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O and chain A and resname HOH and resseq 4
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O and chain A and resname HOH and resseq 7
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 2
atom_selection_2 = name O and chain A and resname HOH and resseq 6
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O3G and chain A and resname ANP and resseq 1
distance_ideal = 2.090000
sigma = 0.250
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O and chain A and resname HOH and resseq 9
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O1B and chain A and resname ANP and resseq 1
distance_ideal = 2.090000
sigma = 0.250
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O and chain A and resname HOH and resseq 8
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O and chain A and resname HOH and resseq 6
distance_ideal = 2.070000
sigma = 0.050
}
bond {
action = *add
atom_selection_1 = name MG and chain A and resname MG and resseq 3
atom_selection_2 = name O and chain A and resname HOH and resseq 5
distance_ideal = 2.070000
sigma = 0.050
}
}"""
params2 = "refinement {\n%s\n}" % params1
open("tst_geo_min_metal_coord_1.phil", "w").write(params1)
open("tst_geo_min_metal_coord_2.phil", "w").write(params2)
# phenix.geometry_minimization
from mmtbx.command_line import geometry_minimization
args = [
"file_name=tst_geo_min_metal_coord.pdb",
"output_file_name_prefix=tst_geo_min_metal_coord_1",
"write_geo_file=True",
"tst_geo_min_metal_coord_1.phil",
]
geometry_minimization.run(args=args, log=null_out())
geo_file_1 = open("tst_geo_min_metal_coord_1.geo").read()
args = [
"file_name=tst_geo_min_metal_coord.pdb",
"output_file_name_prefix=tst_geo_min_metal_coord_2",
"write_geo_file=True",
"tst_geo_min_metal_coord_2.phil",
]
geometry_minimization.run(args=args, log=null_out())
geo_file_2 = open("tst_geo_min_metal_coord_2.geo").read()
show_diff(geo_file_1, geo_file_2)
# phenix.pdbtools
from mmtbx import pdbtools
args = [
"tst_geo_min_metal_coord.pdb",
"tst_geo_min_metal_coord_1.phil",
"model_statistics=True",
]
out1 = StringIO()
pdbtools.run(args=args, out=out1, replace_stderr=False)
args = [
"tst_geo_min_metal_coord.pdb",
"tst_geo_min_metal_coord_2.phil",
"model_statistics=True",
]
out2 = StringIO()
pdbtools.run(args=args, out=out2, replace_stderr=False)
assert (""" atom 1: \"HETATM 37 MG MG A 2 .*. Mg \"""" in
out1.getvalue())
assert (""" atom 1: \"HETATM 37 MG MG A 2 .*. Mg \"""" in
out2.getvalue())
for line1, line2 in zip(out1.getvalue().splitlines(),
out2.getvalue().splitlines()) :
line1 = line1.strip()
line2 = line2.strip()
if (line1.startswith("Date") or line1.startswith("PID") or
line1.startswith("Command line") or line1.startswith("Time")):
continue
else :
assert not show_diff(line1, line2)
def exercise_secondary_structure () :
