def exercise(space_group_info, n_scatterers=1, d_min=2, verbose=0):
structure = random_structure.xray_structure(space_group_info,
elements=["Hg"] * n_scatterers,
volume_per_atom=500,
min_distance=2.,
general_positions_only=True)
if (1 or verbose):
structure.show_summary().show_scatterers()
reduced_peaks = phase_o_phrenia.calculate_exp_i_two_phi_peaks(
structure, d_min, min_peak_distance=3, max_reduced_peaks=20)
for peak in reduced_peaks:
print("%.6g" % peak.height, "%8.5f %8.5f %8.5f" % peak.site)
def exercise(space_group_info, n_scatterers=1, d_min=2, verbose=0):
structure = random_structure.xray_structure(
space_group_info,
elements=["Hg"]*n_scatterers,
volume_per_atom=500,
min_distance=2.,
general_positions_only=True)
if (1 or verbose):
structure.show_summary().show_scatterers()
reduced_peaks = phase_o_phrenia.calculate_exp_i_two_phi_peaks(
structure, d_min, min_peak_distance=3, max_reduced_peaks=20)
for peak in reduced_peaks:
print "%.6g" % peak.height, "%8.5f %8.5f %8.5f" % peak.site
def run(server_info, inp, status):
print("<pre>")
if (inp.format == "cns_sdb"):
print("Minimum distance between symmetrically equivalent sites:",
end=' ')
print(float(inp.min_distance_sym_equiv))
print()
structures = inp_as_xray_structures(inp)
if (len(structures) == 0):
print("No CNS sdb files found!")
print()
print(
"Note that each file must start with {+ file: some_file_name +}"
)
print("in order to be recognized.")
print()
else:
if (inp.ucparams is None): inp.ucparams = ""
if (inp.sgsymbol is None): inp.sgsymbol = "P1"
special_position_settings = io_utils.special_position_settings_from_inp(
inp)
special_position_settings.show_summary()
print("Minimum distance between symmetrically equivalent sites:",
end=' ')
print(special_position_settings.min_distance_sym_equiv())
print()
structures = [
io_utils.structure_from_inp(inp, status, special_position_settings)
]
d_min = float(inp.d_min)
print("Minimum d-spacing:", d_min)
if (d_min <= 0.):
raise ValueError("d-spacing must be greater than zero.")
print()
min_peak_distance = float(inp.min_peak_distance)
print("Minimum peak distance:", min_peak_distance)
if (min_peak_distance <= 0.):
raise ValueError("min_peak_distance must be greater than zero.")
print()
max_reduced_peaks = int(inp.max_reduced_peaks)
print("Maximum number of peaks:", max_reduced_peaks)
if (max_reduced_peaks <= 0):
raise ValueError("max_reduced_peaks must be greater than zero.")
print()
for structure in structures:
if (inp.format == "cns_sdb"):
structure.show_summary().show_scatterers()
print()
if (structure.scatterers().size() == 0): continue
reduced_peaks = phase_o_phrenia.calculate_exp_i_two_phi_peaks(
xray_structure=structure,
d_min=d_min,
min_peak_distance=min_peak_distance,
max_reduced_peaks=max_reduced_peaks)
print("Actual number of peaks:", len(reduced_peaks))
print()
plot_nx = min(len(reduced_peaks), 60)
if (plot_nx > 0):
plot_ny = max(10, plot_nx // 3)
if (plot_nx != max_reduced_peaks):
print("Number of peaks used for plot:", plot_nx)
print()
print("Plot of relative peak heights:")
print()
plot = flex.bool(flex.grid(plot_nx, plot_ny))
for i in range(plot_nx):
height = reduced_peaks[i].height
h = int(round(height * plot_ny))
h = max(0, min(plot_ny, h))
for j in range(h):
plot[(i, j)] = True
for j in range(plot_ny - 1, -1, -1):
line = ""
for i in range(plot_nx):
if (plot[(i, j)]): line += "*"
else: line += " "
print(" |" + line.rstrip())
print(" -" + "-" * plot_nx)
print()
print("Peak list:")
print(" Relative")
print(" height Fractional coordinates")
for peak in reduced_peaks:
print(" %5.1f" % (peak.height * 100),
" %8.5f %8.5f %8.5f" % peak.site)
print()
print("</pre>")
def run(server_info, inp, status):
print "<pre>"
if (inp.format == "cns_sdb"):
print "Minimum distance between symmetrically equivalent sites:",
print float(inp.min_distance_sym_equiv)
print
structures = inp_as_xray_structures(inp)
if (len(structures) == 0):
print "No CNS sdb files found!"
print
print "Note that each file must start with {+ file: some_file_name +}"
print "in order to be recognized."
print
else:
if (inp.ucparams is None): inp.ucparams = ""
if (inp.sgsymbol is None): inp.sgsymbol = "P1"
special_position_settings = io_utils.special_position_settings_from_inp(inp)
special_position_settings.show_summary()
print "Minimum distance between symmetrically equivalent sites:",
print special_position_settings.min_distance_sym_equiv()
print
structures = [io_utils.structure_from_inp(inp, status, special_position_settings)]
d_min = float(inp.d_min)
print "Minimum d-spacing:", d_min
if (d_min <= 0.):
raise ValueError, "d-spacing must be greater than zero."
print
min_peak_distance = float(inp.min_peak_distance)
print "Minimum peak distance:", min_peak_distance
if (min_peak_distance <= 0.):
raise ValueError, "min_peak_distance must be greater than zero."
print
max_reduced_peaks = int(inp.max_reduced_peaks)
print "Maximum number of peaks:", max_reduced_peaks
if (max_reduced_peaks <= 0):
raise ValueError, "max_reduced_peaks must be greater than zero."
print
for structure in structures:
if (inp.format == "cns_sdb"):
structure.show_summary().show_scatterers()
print
if (structure.scatterers().size() == 0): continue
reduced_peaks = phase_o_phrenia.calculate_exp_i_two_phi_peaks(
xray_structure=structure,
d_min=d_min,
min_peak_distance=min_peak_distance,
max_reduced_peaks=max_reduced_peaks)
print "Actual number of peaks:", len(reduced_peaks)
print
plot_nx = min(len(reduced_peaks), 60)
if (plot_nx > 0):
plot_ny = max(10, plot_nx//3)
if (plot_nx != max_reduced_peaks):
print "Number of peaks used for plot:", plot_nx
print
print "Plot of relative peak heights:"
print
plot = flex.bool(flex.grid(plot_nx, plot_ny))
for i in xrange(plot_nx):
height = reduced_peaks[i].height
h = int(round(height * plot_ny))
h = max(0, min(plot_ny, h))
for j in xrange(h): plot[(i,j)] = True
for j in xrange(plot_ny-1,-1,-1):
line = ""
for i in xrange(plot_nx):
if (plot[(i,j)]): line += "*"
else: line += " "
print " |" + line.rstrip()
print " -" + "-" * plot_nx
print
print "Peak list:"
print " Relative"
print " height Fractional coordinates"
for peak in reduced_peaks:
print " %5.1f" % (peak.height*100), " %8.5f %8.5f %8.5f" % peak.site
print
print "</pre>"
