def read_table(file_name):
atomic_number = None
number_of_electrons = None
x = flex.double()
y = flex.double()
sigmas = flex.double()
lf = line_feeder(open(file_name))
while 1:
line = next(lf)
if (lf.eof): break
if (line.startswith(" FORM: ATOMIC NUMBER=")):
atomic_number = float(line.split("=")[1])
assert int(atomic_number) == atomic_number
elif (line.startswith(" FORM: # ELECTRONS=")):
number_of_electrons = float(line.split("=")[1])
assert int(number_of_electrons) == number_of_electrons
elif (line.startswith(" X (1/A)")):
assert atomic_number == number_of_electrons
while 1:
line = next(lf)
assert not lf.eof
if (line == " *** END OF DATA ***"):
lf.eof = True
break
vals_str = line.split()
for val_str in vals_str:
assert len(val_str) == 13
x.append(float(vals_str[0]))
y.append(float(vals_str[1]))
assert vals_str[1][-4] == "E"
sigmas.append(float("0.00000005" + vals_str[1][-4:]))
return table(int(atomic_number), x, y * atomic_number, sigmas)
def read_table(file_name):
atomic_number = None
number_of_electrons = None
x = flex.double()
y = flex.double()
sigmas = flex.double()
lf = line_feeder(open(file_name))
while 1:
line = lf.next()
if lf.eof:
break
if line.startswith(" FORM: ATOMIC NUMBER="):
atomic_number = float(line.split("=")[1])
assert int(atomic_number) == atomic_number
elif line.startswith(" FORM: # ELECTRONS="):
number_of_electrons = float(line.split("=")[1])
assert int(number_of_electrons) == number_of_electrons
elif line.startswith(" X (1/A)"):
assert atomic_number == number_of_electrons
while 1:
line = lf.next()
assert not lf.eof
if line == " *** END OF DATA ***":
lf.eof = True
break
vals_str = line.split()
for val_str in vals_str:
assert len(val_str) == 13
x.append(float(vals_str[0]))
y.append(float(vals_str[1]))
assert vals_str[1][-4] == "E"
sigmas.append(float("0.00000005" + vals_str[1][-4:]))
return table(int(atomic_number), x, y * atomic_number, sigmas)
def read_table6111(file_name):
tab = table6111(file_name)
lf = line_feeder(open(file_name))
while 1:
line = next(lf)
if (lf.eof): break
if (line.startswith("Element")):
elements = line.split()[1:]
line = next(lf)
assert line.lstrip().startswith("Z"), line
atomic_numbers = [int(z) for z in line.split()[1:]]
assert len(atomic_numbers) == len(elements), line
line = next(lf)
assert line.startswith("Method"), line
methods = line.split()[1:]
assert len(methods) == len(elements), line
line = next(lf)
assert line.find("sin") > 0, line
stols = flex.double()
value_rows = []
sigma_rows = []
while 1:
line = next(lf)
assert not lf.eof
if (len(line.strip()) == 0): continue
raw_value_row = line.rstrip().split("\t")
assert len(raw_value_row) == len(elements) + 1, line
stols.append(float(raw_value_row[0]))
assert stols[-1] == international_tables_stols[stols.size() -
1], line
value_row = flex.double()
sigma_row = flex.double()
for value in raw_value_row[1:]:
if (len(value.strip()) == 0):
value_row.append(-1)
sigma_row.append(-1)
else:
try:
value_row.append(float(value))
except ValueError as e:
raise ValueError(line)
assert value.count(".") == 1
sigma = ""
for c in value.strip():
if (c == "."):
sigma += "."
else:
assert c in "0123456789"
sigma += "0"
sigma += "5"
sigma_row.append(float(sigma))
value_rows.append(value_row)
sigma_rows.append(sigma_row)
if (stols.size() == 62):
assert stols[-1] == 6, line
break
tab.enter_block(elements, atomic_numbers, methods, value_rows,
sigma_rows)
return tab
def read_table6111(file_name):
tab = table6111(file_name)
lf = line_feeder(open(file_name))
while 1:
line = lf.next()
if (lf.eof): break
if (line.startswith("Element")):
elements = line.split()[1:]
line = lf.next()
assert line.lstrip().startswith("Z"), line
atomic_numbers = [int(z) for z in line.split()[1:]]
assert len(atomic_numbers) == len(elements), line
line = lf.next()
assert line.startswith("Method"), line
methods = line.split()[1:]
assert len(methods) == len(elements), line
line = lf.next()
assert line.find("sin") > 0, line
stols = flex.double()
value_rows = []
sigma_rows = []
while 1:
line = lf.next()
assert not lf.eof
if (len(line.strip()) == 0): continue
raw_value_row = line.rstrip().split("\t")
assert len(raw_value_row) == len(elements) + 1, line
stols.append(float(raw_value_row[0]))
assert stols[-1] == international_tables_stols[stols.size()-1], line
value_row = flex.double()
sigma_row = flex.double()
for value in raw_value_row[1:]:
if (len(value.strip()) == 0):
value_row.append(-1)
sigma_row.append(-1)
else:
try: value_row.append(float(value))
except ValueError, e: raise ValueError(line)
assert value.count(".") == 1
sigma = ""
for c in value.strip():
if (c == "."):
sigma += "."
else:
assert c in "0123456789"
sigma += "0"
sigma += "5"
sigma_row.append(float(sigma))
value_rows.append(value_row)
sigma_rows.append(sigma_row)
if (stols.size() == 62):
assert stols[-1] == 6, line
break
tab.enter_block(elements,atomic_numbers,methods,value_rows,sigma_rows)
return tab
def run():
assert len(sys.argv) == 2
f = open(sys.argv[1], "r")
lf = line_feeder(f)
lookup_dict = {}
while 1:
entry = dtrek_symmetry_entry(lf)
if (entry.symbol is None):
break
cctbx_lookup_symbol = str(entry.space_group_info).replace(" ", "")
if (cctbx_lookup_symbol != entry.symbol):
lookup_dict[entry.symbol] = cctbx_lookup_symbol
pprint.pprint(lookup_dict)
def run():
assert len(sys.argv) == 2
f = open(sys.argv[1], "r")
lf = line_feeder(f)
lookup_dict = {}
while 1:
entry = dtrek_symmetry_entry(lf)
if (entry.symbol is None):
break
cctbx_lookup_symbol = str(entry.space_group_info).replace(" ", "")
if (cctbx_lookup_symbol != entry.symbol):
lookup_dict[entry.symbol] = cctbx_lookup_symbol
pprint.pprint(lookup_dict)