# what is tested here? Not a single assert or check.
pdb_in_p1 = """\
CRYST1 21.348 25.003 18.365 90.00 90.00 90.00 P 1
ATOM 1 N SER A 1 10.914 5.773 13.123 1.00 0.00
ATOM 2 CA SER A 1 12.373 5.809 13.123 1.00 0.00
ATOM 3 C SER A 1 12.880 7.231 13.123 1.00 0.00
ATOM 4 O SER A 1 12.115 8.196 13.123 1.00 0.00
ATOM 5 CB SER A 1 12.944 5.000 11.931 1.00 0.00
ATOM 6 N ASP A 2 14.192 7.378 13.123 1.00 0.00
ATOM 7 CA ASP A 2 14.822 8.695 13.123 1.00 0.00
ATOM 8 C ASP A 2 14.519 9.440 11.845 1.00 0.00
ATOM 9 O ASP A 2 14.263 10.684 11.836 1.00 0.00
ATOM 10 CB ASP A 2 16.348 8.559 13.365 1.00 0.00
ATOM 11 N PRO A 3 14.535 8.722 10.738 1.00 0.00
ATOM 12 CA PRO A 3 14.264 9.228 9.323 1.00 0.00
ATOM 13 C PRO A 3 12.793 9.507 9.027 1.00 0.00
ATOM 14 O PRO A 3 12.513 10.527 8.347 1.00 0.00
ATOM 15 CB PRO A 3 14.734 8.129 8.381 1.00 0.00
ATOM 16 N ALA A 4 11.844 8.703 9.470 1.00 0.00
ATOM 17 CA ALA A 4 10.431 8.949 9.199 1.00 0.00
ATOM 18 C ALA A 4 9.967 10.223 9.865 1.00 0.00
ATOM 19 O ALA A 4 9.185 11.004 9.310 1.00 0.00
ATOM 20 CB ALA A 4 9.645 7.712 9.664 1.00 0.00
ATOM 21 N ALA A 5 10.435 10.445 11.079 1.00 0.00
ATOM 22 CA ALA A 5 10.071 11.635 11.842 1.00 0.00
ATOM 23 C ALA A 5 10.591 12.886 11.175 1.00 0.00
ATOM 24 O ALA A 5 9.928 13.929 11.130 1.00 0.00
ATOM 25 CB ALA A 5 10.609 11.453 13.272 1.00 0.00
ATOM 26 N LEU A 6 11.801 12.803 10.654 1.00 0.00
ATOM 27 CA LEU A 6 12.432 13.934 9.979 1.00 0.00
ATOM 28 C LEU A 6 11.678 14.303 8.724 1.00 0.00
ATOM 29 O LEU A 6 11.492 15.483 8.391 1.00 0.00
ATOM 30 CB LEU A 6 13.921 13.618 9.660 1.00 0.00
ATOM 31 N LYS A 7 11.228 13.293 8.001 1.00 0.00
ATOM 32 CA LYS A 7 10.483 13.500 6.763 1.00 0.00
ATOM 33 C LYS A 7 9.162 14.181 7.033 1.00 0.00
ATOM 34 O LYS A 7 8.713 15.063 6.287 1.00 0.00
ATOM 35 CB LYS A 7 10.269 12.135 6.054 1.00 0.00
ATOM 36 N ARG A 8 8.515 13.780 8.112 1.00 0.00
ATOM 37 CA ARG A 8 7.227 14.350 8.498 1.00 0.00
ATOM 38 C ARG A 8 7.367 15.810 8.856 1.00 0.00
ATOM 39 O ARG A 8 6.516 16.641 8.545 1.00 0.00
ATOM 40 CB ARG A 8 6.648 13.528 9.682 1.00 0.00
ATOM 41 N ALA A 9 8.444 16.136 9.545 1.00 0.00
ATOM 42 CA ALA A 9 8.710 17.511 9.960 1.00 0.00
ATOM 43 C ALA A 9 8.937 18.403 8.764 1.00 0.00
ATOM 44 O ALA A 9 8.495 19.558 8.714 1.00 0.00
ATOM 45 CB ALA A 9 9.912 17.483 10.921 1.00 0.00
ATOM 46 N ARG A 10 9.646 17.883 7.780 1.00 0.00
ATOM 47 CA ARG A 10 9.944 18.630 6.562 1.00 0.00
ATOM 48 C ARG A 10 8.683 18.929 5.788 1.00 0.00
ATOM 49 O ARG A 10 8.510 20.003 5.215 1.00 0.00
ATOM 50 CB ARG A 10 10.955 17.817 5.707 1.00 0.00
ATOM 51 N ASN A 11 7.788 17.960 5.742 1.00 0.00
ATOM 52 CA ASN A 11 6.522 18.108 5.030 1.00 0.00
ATOM 53 C ASN A 11 5.662 19.170 5.672 1.00 0.00
ATOM 54 O ASN A 11 5.000 19.964 5.005 1.00 0.00
ATOM 55 CB ASN A 11 5.780 16.740 5.000 1.00 0.00
TER
END
"""
open("tst_geo_min_ss_phil.pdb", "w").write(pdb_in_p1)
from mmtbx.command_line import secondary_structure_restraints
out = StringIO()
args = [
"tst_geo_min_ss_phil.pdb",
# "use_ksdssp=False",
]
secondary_structure_restraints.run(args, out=out, log=null_out())
# phenix.geometry_minimization
from mmtbx.command_line import geometry_minimization
open("tst_geo_min_ss_phil.phil", "w").write(out.getvalue())
args = [
"tst_geo_min_ss_phil.pdb",
"tst_geo_min_ss_phil.phil",
"secondary_structure.enabled=True",
]
geometry_minimization.run(args=args, log=null_out())
