def __init__(self,
file_path=None,
file_object=None,
input_string=None,
cif_object=None,
builder=None,
raise_if_errors=True,
strict=True):
assert [file_path, file_object, input_string].count(None) == 2
self.file_path = file_path
if builder is None:
builder = builders.cif_model_builder(cif_object)
else:
assert cif_object is None
self.builder = builder
if file_path is not None:
file_object = smart_open.for_reading(file_path)
else:
file_path = "memory"
if file_object is not None:
input_string = file_object.read()
# check input_string for binary, and abort if necessary
binary_detector = detect_binary_file()
binary_detector.monitor_initial = min(len(input_string),
binary_detector.monitor_initial)
if binary_detector.is_binary_file(block=input_string):
raise CifParserError("Binary file detected, aborting parsing.")
self.parser = ext.fast_reader(builder, input_string, file_path, strict)
if raise_if_errors and len(self.parser.lexer_errors()):
raise CifParserError(self.parser.lexer_errors()[0])
if raise_if_errors and len(self.parser.parser_errors()):
raise CifParserError(self.parser.parser_errors()[0])
def extract_from(file_name=None, file=None, monitor_initial=None):
assert [file_name, file].count(None) == 1
if (file is None):
file = open(file_name)
lines = file.readlines()
file.close()
detect_binary = detect_binary_file(monitor_initial=monitor_initial)
unit_cell = None
space_group_symbol = None
for line in lines:
if (detect_binary is not None):
is_binary = detect_binary.is_binary_file(block=line)
if (is_binary is not None):
if (is_binary): break
detect_binary = None
flds = line.split("!", 1)[0].split()
if (len(flds) > 0):
keyword = flds[0].upper()
if (keyword == "CELL"):
assert len(flds) > 1
unit_cell = " ".join(flds[1:])
if (space_group_symbol is not None):
break
elif (keyword == "SYMFILE"):
assert len(flds) > 1
space_group_symbol = flds[1].replace("\\", "/").split("/")[-1]
if (space_group_symbol.lower().endswith(".sym")):
space_group_symbol = space_group_symbol[:-4]
if (unit_cell is not None):
break
assert [unit_cell, space_group_symbol].count(None) < 2
return crystal.symmetry(unit_cell=unit_cell,
space_group_symbol=space_group_symbol)
def run(args):
if (len(args) != 2):
raise Usage("""\
iotbx.cns.transfer_crystal_symmetry any_symmetry_source_file cns_input_file
*********************************************
NOTE: the cns_input_file is changed in place.
*********************************************""")
#
for file_name in args:
if (not os.path.exists(file_name)):
raise Sorry("No such file: %s" % show_string(file_name))
source, target = args
crystal_symmetry = crystal_symmetry_from_any.extract_from(source)
if (crystal_symmetry is None):
raise Sorry(
"Unknown file format or unit cell and/or space group"
" missing from file: " + show_string(source))
cns_space_group_symbol = cns.space_group_symbols.cns_format(
space_group_info=crystal_symmetry.space_group_info())
if (cns_space_group_symbol is None):
raise Sorry("Space group not available in CNS: %s" %
show_string(str(crystal_symmetry.space_group_info())))
sg = '"%s"' % cns_space_group_symbol
a,b,c,alpha,beta,gamma = ["%.6g" % p
for p in crystal_symmetry.unit_cell().parameters()]
parameter_names = ["sg", "a", "b", "c", "alpha", "beta", "gamma"]
parameters_found = dict(zip(parameter_names, [0]*len(parameter_names)))
parameters_changed = []
lines_out = []
detect_binary = detect_binary_file(monitor_initial=100)
try: cns_inp = open(target).read().splitlines()
except IOError, e:
raise Sorry("Error reading file %s (%s)" % (show_string(target), str(e)))
def __init__(self,
file_path=None,
file_object=None,
input_string=None,
cif_object=None,
builder=None,
raise_if_errors=True,
strict=True):
assert [file_path, file_object, input_string].count(None) == 2
self.file_path = file_path
if builder is None:
builder = builders.cif_model_builder(cif_object)
else: assert cif_object is None
self.builder = builder
if file_path is not None:
file_object = smart_open.for_reading(file_path)
else:
file_path = "memory"
if file_object is not None:
input_string = file_object.read()
# check input_string for binary, and abort if necessary
binary_detector = detect_binary_file()
binary_detector.monitor_initial = min(
len(input_string), binary_detector.monitor_initial)
if binary_detector.is_binary_file(block=input_string):
raise CifParserError("Binary file detected, aborting parsing.")
self.parser = ext.fast_reader(builder, input_string, file_path, strict)
if raise_if_errors and len(self.parser.lexer_errors()):
raise CifParserError(self.parser.lexer_errors()[0])
if raise_if_errors and len(self.parser.parser_errors()):
raise CifParserError(self.parser.parser_errors()[0])
def extract_from(file_name=None, file=None, monitor_initial=None):
assert [file_name, file].count(None) == 1
if (file is None):
file = open(file_name)
detect_binary = detect_binary_file(monitor_initial=monitor_initial)
unit_cell = None
space_group_symbol = None
for line in file:
if (detect_binary is not None):
is_binary = detect_binary.is_binary_file(block=line)
if (is_binary is not None):
if (is_binary): break
detect_binary = None
flds = line.split("!",1)[0].split()
if (len(flds) > 0):
keyword = flds[0].upper()
if (keyword == "CELL"):
assert len(flds) > 1
unit_cell = " ".join(flds[1:])
if (space_group_symbol is not None):
break
elif (keyword == "SYMFILE"):
assert len(flds) > 1
space_group_symbol = flds[1].replace("\\","/").split("/")[-1]
if (space_group_symbol.lower().endswith(".sym")):
space_group_symbol = space_group_symbol[:-4]
if (unit_cell is not None):
break
assert [unit_cell, space_group_symbol].count(None) < 2
return crystal.symmetry(
unit_cell=unit_cell,
space_group_symbol=space_group_symbol)
def run(args):
if (len(args) != 2):
raise Usage("""\
iotbx.cns.transfer_crystal_symmetry any_symmetry_source_file cns_input_file
*********************************************
NOTE: the cns_input_file is changed in place.
