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)
from __future__ import division
# LIBTBX_SET_DISPATCHER_NAME phenix.pdbtools
from mmtbx import pdbtools
import sys
if (__name__ == "__main__"):
pdbtools.run(args=sys.argv[1:])
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)
from __future__ import division # LIBTBX_SET_DISPATCHER_NAME phenix.pdbtools from mmtbx import pdbtools import sys if (__name__ == "__main__"): pdbtools.run(args=sys.argv[1:])