def run(args):
#log = StringIO()
if len(args) != 3:
raise Usage(
"mmtbx.nqh_minimize input.pdb output.pdb temp_dir_path")
filename = args[0]
outfile = args[1]
temp_dir = args[2]
basename = os.path.basename(filename)
flipped_residues = parse_user_mods(filename=filename)
selection = "selection = (not (name ' CA ' or name ' N ' or name ' C ' " +\
"or name ' O ' or name ' HA ' or name ' H ' " +\
"or name ' OXT')) and ("
restrain = "pdb_interpretation.reference_coordinate_restraints.selection = " +\
"(not (name ' CA ' or name ' N ' or name ' C ' " +\
"or name ' O ' or name ' HA ' or name ' H ' " +\
"or name ' OXT')) and ("
is_first = True
for flip in flipped_residues:
if not is_first:
selection += " or"
restrain += " or"
else:
is_first = False
chain_id = flip[0:2]
if (len(flip) == 10): #not an altloc
if chain_id == ' ':
selection += " (resseq %s and resname %s)" % \
(flip[2:6].strip(), flip[7:])
restrain += " (resseq %s and resname %s)" % \
(flip[2:6].strip(), flip[7:])
else:
selection += " (chain '%s' and resseq %s and resname %s)" % \
(flip[0:2], flip[2:6].strip(), flip[7:])
restrain += " (chain '%s' and resseq %s and resname %s)" % \
(flip[0:2], flip[2:6].strip(), flip[7:])
else: #is an alternate
if chain_id == ' ':
selection += \
" (resseq %s and resname %s and altid '%s')" % \
(flip[2:6].strip(), flip[7:10], flip[-1:])
restrain += \
" (resseq %s and resname %s and altid '%s')" % \
(flip[2:6].strip(), flip[7:10], flip[-1:])
else:
selection += \
" (chain '%s' and resseq %s and resname %s and altid '%s')" % \
(flip[0:2], flip[2:6].strip(), flip[7:10], flip[-1:])
restrain += \
" (chain '%s' and resseq %s and resname %s and altid '%s')" % \
(flip[0:2], flip[2:6].strip(), flip[7:10], flip[-1:])
selection += " )"
restrain += " )"
sigma = "pdb_interpretation.reference_coordinate_restraints.sigma=0.05"
directory = "directory="+temp_dir
params = os.path.join(temp_dir, "nqh.params")
p = file(params, 'w')
print >> p, selection
print >> p, restrain
print >> p, sigma
print >> p, "pdb_interpretation.reference_coordinate_restraints.enabled=True"
print >> p, directory
print >> p, "stop_for_unknowns=False"
print >> p, "pdb_interpretation.clash_guard.nonbonded_distance_threshold=None"
p.close()
temp_pdb = os.path.join(temp_dir, "nqh_flips.pdb")
out = file(temp_pdb, 'w')
f = file(filename, 'rb')
for line in f.readlines():
if line.startswith("ATOM "):
id_str = line[16:26]
key = id_str[4:6]+id_str[6:]+' '+id_str[1:4]
if id_str[0] != ' ':
key = key+" %s" % id_str[0]
if key in flipped_residues:
print >> out, line.strip()
out.close()
f.close()
min_args = []
min_args.append(filename)
min_args.append(params)
log_file = os.path.join(temp_dir, "nqh.log")
log = file(log_file, 'w')
o = geometry_minimization.run(min_args, log=log)
updated_coords = {}
ind = max(0,basename.rfind("."))
ofn = \
basename+"_minimized.pdb" if ind==0 else basename[:ind]+"_minimized.pdb"
min_file = file(os.path.join(temp_dir, ofn), 'rb')
for line in min_file.readlines():
if line.startswith("ATOM "):
id_str = line[16:26]
check_key = id_str[4:6]+id_str[6:]+' '+id_str[1:4]
if id_str[0] != ' ':
check_key = check_key+" %s" % id_str[0]
if check_key in flipped_residues:
key = line[12:26]
coords = line[30:54]
updated_coords[key] = coords
min_file.close()
finalize_coords(
filename=filename,
outfile=outfile,
updated_coords=updated_coords)