*********************************************""")
#
for file_name in args:
if (not os.path.exists(file_name)):
raise Sorry("No such file: %s" % show_string(file_name))
source, target = args
crystal_symmetry = crystal_symmetry_from_any.extract_from(source)
if (crystal_symmetry is None):
raise Sorry("Unknown file format or unit cell and/or space group"
" missing from file: " + show_string(source))
cns_space_group_symbol = cns.space_group_symbols.cns_format(
space_group_info=crystal_symmetry.space_group_info())
if (cns_space_group_symbol is None):
raise Sorry("Space group not available in CNS: %s" %
show_string(str(crystal_symmetry.space_group_info())))
sg = '"%s"' % cns_space_group_symbol
a, b, c, alpha, beta, gamma = [
"%.6g" % p for p in crystal_symmetry.unit_cell().parameters()
]
parameter_names = ["sg", "a", "b", "c", "alpha", "beta", "gamma"]
parameters_found = dict(zip(parameter_names, [0] * len(parameter_names)))
parameters_changed = []
lines_out = []
detect_binary = detect_binary_file(monitor_initial=100)
try:
cns_inp = open(target).read().splitlines()
except IOError, e:
raise Sorry("Error reading file %s (%s)" %
(show_string(target), str(e)))
def extract_from(file_name=None, file=None, monitor_initial=None):
assert [file_name, file].count(None) == 1
if (file is None):
file = smart_open.for_reading(file_name=file_name)
detect_binary = detect_binary_file(monitor_initial=monitor_initial)
line_number = 0
for line in file:
line_number += 1
if (detect_binary is not None):
is_binary = detect_binary.is_binary_file(block=line)
if (is_binary is not None):
if (is_binary): break
detect_binary = None
if (line.startswith("CRYST1")):
return cryst1_interpretation.crystal_symmetry(cryst1_record=line)
crystal_symmetry = cns_pdb_remarks.extract_symmetry(pdb_record=line)
if (crystal_symmetry is not None):
return crystal_symmetry
raise RuntimeError("No CRYST1 record.")
def run(args):
if (len(args) != 2):
raise Usage("""\
iotbx.cns.transfer_crystal_symmetry any_symmetry_source_file cns_input_file
*********************************************
NOTE: the cns_input_file is changed in place.
*********************************************""")
#
for file_name in args:
if (not os.path.exists(file_name)):
raise Sorry("No such file: %s" % show_string(file_name))
source, target = args
crystal_symmetry = crystal_symmetry_from_any.extract_from(source)
if (crystal_symmetry is None):
raise Sorry("Unknown file format or unit cell and/or space group"
" missing from file: " + show_string(source))
cns_space_group_symbol = cns.space_group_symbols.cns_format(
space_group_info=crystal_symmetry.space_group_info())
if (cns_space_group_symbol is None):
raise Sorry("Space group not available in CNS: %s" %
show_string(str(crystal_symmetry.space_group_info())))
sg = '"%s"' % cns_space_group_symbol
a, b, c, alpha, beta, gamma = [
"%.6g" % p for p in crystal_symmetry.unit_cell().parameters()
]
parameter_names = ["sg", "a", "b", "c", "alpha", "beta", "gamma"]
parameters_found = dict(zip(parameter_names, [0] * len(parameter_names)))
parameters_changed = []
lines_out = []
detect_binary = detect_binary_file(monitor_initial=100)
try:
cns_inp = open(target).read().splitlines()
except IOError as e:
raise Sorry("Error reading file %s (%s)" %
(show_string(target), str(e)))
end_block_parameter_definition = False
for line in cns_inp:
if (detect_binary is not None):
is_binary = detect_binary.is_binary_file(block=line)
if (is_binary is not None):
if (is_binary):
raise Sorry("%s appears to be a binary file." %
show_string(target))
detect_binary = None
if (end_block_parameter_definition):
lines_out.append(line)
else:
l = line.strip().replace(" ", "")
if (l == "){-endblockparameterdefinition-}"):
lines_out.append(line)
end_block_parameter_definition = True
else:
line_out = line
for p in parameter_names:
if (l.startswith("{===>}%s=" % p) and l.endswith(";")):
parameters_found[p] += 1
line_out = '{===>} %s=%s;' % (p, vars()[p])
if (line_out != line): parameters_changed.append(p)
break
lines_out.append(line_out)
if (list(parameters_found.values()).count(1) != 7):
raise Sorry("Unexpected set of variable names in %s:\n counts: %s" %
(show_string(target), str(parameters_found)))
elif (len(parameters_changed) == 0):
print("Info: no changes, %s was not modified." % show_string(target))
else:
string_out = "\n".join(lines_out)
print("Info: %d change%s" % plural_s(len(parameters_changed)), \
"(%s)," % ", ".join(parameters_changed), \
"writing modified file %s." % show_string(target))
try:
print(string_out, file=open(target, "w"))
except IOError as e:
raise Sorry("Error writing file %s (%s)" %
(show_string(target), str(e)))
